(en)This disclosure provides, inter alia, an optimized strain of Nitrosomonas eutropha ( N. eutropha ) designated D23, D23-100, or AOB D23-100. N. eutropha bacteria disclosed in this application have desirable properties, e.g., optimized properties, such as the ability to suppress growth of pathogenic bacteria, and an enhanced ability to produce nitric oxide and nitric oxide precursors. The N. eutropha herein may be used, for instance, to treat diseases associated with low nitrite levels, skin diseases, and diseases caused by pathogenic bacteria.

1.ApplicationNumber: US-201515304151-A
1.PublishNumber: US-2017037363-A1
2.Date Publish: 20170209
3.Inventor: WHITLOCK DAVID R.
JAMAS SPIROS
WEISS LARRY
GRYLLOS IOANNIS

4.Inventor Harmonized: WHITLOCK DAVID R(US)
JAMAS SPIROS(US)
WEISS LARRY(US)
GRYLLOS IOANNIS(US)

5.Country: US
6.Claims:
(en)This disclosure provides, inter alia, an optimized strain of Nitrosomonas eutropha ( N. eutropha ) designated D23, D23-100, or AOB D23-100. N. eutropha bacteria disclosed in this application have desirable properties, e.g., optimized properties, such as the ability to suppress growth of pathogenic bacteria, and an enhanced ability to produce nitric oxide and nitric oxide precursors. The N. eutropha herein may be used, for instance, to treat diseases associated with low nitrite levels, skin diseases, and diseases caused by pathogenic bacteria.

7.Description:
(en)This application claims priority to Greek Patent Application Number 20140100217, filed Apr. 15, 2014, U.S. Provisional Application No. 62/002,084, filed May 22, 2014, U.S. Provisional Application No. 62/012,811, filed Jun. 16, 2014, U.S. Provisional Application No. 62/053,588, filed Sep. 22, 2014, and Greek Patent Application Number 20150100115, filed Mar. 13, 2015, the contents of which are incorporated herein by reference in their entireties.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Apr. 13, 2015, is named N2060-7001WO.txt and is 3,590,980 bytes in size.
BACKGROUND
Beneficial bacteria can be used to suppress the growth of pathogenic bacteria. Bacteria and other microorganisms are ubiquitous in the environment. The discovery of pathogenic bacteria and the germ theory of disease have had a tremendous effect on health and disease states. Bacteria are a normal part of the environment of all living things. In the gut, these bacteria are not pathogenic under normal conditions, and in fact improve health by rendering the normal intestinal contents less hospitable for disease causing organisms. Disease prevention is accomplished in a number of ways: nutrients are consumed, leaving less for pathogens; conditions are produced, such as pH and oxygen tension, which are not hospitable for pathogens; compounds are produced that are toxic to pathogens; pathogens are consumed as food by these microorganisms; less physical space remains available for pathogens; and specific binding sites are occupied leaving fewer binding sites available for pathogens. The presence of these desirable bacteria is seen as useful in preventing disease states.
There is a need in the art for improved beneficial bacteria that can suppress the growth of pathogenic bacteria.
SUMMARY
This disclosure provides, inter alia, an optimized strain of Nitrosomonas eutropha ( N. eutropha ) designated D23, D23-100 or AOB D23-100, the terms which may be used interchangeably throughout the disclosure.
Ammonia oxidizing bacterial of the genus Nitrosomonas are ubiquitous Gram-negative obligate chemolithoautotrophic bacteria with a unique capacity to generate energy exclusively from the conversion of ammonia to nitrite.
N. eutropha bacteria disclosed in this application have desirable, e.g. optimized, properties such as the ability to suppress growth of pathogenic bacteria, and an enhanced ability to produce nitric oxide (NO) and nitric oxide (NO 2 − ) precursors. The N. eutropha , e.g., optimized N. eutropha , e.g., purified preparations of optimized N. eutropha herein may be used, for instance, to treat diseases, e.g., diseases associated with low nitrite levels, skin disorders, and diseases caused by pathogenic bacteria. When referring to N. eutropha throughout the disclosure, it may be referring to an optimized strain of N. eutropha or a purified preparation of optimized N. eutropha.
The present disclosure provides, inter alia, a Nitrosomonas eutropha ( N. eutropha ) bacterium, e.g., an optimized N. eutropha , e.g., a purified preparation of optimized N. eutropha , having at least one property selected from:
an optimized growth rate; an optimized NH 4 + oxidation rate; and an optimized resistance to ammonium ion (NH 4 + ).

The bacterium is optionally axenic.
In embodiments, the optimized growth rate is a rate allowing a continuous culture of N. eutropha at an OD600 (optical density at 600 nm) of about 0.15-0.18 to reach an OD600 of about 0.5-0.6 in about 1-2 days. In embodiments, optimized growth rate is a doubling time of about 8 hours when cultured under batch culture conditions. In embodiments, the optimized NH 4 + oxidation rate is a rate of at least about 125 micromoles per minute of oxidizing NH 4 + to NO 2 − . In embodiments, the optimized resistance to NH 4 + is an ability to grow in medium comprising about 200 mM NH 4 + for at least about 48 hours.
In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) has at least two properties selected from an optimized growth rate, an optimized NH 4 + oxidation rate, and an optimized resistance to NH 4 + . In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) has an optimized growth rate, an optimized NH 4 + oxidation rate, and an optimized resistance to NH 4 + . In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) comprises a chromosome that hybridizes under very high stringency to SEQ ID NO: 1.
In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) comprises an AmoA protein having an identity to SEQ ID NO: 6 or 12 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, an AmoB protein having an identity to SEQ ID NO: 8 or 14 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, an amoC gene having an identity to SEQ ID NO: 4, 10, or 16 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, a hydroxylamine oxidoreductase protein having an identity to SEQ ID NO: 18, 20, or 22 selected from at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, a cytochrome c554 protein having an identity to SEQ ID NO: 24, 26, or 28 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, or a cytochrome c M 552 protein having an identity to SEQ ID NO: 30 or 32 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical.
In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) comprises 1-5, 5-10, 10-15, 15-20, 20-25, 25-30, or all of the sequence characteristics of Table 2. For instance, in some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1. In some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160. In some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167. In some embodiments, the bacterium or preparation comprises an AmoB1 or AmoB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 33, e.g., a V at position 33. In some embodiments, the bacterium or preparation comprises an AmoB1 or AmoB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 165, e.g., an I at position 165. In some embodiments, the bacterium or preparation comprises an AmoC3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 79, e.g., an A at position 79. In some embodiments, the bacterium or preparation comprises an AmoC3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 271, e.g., a V at position 271. In some embodiments, the bacterium or preparation comprises a Hao1, Hao2, or Hao3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85. In some embodiments, the bacterium or preparation comprises a Hao1, Hao2, or Hao3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312. In some embodiments, the bacterium or preparation comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163. In some embodiments, the bacterium or preparation comprises a c554 CycA1, c554 CycA2, or c554 CycA3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 65, e.g., a T at position 65. In some embodiments, the bacterium or preparation comprises a c554 CycA1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 186, e.g., a T at position 186. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 or c M 552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 63, e.g., a V at position 63. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 or c M 552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 189, e.g., a P at position 189. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 or c M 552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 206, e.g., an insE at position 206. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 or c M 552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 207, e.g., an insE at position 207. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 195, e.g., an insD at position 195. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 196, e.g., an insD at position 196. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 197, e.g., an insD at position 197.
Combinations of two or more sequence characteristics of Table 2 are also described. The two or more sequence characteristics may be in the same gene or different genes. The two or more sequence characteristics may be in the same protein or different proteins. For instance, in some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1 and a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160. In some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1 and a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167. In some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160 and a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167.
In some embodiments, the bacterium or preparation comprises an AmoB1 or AmoB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 33, e.g., a V at position 33 and a mutation relative to N. eutropha strain C91 at position 165, e.g., an I at position 165.
In some embodiments, the bacterium or preparation comprises an AmoC3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 79, e.g., an A at position 79 and a mutation relative to N. eutropha strain C91 at position 271, e.g., a V at position 271.
In some embodiments, the bacterium or preparation comprises a Hao1, Hao2, or Hao3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85 and a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312. In some embodiments, the bacterium or preparation comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85 and a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163. In some embodiments, the bacterium or preparation comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312 and a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163.
In some embodiments, the bacterium or preparation comprises a c554 CycA1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 65, e.g., a T at position 65 and a mutation relative to N. eutropha strain C91 at position 186, e.g., a T at position 186.
In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 protein having (or gene encoding) mutations at any two or more of the following amino acid positions: 63, 189, 194, 195, 196, 197, 206, and 207. For instance, the two or more amino acid positions may comprise: 63 and 189, 63 and 194, 63 and 195, 63 and 196, 63 and 197, 63 and 206, 63 and 207, 189 and 194, 189 and 195, 189 and 196, 189 and 194, 189 and 195, 189 and 196, 189 and 197, 189 and 206, 189 and 207, 194 and 195, 194 and 196, 194 and 197, 194 and 206, 194 and 207, 195 and 196, 195 and 197, 195 and 206, 195 and 207, 196 and 197, 196 and 206, 196 and 207, 197 and 206, 197 and 207, or 206 and 207. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 protein having (or gene encoding) any two or more mutations selected from the group consisting of: I63V, S189P, D194G, 195insD, 196insD, 197insD, 206insE, and 207insE. For instance, the two or more mutations can be selected from the group consisting of: I63V and S189P, I63V and D194G, I63V and 195insD, I63V and 196insD, I63V and 197insD, I63V and 206insE, I63V and 207insE, S189P and D194G, S189P and 195insD, S189P and 196insD, S189P and 197insD, S189P and 206insE, S189P and 207insE, D194G and 195insD, D194G and 196insD, D194G and 197insD, D194G and 206insE, D194G and 207insE, 195insD and 196insD, 195insD and 197insD, 195insD and 206insE, 195insD and 207insE, 196insD and 197insD, 196insD and 206insE, 196insD and 207insE, 197insD and 206insE, 197insD and 207insE, and 206insE and 207insE.
In some embodiments, the bacterium or preparation comprises a c M 552 CycB2 protein having (or gene encoding) mutations at any two or more of the following amino acid positions: 63, 189, 206, and 207. For instance, the two or more amino acid positions may comprise: 63 and 189, 63 and 206, 63 and 207, 189 and 206, 189 and 207, or 206 and 207. In some embodiments, the bacterium or preparation comprises a c M 552 CycB2 protein having (or gene encoding) any two or more mutations selected from the group consisting of: I63V, S189P, 206insE, and 207insE. For instance, the two or more mutations can be selected from the group consisting of: I63V and S189P, I63V and 206insE, I63V and 207insE, S189P and 206insE, S189P and 207insE, and 206insE and 207insE.
Combinations of three or more sequence characteristics of Table 2 are also described. For instance, in some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1 and a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160, and a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167.
In some embodiments, the bacterium or preparation comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85 and a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312, and a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163.
In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 protein having (or gene encoding) mutations at any three or more (e.g., 4, 5, 6, 7, or all) of the following amino acid positions: 63, 189, 194, 195, 196, 197, 206, and 207. For instance, the three mutations may be at positions 195, 196, and 197. In some embodiments, the bacterium or preparation comprises a c M 552 CycB1 protein having (or gene encoding) any three or more (e.g., 4, 5, 6, 7, or all) mutations selected from the group consisting of: I63V, S189P, D194G, 195insD, 196insD, 197insD, 206insE, and 207insE. For instance, the three mutations may be 195insD, 196insD, and 197insD.
In some embodiments, the bacterium or preparation comprises a c M 552 CycB2 protein having (or gene encoding) mutations at any three or more (e.g., all) of the following amino acid positions: 63, 189, 206, and 207. In some embodiments, the bacterium or preparation comprises a c M 552 CycB2 protein having (or gene encoding) any three or more (e.g., all) mutations selected from the group consisting of: I63V, S189P, 206insE, and 207insE.
In some embodiments, the bacterium or preparation comprises mutations relative to N. eutropha strain C91 in at least two genes, e.g., at least two genes listed in Table 2. The two genes may be, for instance, AmoA1 and AmoA2, AmoA1 and AmoB1, AmoA1 and AmoB2, AmoA1 and AmoC1, AmoA1 and AmoC2, AmoA1 and AmoC3, AmoA1 and Hao1, AmoA1 and Hao2, AmoA1 and Hao3, AmoA1 and c554 CycA1, AmoA1 and c554 CycA2, AmoA1 and c554 CycA3, AmoA1 and cM552 CycB1, AmoA1 and cM552 CycB2, AmoA2 and AmoB1, AmoA2 and AmoB2, AmoA2 and AmoC1, AmoA2 and AmoC2, AmoA2 and AmoC3, AmoA2 and Hao1, AmoA2 and Hao2, AmoA2 and Hao3, AmoA2 and c554 CycA1, AmoA2 and c554 CycA2, AmoA2 and c554 CycA3, AmoA2 and cM552 CycB1, AmoA2 and cM552 CycB2, AmoB1 and AmoB2, AmoB1 and AmoC1, AmoB1 and AmoC2, AmoB1 and AmoC3, AmoB1 and Hao1, AmoB1 and Hao2, AmoB1 and Hao3, AmoB1 and c554 CycA1, AmoB1 and c554 CycA2, AmoB1 and c554 CycA3, AmoB1 and cM552 CycB1, AmoB1 and cM552 CycB2, AmoB2 and AmoC1, AmoB2 and AmoC2, AmoB2 and AmoC3, AmoB2 and Hao1, AmoB2 and Hao2, AmoB2 and Hao3, AmoB2 and c554 CycA1, AmoB2 and c554 CycA2, AmoB2 and c554 CycA3, AmoB2 and cM552 CycB1, AmoB2 and cM552 CycB2, AmoC1 and AmoC2, AmoC1 and AmoC3, AmoC1 and Hao1, AmoC1 and Hao2, AmoC1 and Hao3, AmoC1 and c554 CycA1, AmoC1 and c554 CycA2, AmoC1 and c554 CycA3, AmoC1 and cM552 CycB1, AmoC1 and cM552 CycB2, AmoC2 and AmoC3, AmoC2 and Hao1, AmoC2 and Hao2, AmoC2 and Hao3, AmoC2 and c554 CycA1, AmoC2 and c554 CycA2, AmoC2 and c554 CycA3, AmoC2 and cM552 CycB1, AmoC2 and cM552 CycB2, AmoC3 and Hao1, AmoC3 and Hao2, AmoC3 and Hao3, AmoC3 and c554 CycA1, AmoC3 and c554 CycA2, AmoC3 and c554 CycA3, AmoC3 and cM552 CycB1, AmoC3 and cM552 CycB2, Hao1 and Hao2, Hao1 and Hao3, Hao1 and c554 CycA1, Hao1 and c554 CycA2, Hao1 and c554 CycA3, Hao1 and cM552 CycB1, Hao1 and cM552 CycB2, Hao2 and Hao3, Hao2 and c554 CycA1, Hao2 and c554 CycA2, Hao2 and c554 CycA3, Hao2 and cM552 CycB1, Hao2 and cM552 CycB2, Hao3 and c554 CycA1, Hao3 and c554 CycA2, Hao3 and c554 CycA3, Hao3 and cM552 CycB1, Hao3 and cM552 CycB2, c554 CycA1 and c554 CycA2, c554 CycA1 and c554 CycA3, c554 CycA1 and cM552 CycB1, c554 CycA1 and cM552 CycB2, c554 CycA2 and c554 CycA3, c554 CycA2 and cM552 CycB1, c554 CycA2 and cM552 CycB2, c554 CycA3 and cM552 CycB1, c554 CycA3 and cM552 CycB2, or cM552 CycB1 and cM552 CycB2.
In some embodiments, the bacterium or preparation comprises mutations relative to N. eutropha strain C91 in at least three genes, e.g., at least three (e.g., 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all) genes listed in Table 2. The three genes may be, for instance AmoA1 and AmoA2 and AmoA3; AmoC1 and AmoC2 and AmoC3; or Hao1 and Hao2 and Hao3.
In some embodiments, the bacterium or preparation comprises at least one structural difference, e.g., at least one mutation, relative to a wild-type bacterium such as N. eutropha strain C91. In some embodiments, the bacterium or preparation comprises a nucleic acid that can be amplified using a pair of primers described herein, e.g., a primer comprising a sequence of SEQ ID NO: 64 and a primer comprising a sequence of SEQ ID NO: 65. In some embodiments, the bacterium or preparation comprises a nucleic acid or protein at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, or 100% identical to a gene of FIG. 6, 7 , or 8 , or a protein encoded by a gene of FIG. 6, 7 , or 8 . In some embodiments, the bacterium or preparation comprises a nucleic acid or protein at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, or 100% identical to a sequence of any of SEQ ID NOS: 64-66 or a protein encoded by a sequence of any of SEQ ID NOS: 64-66.
In some aspects, the present disclosure provides, inter alia, an N. eutropha bacterium, or a purified preparation thereof, comprising a mutation in an ammonia monooxygenase gene, a hydroxylamine oxidoreductase gene, a cytochrome c554 gene, or a cytochrome c M 552 gene. The mutation may be relative to a wild-type bacterium such as N. eutropha strain C91. The mutation may be in one or more of the amoA1 gene, the amoA2 gene, amoB1 gene, the amoB2 gene, and the amoC3 gene. The N. eutropha bacterium, or a purified preparation thereof may have a mutation at a position described herein, e.g., in Table 2. The N. eutropha bacterium, or a purified preparation thereof may have a mutation wherein said mutation is a mutation described herein, e.g., in Table 2.
In some embodiments, the mutation may be in one or more of the hao1 gene, the hao2 gene, or the hao3 gene. The N. eutropha bacterium, or a purified preparation thereof may have a mutation at a position described herein, e.g., in Table 2. The N. eutropha bacterium, or a purified preparation thereof may have a mutation wherein said mutation is a mutation described herein, e.g., in Table 2.
In some embodiments, the mutation may be in one or more of the c554 cycA1 gene, the c554 cycA2 gene, and the c554 cycA3 gene. The N. eutropha bacterium, or a purified preparation thereof may have a mutation at a position described herein, e.g., in Table 2. The N. eutropha bacterium, or a purified preparation thereof may have a mutation wherein said mutation is a mutation described herein, e.g., in Table 2.
In some embodiments, the mutation may be in one or more of the c M 552 cycB1 gene and the c M 552 cycB2 gene. The N. eutropha bacterium, or a purified preparation thereof may have a mutation at a position described herein, e.g., in Table 2. The N. eutropha bacterium, or a purified preparation thereof may have a mutation wherein said mutation is a mutation described herein, e.g., in Table 2.
In certain aspects the N. eutropha bacterium, or a purified preparation thereof, described in the preceding four paragraphs may be based on a N. eutropha bacterium, e.g., an optimized N. eutropha , e.g., a purified preparation of optimized N. eutropha , having at least one property selected from:
an optimized growth rate; an optimized NH 4 + oxidation rate; and an optimized resistance to ammonium ion (NH 4 + ).

In certain aspects, the N. eutropha bacterium, or a purified preparation thereof, described in the preceding five paragraphs may have a mutation in at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 positions of one or more of amoA1 gene, amoA2 gene, amoB1 gene, amoB2 gene, amoC3 gene, hao1 gene, hao2 gene, hao3 gene, c554 cycA1 gene, c554 cycA2 gene, c554 cycA3 gene, c M 552 cycB1 gene, and c554 cycB2 gene.
In some embodiments, the N. eutropha bacterium has an optimized growth rate, e.g., an optimized growth rate described herein, and a structural difference such as a mutation (e.g., relative to a wild-type strain such as N. eutropha strain C91), e.g., a mutation described herein, e.g., a mutation of Table 2. In some embodiments, the N. eutropha bacterium has an optimized NH 4 + oxidation rate, e.g., an optimized NH 4 + oxidation rate described herein, and a structural difference such as a mutation (e.g., relative to a wild-type strain such as N. eutropha strain C91), e.g., a mutation described herein, e.g., a mutation of Table 2. In some embodiments, the N. eutropha bacterium has an optimized resistance to NH 4 + , e.g., an optimized resistance to NH 4 + described herein, and a structural difference such as a mutation (e.g., relative to a wild-type strain such as N. eutropha strain C91), e.g., a mutation described herein, e.g., a mutation of Table 2.
In some embodiments, the N. eutropha bacterium comprises a nucleic acid that can be amplified using a pair of primers described herein, e.g., a primer comprising a sequence of SEQ ID NO: 64 and a primer comprising a sequence of SEQ ID NO: 65.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising a chromosome that hybridizes at high stringency to SEQ ID NO: 1.
In embodiments, the chromosome hybridizes at very high stringency to SEQ ID NO: 1. In embodiments, the N. eutropha bacterium (which is optionally axenic) comprises a gene that is at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% identical to one or more genes of FIGS. 6-8 (e.g., 10, 20, 30, 40, 50, 100, or all genes of any one or more of FIGS. 6, 7, and 8 ).
In embodiments, the N. eutropha bacterium (which is optionally axenic) lacks any plasmid that is at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 2 (pNeut1) or SEQ ID NO: 3 (pNeut2), as described by Stein et al. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environmental Microbiology (2007) 9(12), 2993-3007. In embodiments, the N. eutropha (which is optionally axenic) lacks one or more genes present on the plasmids of SEQ ID NO: 2 or SEQ ID NO: 3. For instance, the N. eutropha (which is optionally axenic) may lack at least 2, 3, 4, 5, 10, 15, or 20 genes present on one or both of pNeut1 and pNeut2. pNeut1 contains 55 protein-coding sequences while pNeutP2 contains 52 protein-coding sequences. In embodiments, the N. eutropha bacterium (which is optionally axenic) lacks any plasmid.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7 and an amoA2 gene at least about 98.8% identical to SEQ ID NO: 13.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6 and an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9 and an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 or amoA2 gene at least about 98.9% identical to SEQ ID NO: 7 or 13.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8 and an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6 and an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, and an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, and an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, and an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, and a hao3 gene at least about 99.3% identical to SEQ ID NO: 23.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, and an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, and a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, or an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a cycA1 gene at least about 98.1% identical to SEQ ID NO: 25, a cycA2 gene at least about 98.8% identical to SEQ ID NO: 27, and a cycA3 gene at least about 99.4% identical to SEQ ID NO: 28.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17, a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, and a hao3 gene at least about 99.3% identical to SEQ ID NO: 23.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a CycA1 protein at least about 99.2% identical to SEQ ID NO: 24, a CycA2 protein at least about 99.7% identical to SEQ ID NO: 26, and a CycA3 protein at least about 99.7% identical to SEQ ID NO: 28.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16, a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, and a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a cycB1 gene at least about 96.8% identical to SEQ ID NO: 31 and a cycB2 gene at least about 97.2% identical to SEQ ID NO: 33.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17, a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, a hao3 gene at least about 99.3% identical to SEQ ID NO: 23, a cycA1 gene at least about 98.1% identical to SEQ ID NO: 25, a cycA2 gene at least about 98.8% identical to SEQ ID NO: 27, and a cycA3 gene at least about 99.4% identical to SEQ ID NO: 28.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a CycB1 protein at least about 97.2% identical to SEQ ID NO: 30 or a CycB2 protein at least about 98.8% identical to SEQ ID NO: 32.
In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16, a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22, a CycA1 protein at least about 99.2% identical to SEQ ID NO: 24, a CycA2 protein at least about 99.7% identical to SEQ ID NO: 26, and a CycA3 protein at least about 99.7% identical to SEQ ID NO: 28.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more genes according to SEQ ID NOS: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, and 33.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more proteins according to SEQ ID NOS: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, and 32.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising a protein that is mutant relative to N. eutropha strain C91 at at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, or all of the amino acid positions listed in Table 2.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising proteins that are mutant relative to N. eutropha strain C91 at all of the amino acid positions listed in Table 2.
In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) of strain D23, 25 vials of said bacterium, designated AOB D23-100, having been deposited with the ATCC patent depository on Apr. 8, 2014 under ATCC accession number PTA-121157.
In embodiments, the N. eutropha bacterium (which is optionally axenic) is transgenic.
In embodiments, the N. eutropha bacterium (which is optionally axenic) has at least one property selected from an optimized growth rate, an optimized NH 4 + oxidation rate, and an optimized resistance to NH 4 + .
In embodiments, the N. eutropha bacterium (which is optionally axenic) has at least two properties selected from an optimized growth rate, an optimized NH 4 + oxidation rate, and an optimized resistance to NH 4 + .
In embodiments, the N. eutropha bacterium (which is optionally axenic) has an optimized growth rate, an optimized NH 4 + oxidation rate, and an optimized resistance to NH 4 + .
In embodiments, the N. eutropha bacterium as described herein (e.g., strain D23) is substantially free of bacteria, other ammonia oxidizing bacteria, fungi, viruses, or pathogens (e.g., animal pathogens, e.g., human pathogens), or any combination thereof.
In certain aspects, this disclosure provides a composition comprising the N. eutropha bacterium as described herein (e.g., strain D23), wherein the composition is substantially free of other organisms.
In certain aspects, this disclosure provides a composition comprising the N. eutropha bacterium as described herein (e.g., strain D23) and further comprising a second organism (e.g., a second strain or species), wherein the composition is substantially free of other organisms (e.g., strains or species). In embodiments, the second organism is an ammonia oxidizing bacterium. In embodiments, the second organism is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, Lactobacillus, Streptococcus , and Bifidobacter , and combinations thereof.
This disclosure also provides a composition comprising the N. eutropha bacterium as described herein (e.g., strain D23) and further comprising a second and a third organism (e.g., of other strains or species), wherein the composition is substantially free of other organisms (e.g., strains or species). This disclosure also provides a composition comprising the N. eutropha bacterium as described herein (e.g., strain D23) and further comprising 2, 3, 4, 5, 6, 7, 8, 9, or 10 other organisms (e.g., of other strains or species), wherein the composition is substantially free of other organisms (e.g., strains or species).
In some aspects, this disclosure provides a composition comprising a cell suspension of an actively dividing culture of N. eutropha bacteria having an OD600 of at least about 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.6, 0.7, or 0.8, wherein the composition is substantially free of other organisms.
In some aspects, this disclosure provides a composition for topical administration, comprising the N. eutropha bacterium as described herein (e.g., strain D23) and a pharmaceutically or cosmetically acceptable excipient suitable for topical administration. In embodiments, the composition is substantially free of other organisms. In embodiments, the composition further comprises a second organism (e.g., of another strain or specie). In embodiments, the composition further comprises 2, 3, 4, 5, 6, 7, 8, 9, or 10 other organisms (e.g., of other strains or species). The second organism may be, for example, an ammonia oxidizing bacterium. In embodiments, the second organism is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, Lactobacillus, Streptococcus , and Bifidobacter , and combinations thereof.
In embodiments, the composition is a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage. In embodiments, the composition further comprises a moisturizing agent, deodorizing agent, scent, colorant, insect repellant, cleansing agent, or UV-blocking agent. In embodiments, the excipient is an anti-adherent, binder, coat, disintegrant, filler, flavor, color, lubricant, glidant, sorbent, preservative, or sweetener. In embodiments, the concentration of N. eutropha in the composition is about 10 11 -10 13 CFU/L. In embodiments, the concentration of N. eutropha in the composition is about 10 9 CFU/ml. In embodiments, the mass ratio of N. eutropha to pharmaceutical excipient may be about 0.1 gram per liter to about 100 grams per liter. In some embodiments, the mass ratio of N. eutropha to pharmaceutical excipient is 1 gram per liter.
In some aspects the composition and/or excipient may be in the form of one or more of a liquid, a solid, or a gel. For example, liquid suspensions may include, but are not limited to, water, saline, phosphate-buffered saline, or an ammonia oxidizing storage buffer. Gel formulations may include, but are not limited to agar, silica, polyacrylic acid (for example Carbopol®), carboxymethyl cellulose, starch, guar gum, alginate or chitosan. In some embodiments, the formulation may be supplemented with an ammonia source including, but not limited to ammonium chloride or ammonium sulfate.
In some aspects, this disclosure provides a composition comprising at least about 10, 20, 50, 100, 200, 500, 1,000, 2,000, or 10,000 L, e.g., at about 10 11 CFU/L, 10 12 CFU/L, 10 13 CFU/L of the N. eutropha bacterium as described herein (e.g., strain D23). In some embodiments, the composition is at a concentration of at least about 10 9 CFU/L, 10 10 CFU/L, 10 11 CFU/L, or 10 12 CFU/L. In some aspects, this disclosure provides a composition comprising at least about 1, 2, 5, 10, 20, 50, 100, 200, or 500 g of the N. eutropha bacterium described herein, e.g., as a dry formulation such as a powder.
In some aspects, this disclosure provides an article of clothing comprising the N. eutropha as described herein (e.g., strain D23). In embodiments, the article of clothing is packaged. In embodiments, the article of clothing is packaged in a material that is resistant to gaseous exchange or resistant to water. The article of clothing may be provided, e.g., at a concentration that provides one or more of a treatment or prevention of a skin disorder, a treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, or a treatment to inhibit microbial growth.
In some aspects, this disclosure provides a cloth comprising the N. eutropha as described herein (e.g., strain D23).
In some aspects, this disclosure provides a yarn comprising the N. eutropha as described herein (e.g., strain D23).
In some aspects, this disclosure provides a thread comprising the N. eutropha as described herein (e.g., strain D23).
In some aspects, this disclosure provides a method of obtaining, e.g., manufacturing, an (optionally axenic) N. eutropha bacterium having an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + , comprising:
(a) culturing the bacterium under conditions that select for one or more of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + , thereby producing a culture;
(b) testing a sample from the culture for an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + ; and
(c) repeating the culturing and testing steps until a bacterium having an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + is obtained.
In embodiments, the method comprises a step of obtaining an N. eutropha bacterium from a source, such as soil or the skin of an individual. In embodiments, culturing the bacterium under conditions that select for one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + comprises culturing the bacterium in N. europaea medium that comprises about 200 mM NH 4 + . In embodiments, the method comprises a step of creating an axenic culture. In embodiments, the method comprises a step of co-culturing the N. eutropha together with at least one other type of ammonia oxidizing bacteria. In embodiments, the N. eutropha of step (a) lack an optimized growth rate, an optimized NH 4 + oxidation rate, and an optimized resistance to NH 4 + In embodiments, step (c) comprises repeating the culturing and testing steps until a bacterium having at least two of an optimized growth rate, an optimized NH 4 + oxidation rate, and an optimized resistance to NH 4 + is obtained.
In some aspects, this disclosure provides an N. eutropha bacterium as described herein (e.g., strain D23), produced by the methods described above.
In some aspects, this disclosure provides a method of testing a preparation of (optionally axenic) N. eutropha , comprising:
assaying the N. eutropha for one or more of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + ; and
if the N. eutropha has one or more of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + , classifying the N. eutropha as accepted.
In embodiments, the method further comprises a step of testing the preparation for contaminating organisms. In embodiments, the method further comprises a step of removing a sample from the preparation and conducting testing on the sample. In embodiments, the method further comprises testing medium in which the N. eutropha is cultured. In embodiments, the method further comprises packaging N. eutropha from the preparation into a package. In embodiments, the method further comprises placing N. eutropha from the preparation into commerce.
In some aspects, this disclosure provides a method of producing, e.g., manufacturing N. eutropha , comprising contacting N. eutropha with culture medium and culturing the N. eutropha until an OD600 of at least about 0.3, 0.4, 0.5, 0.6, 0.7, or 0.8 is reached. In some embodiments, the method comprises culturing the N. eutropha until an OD600 of at about 0.3-0.4, 0.4-0.5, 0.5-0.6, 0.6-0.7, or 0.7-0.8 is reached.
In embodiments, the method further comprises assaying the N. eutropha and culture medium for contaminating organisms. In embodiments, the method further comprises assaying the N. eutropha for one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + In embodiments, the method comprises producing at least at least about 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, or 10,000 L per day of N. eutropha , e.g., at about 10 12 CFUs/L. In some embodiments, the N. eutropha is at a concentration of about 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , or 10 14 CFUs/L. In some embodiments, the N. eutropha is at a concentration of least about 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , or 10 14 CFUs/L.
In some aspects, this disclosure provides a method of producing, e.g., manufacturing, N. eutropha , comprising contacting N. eutropha with culture medium and culturing the N. eutropha until about at least about 1,000 L at about 10 12 CFU/L N. eutropha are produced.
In embodiments, the method further comprises a step of assaying the N. eutropha for one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + .
In embodiments, the method further comprises a step of testing the N. eutropha or culture medium for contaminating organisms. In embodiments, the N. eutropha brought into contact with the culture medium is an N. eutropha having one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + .
In some aspects, this disclosure provides a method of producing, e.g., manufacturing N. eutropha , comprising:
(a) contacting N. eutropha with a culture medium; and
(b) culturing the N. eutropha for 1-2 days, thereby creating a culture, until the culture reaches an OD600 of about 0.5-0.6.
In embodiments, the method further comprises a step of assaying the N. eutropha for one or more of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + . In embodiments, the method further comprises a step of testing the culture for contaminating organisms, e.g., bacteria, viruses, fungi, or pathogens, or a combination thereof. In embodiments, the N. eutropha of step (a) is an N. eutropha having one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH 4 + oxidation rate, or an optimized resistance to NH 4 + . In embodiments, the method comprises producing at least at least about 1,000 L per day at about 10 12 CFUs/L of N. eutropha.
In some aspects, this disclosure provides a N. eutropha bacterium produced by the methods described above.
In embodiments, a preparation of N. eutropha made by the methods described above. In some aspects, the preparation may comprise about 0.1 milligrams to about 100 milligrams (mg) of N. eutropha.
In some aspects, a reaction mixture may be provided comprising N. eutropha at an optical density of about 0.5 to about 0.6. In some aspects, this disclosure provides a method of producing N. eutropha -bearing clothing, comprising contacting an article of clothing with of the N. eutropha as described herein (e.g., strain D23).
In embodiments, the method comprises producing at least 10, 100, or 1000 articles of clothing. In embodiments, the method comprises contacting the article of clothing with at least 10 10 CFUs of N. eutropha . In embodiments, the method further comprises packaging the clothing.
In certain aspects, the present disclosure provides a method of obtaining a formulation of N. eutropha , combining contacting N. eutropha described herein (e.g., strain D23) with a pharmaceutically or cosmetically acceptable excipient.
In embodiments, the method further comprises mixing the N. eutropha and the excipient. In embodiments, the method is performed under conditions that are substantially free of contaminating organisms, e.g., bacteria, viruses, fungi, or pathogens.
In certain aspects, the present disclosure provides a method of packaging N. eutropha , comprising assembling N. eutropha described herein (e.g., strain D23) into a package.
In embodiments, the package is resistant to gaseous exchange or resistant to water. In embodiments, the package is permeable to gaseous exchange, NH 3 , NH 4 + , or NO 2 − .
In certain aspects, the present disclosure provides a method of inhibiting microbial growth on a subject's skin, comprising topically administering to a subject in need thereof an effective dose of the N. eutropha bacteria described herein (e.g., strain D23).
In embodiments, the effective dose is approximately 1×10 9 CFU, 2×10 9 CFU, 5×10 9 CFU, 1×10 10 CFU, 1.5×10 10 CFU, 2×10 10 CFU, 5×10 10 CFU, or 1×10 11 CFU. In embodiments, the effective dose is at least about 1×10 9 CFU, 2×10 9 CFU, 5×10 9 CFU, 1×10 10 CFU, 1.5×10 10 CFU, 2×10 10 CFU, 5×10 10 CFU, or 1×10 11 CFU. In embodiments, the effective dose is approximately 1×10 9 CFU-2×10 9 CFU, 2×10 9 CFU-5×10 9 CFU, 5×10 9 CFU-1×10 10 CFU, 1×10 10 CFU-1.5×10 10 CFU, 1×10 10 CFU-2×10 10 CFU 1.5×10 10 CFU-2×10 10 CFU, 2×10 10 CFU-5×10 10 CFU, or 5×10 10 CFU-1×10 11 CFU. In embodiments, the bacterium is administered at a concentration of about 1×10 8 , 2×10 8 , 5×10 8 , 1×10 9 , 2×10 9 , 5×10 9 , or 1×10 10 CFU/ml. In embodiments, the bacterium is administered at a concentration of at least about 1×10 8 , 2×10 8 , 5×10 8 , 1×10 9 , 2×10 9 , 5×10 9 , or 1×10 10 CFU/ml. In embodiments, the bacterium is administered at a concentration of about 1×10 8 -2×10 8 , 2×10 8 -5×10 8 , 5×10 8 -1×10 9 , 1×10 9 -2×10 9 , 2×10 9 -5×10 9 , or 5×10 9 -1×10 10 CFU/ml. In embodiments, the administration is performed twice per day. In embodiments, the subject is a human. In embodiments, the microbial growth to be inhibited is growth of Pseudomonas aeruginosa or Staphylococcus aureus ( S. aureus or SA), Streptococcus pyogenes ( S. pyogenes or SP), or Acinetobacter baumannii ( A. baumannii or AB).
In certain aspects, the present disclosure provides a method of supplying nitric oxide to a subject, comprising positioning an effective dose of the N. eutropha bacteria described herein (e.g., strain D23) in close proximity to the subject.
In certain aspects, the present disclosure provides a method of reducing body odor, comprising topically administering to a subject in need thereof an effective dose of the N. eutropha bacteria described herein (e.g., strain D23).
In certain aspects, the present disclosure provides a method of treating a disease associated with low nitrite levels, comprising topically administering to a subject in need thereof a therapeutically effective dose of the N. eutropha bacteria described herein (e.g., strain D23).
In embodiments, the disease is HIV dermatitis, infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, or cancer.
In certain aspects, the present disclosure provides a method of treating a skin disorder, comprising topically administering to a subject in need thereof a therapeutically effective dose of the N. eutropha bacteria as described herein (e.g., strain D23). In related aspects, the disclosure provides an N. eutropha bacteria as described herein (e.g., strain D23) for treating a disorder such as a skin disorder. In related aspects, the disclosure provides an N. eutropha bacteria as described herein (e.g., strain D23) for the manufacture of a medicament, e.g., a medicament for treating a skin disorder.
In embodiments, the skin disorder is acne, e.g., acne vulgaris, rosacea, eczema, or psoriasis. In some embodiments, the skin disorder is an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer. In some embodiments, topically administering comprises pre-treating the subject with N. eutropha , e.g., an N. eutropha described herein. In some embodiments, topically administering comprises topically administering prior to occurrence of the skin disorder. In some embodiments, topically administering comprises topically administering subsequent to occurrence of the skin disorder.
In certain aspects, the present disclosure provides a method of promoting wound healing or closure, comprising administering to a wound an effective dose of the N. eutropha bacteria as described herein (e.g., strain D23). In related aspects, the disclosure provides an N. eutropha bacteria as described herein (e.g., strain D23) for promoting wound healing. In related aspects, the disclosure provides an N. eutropha bacteria as described herein (e.g., strain D23) for the manufacture of a medicament, e.g., a medicament for promoting wound healing.
In embodiments, the wound comprises one or more undesirable bacteria, e.g., pathogenic bacteria. In embodiments, the wound comprises S. aureus, P. aeruginosa, P. aeroginosa , or A. baunannii.
In embodiments, the N. eutropha is administered to the subject prior to occurrence of the wound. In embodiments, administering to the wound comprises administering to the subject prior to occurrence of the wound. In embodiments, the method further comprises administering N. eutropha (e.g., an N. eutropha described herein, e.g., strain D23) to the wound subsequent to occurrence of the wound. In some aspects, the disclosure provides a method of killing or inhibiting growth of pathogenic bacteria comprising contacting, e.g., applying, N. eutropha bacteria (e.g., N. eutropha described herein, e.g., strain D23) to the skin.
In embodiments, the pathogenic bacteria contribute to one or more of the following conditions: HIV dermatitis, an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, uticaria, rosacea, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, pneumonia, primary immunodeficiency, epidermal lysis bulosa, or cancer.
In embodiments, the condition is an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer. In embodiments, the condition is a venous leg ulcer. In embodiments, the condition is acne, e.g., acne vulgaris. In embodiments, the condition is acne vulgaris. In embodiments, the pathogenic bacteria is one or more of Propionibacterium acnes, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes , or Acinetobacter baumannii . In embodiments, the method further comprises determining whether the subject is in need of killing or inhibiting growth of pathogenic bacteria, e.g., determining that the subject is in need of killing or inhibiting growth of pathogenic bacteria. In embodiments, the method further comprises selecting the subject in need of killing or inhibiting growth of pathogenic bacteria.
In some embodiments, the N. eutropha catalyze the following reactions.
At a neutral pH, ammonia generated from ammonium around neutral pH conditions is the substrate of the initial reaction. The conversion of ammonia to nitrite takes place in two steps catalyzed respectively by ammonia monooxygenase (Amo) and hydroxylamine oxidoreductase (Hao), as follows:
NH 3 +2H + +2 e −+O 2 →NH 2 OH+H 2 O (A)

NH 2 OH+H 2 O→NO 2 − +4 e −+5H + (B)

In some instances, reaction B is reported as follows, to indicate nitrous acid (HNO 2 ) formation at low pH:
NH 2 OH+H 2 O→HNO 2 +4 e −+4H +

In certain embodiments, the N. eutropha has a doubling time of less than 4, 5, 6, 7, 8, 9, or 10 hours, for instance about 8 hours, e.g., 7-9 hours or 6-10 hours, when grown under batch culture conditions. In some embodiments, the doubling time is at least 3, 4, 5, or 6 hours under batch culture conditions. In some embodiments, the N. eutropha has a doubling time of less than 16, 18, 20, 22, 24, or 26 hours, for instance about 20 hours, e.g., 19-21 hours or 18-22 hours, when grown under chemostat (i.e., continuous culture) conditions. In some embodiments, the doubling time is at least 10, 12, 14, 16, or 18 hours under chemostat conditions.
In certain embodiments, a continuous culture of N. eutropha at an OD600 of about 0.15-0.18 is capable of reaching an OD600 of about 0.5-0.6 in about 1-2 days. For instance, in some embodiments, a continuous culture of N. eutropha may grow from an OD600 of about 0.15 to at least 0.3, 0.4, 0.5, 0.6, 0.7, or 0.8 over about 1 day; in embodiments the culture may reach an OD in range of 0.4-0.6 or 0.3-0.7 over about 1 day. In embodiments, the continuous culture of N. eutropha may grow from an OD600 of about 0.15 to at least 0.3, 0.4, 0.5, 0.6, 0.7, or 0.8 over about 2 days; in embodiments the culture may reach an OD in the range of 0.4-0.6 or 0.3-0.7 over about 2 days. In some embodiments, the continuous culture conditions comprise growth in a bioreactor in N. europaea medium, optionally comprising about 200 mM NH 4 + . In some embodiments, the continuous culture conditions are conditions set out in Example 2.
In certain embodiments, the N. eutropha are capable of converting NH 4 + (e.g., at about 200 mM) to nitrite (e.g., reaching up to about 180 mM) at a rate of at least about 50, 75, 125, or 150 micromoles NO 2 − per minute, e.g., about 100-150, 75-175, 75-125, 100-125, 125-150, or 125-175 micromoles/minute, e.g., about 125 micromoles NO 2 − per minute. In some embodiments, the reaction rates are measured in an about 1 L chemostat culture of about 10 9 CFU/ml over the course of 24 hours.
In certain embodiments, the N. eutropha are capable of growing in medium comprising at least 50 mM, 75 mM, 100 mM, 125 mM, 150 mM, 175 mM, 200 mM, 225 mM, 250 mM, 275 mM, or 300 mM NH 4 + (or NH 3 ), e.g., about 150-200, 175-225, 200-250, 225-275, 250-300 mM, e.g., about 200 or about 250 mM. In certain embodiments, the N. eutropha is grown in a bioreactor under these concentrations of ammonium. In some embodiments, when the N. eutropha is grown under these concentrations of ammonium, the concentration of nitrate or nitrite is capable of reaching at least 60, 80, 100, 120, 140, 160, or 180 mM, e.g., about 140-180, 160-200, or 140-200 mM, e.g., about 160 or 180 mM.
In certain aspects, the present disclosure provides high density cultures of N. eutropha , e.g., N. eutropha strain D23. For instance, the high density culture composition may comprise a cell suspension of an actively dividing culture of N. eutropha bacteria having an OD600 of at least about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, or 0.7, e.g., about 0.2-0.6, 0.3-0.6, 0.4-0.6, 0.5-0.6, or 0.4-0.7, wherein the composition is substantially free of other organisms
In some embodiments, the N. eutropha are stable for at least 2 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, or 6 months when stored at 4° C. In some embodiments, the method of storage comprises resuspending the cells in a buffer comprising one or more of Na 2 HPO 4 and MgCl 2 , for instance 50 mM Na 2 HPO 4 and 2 mM MgCl 2 , for instance the storage buffer described in Example 2. For example, the storage conditions may be those specified in Example 2. In some embodiments, the N. eutropha are continuously cultured at 200 mM NH 4 + at a pH of 6-8, e.g., 7, before storage at 4°. Stability can include one or more of 1) retaining viability, 2) retaining a relevant property such as the ability to produce a given level of nitrite.
In certain embodiments, NH 4 + and NH 3 may be used interchangeably throughout the disclosure.
This disclosure provides, inter alia, a method of changing a composition of a skin microbiome of a subject. The method comprises administering, e.g., applying, a preparation comprising ammonia oxidizing bacteria to a surface of the skin, wherein the amount and frequency of administration, e.g., application, is sufficient to reduce the proportion of pathogenic bacteria on the surface of the skin.
Ammonia oxidizing bacteria are, in some embodiments, ubiquitous Gram-negative obligate chemolithoautotrophic bacteria with a unique capacity to generate energy exclusively from the conversion of ammonia to nitrite.
In some embodiments, the method may further comprise, selecting the subject on the basis of the subject being in need of a reduction in the proportion of pathogenic bacteria on the surface of the skin.
In some embodiments, the preparation comprising ammonia oxidizing bacteria comprises at least one of ammonia, ammonium salts, and urea.
In some embodiments, the preparation comprising ammonia oxidizing bacteria comprises a controlled release material, e.g., slow release material.
In some embodiments, the preparation of ammonia oxidizing bacteria, comprises an excipient, e.g., one of a pharmaceutically acceptable excipient or a cosmetically acceptable excipient. The excipient, e.g., one of the pharmaceutically acceptable excipient and the cosmetically acceptable excipient, may be suitable for one of topical, nasal, pulmonary, and gastrointestinal administration. The excipient, e.g., one of the pharmaceutically acceptable excipient and the cosmetically acceptable excipient may be a surfactant. The surfactant may be selected from the group consisting of cocamidopropyl betaine (ColaTeric COAB), polyethylene sorbitol ester (e.g., Tween 80), ethoxylated lauryl alcohol (RhodaSurf 6 NAT), sodium laureth sulfate/lauryl glucoside/cocamidopropyl betaine (Plantapon 611 L UP), sodium laureth sulfate (e.g., RhodaPex ESB 70 NAT), alkyl polyglucoside (e.g., Plantaren 2000 N UP), sodium laureth sulfate (Plantaren 200), Dr. Bronner's Castile soap, lauramine oxide (ColaLux Lo), sodium dodecyl sulfate (SDS), polysulfonate alkyl polyglucoside (PolySufanate 160 P), sodium lauryl sulfate (Stepanol-WA Extra K), and any combination thereof. Dr. Bronner's Castile soap comprises water, organic coconut oil, potassium hydroxide, organic olive oil, organic fair deal hemp oil, organic jojoba oil, citric acid, and tocopherol. In some embodiments, the excipient comprises one or more of, e.g., all of, water, organic coconut oil, potassium hydroxide, organic olive oil, organic fair deal hemp oil, organic jojoba oil, citric acid, and tocopherol.
In some embodiments, the preparation may be substantially free of other organisms.
In some embodiments, the preparation may be disposed in a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage. The preparation may be provided as a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage.
In some embodiments, the preparation may comprise a moisturizing agent, deodorizing agent, scent, colorant, insect repellant, cleansing agent, or UV-blocking agent.
In some embodiments, the excipient, e.g., the pharmaceutically acceptable excipient or the cosmetically acceptable excipient may comprise an anti-adherent, binder, coat, disintegrant, filler, flavor, color, lubricant, glidant, sorbent, preservative, or sweetener.
In some embodiments, the preparation comprising ammonia oxidizing bacteria may comprise between about 10 8 and about 10 14 CFU/L. In certain aspects, the preparation may comprise between about 1×10 9 CFU/L and about 10×10 9 CFU/L.
In some embodiments, the preparation comprising ammonia oxidizing bacteria may comprise between about 50 milligrams (mg) and about 1000 mg of ammonia oxidizing bacteria.
In some embodiments, the mass ratio of ammonia oxidizing bacteria to the excipient, e.g., the pharmaceutically acceptable excipient or the cosmetically acceptable excipient is in a range of about 0.1 grams per liter to about 1 gram per liter.
In some embodiments, the preparation of ammonia oxidizing bacteria are useful in the treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, or a treatment to inhibit microbial growth, e.g., pathogenic bacterial growth.
In some embodiments, the ammonia oxidizing bacteria is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio , and combinations thereof. The preparation may further comprise an organism selected from the group consisting of Lactobacillus, Streptococcus, Bifidobacter , and combinations thereof. In certain aspects, the preparation is substantially free of organisms other than ammonia oxidizing bacteria.
In some embodiments, the preparation comprising ammonia oxidizing bacteria may comprise ammonia oxidizing bacteria in a growth state. In some embodiments, the preparation comprising ammonia oxidizing bacteria may comprise ammonia oxidizing bacteria in a storage state.
In some embodiments, the methods of the present disclosure may be used to deliver a cosmetic product. In some embodiments, the methods of the present disclosure may be used to deliver a therapeutic product. The preparation may be useful for treatment of at least one of HIV dermatitis, infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, uticaria, rosacea, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, pneumonia, primary immunodeficiency, epidermal lysis bulosa, or cancer.
In certain aspects, the preparation may be useful for treatment of at least one of acne, e.g., acne vulgaris, eczema, psoriasis, uticaria, rosacea, and skin infections.
In some embodiments, the preparation may be provided in a container, the preparation and the container having a weight of less than about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 grams.
In some embodiments, the preparation has less than about 0.1% to about 10% of surfactant. In certain aspects, the preparation may be substantially free of surfactant.
In some embodiments, the preparation may comprise a chelator. In some embodiments, the preparation may be substantially free of a chelator.
In some embodiments, the method may comprise applying the preparation about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 times per day. In certain aspects, the preparation may be applied one time per day. In certain other aspects, the preparation may be applied two times per day.
In some embodiments, the preparation may be applied for about 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, or 84-91 days. In certain aspects, the preparation may be applied for about 16 days.
In some embodiments, the method may further comprise obtaining a sample from the surface of the skin. In certain aspects, the method may further comprise isolating DNA of bacteria in the sample. In certain aspects, the method may further comprise sequencing DNA of bacteria in the sample.
In some embodiments, administering the ammonia oxidizing bacteria provides for an increase in the proportion of non-pathogenic bacteria on the surface. In certain aspects, the non-pathogenic bacteria may be commensal non-pathogenic bacteria. In certain aspects, the non-pathogenic bacteria is commensal non-pathogenic bacteria of a genus of Staphylococcus . In certain aspects, the non-pathogenic bacteria may be commensal non-pathogenic bacteria Staphylococcus epidermidis.
In some embodiments, the proportion of non-pathogenic bacteria Staphylococcus is, or is identified as being, increased after about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks. In certain aspects, the proportion of non-pathogenic bacteria Staphylococcus epidermidis Staphylococcus is, or is identified as being, increased after about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks.
In some embodiments, potentially pathogenic or disease associated Propionibacteria is, or is identified as being, reduced after about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks.
In some embodiments, potentially pathogenic or disease associated Stenotrophomonas is, or is identified as being, reduced after about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks.
In some embodiments, the surface of the skin comprises a wound.
In some embodiments, a method of treating acne e.g., acne vulgaris, may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating eczema may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating psoriasis may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating uticaria may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating rosacea may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating skin infection may be provided by one or more methods of the present disclosure. In some embodiments, a method of reducing an amount of undesirable bacteria on a surface of a subject is provided.
In some embodiments, the method herein (e.g., a method of administering a N. eutropha bacterium, e.g., a bacterium of strain D23 to a subject in need thereof), further comprise treating the subject with an antibiotic. In embodiments, the antibiotic is Tetracycline, a Lincosamide such as Clindamycin, a Macrolide such as Erythromycin, an Aminoglycoside such as Gentamicin, a β-lactam such as Piperacillin, β-lactamase inhibitor such as Tazobactam, or any combination thereof (such as a combination of a β-lactam such as Piperacillin and a β-lactamase inhibitor such as Tazobactam). In some embodiments, the antibiotic is an antibiotic to which the bacterium is sensitive. In embodiments, the antibiotic is administered after the bacterium has achieved the desired therapeutic effect. In embodiments, the antibiotic is an antibiotic to which the bacterium is resistant. In embodiments, the antibiotic is administered before or during the period in which the bacterium is producing its therapeutic effect.
It is understood that compositions and methods herein involving a bacterium can also involve a plurality of bacteria. For instance, a method of administering a N. eutropha bacterium can also involve administering a plurality of N. eutropha bacteria.
The present disclosure also provides, in certain aspects, a nucleic acid comprising a sequence of consecutive nucleotides (e.g., 15-100 nucleotides) from within the D23 genome, e.g., a sequence of a gene provided herein, e.g., a gene described in Table 1, FIG. 6-8 or Supplementary Table 1, or SEQ ID NO: 66, or a reverse complement of any of the foregoing. In a related aspect, the present disclosure provides a nucleic acid comprising a sequence of consecutive nucleotides (e.g., 15-100 nucleotides) from within SEQ ID NO: 1 or a reverse complement thereof. In a related aspect, the present disclosure provides a nucleic acid comprising a sequence of consecutive nucleotides (e.g., 15-100 nucleotides) from within a gene of Table 1 (e.g., a sequence of SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, or 33) or a reverse complement thereof.
In some embodiments, the nucleic acid has a non-naturally occurring sequence or another modification such as a label, or both. In some embodiments, the sequence of consecutive nucleotides is not a sequence found in N. Eutropha strain C91. In some embodiments, the nucleic acid comprises a heterologous sequence 5′ to the sequence of 15-100 consecutive nucleotides, or a heterologous sequence 3′ to the sequence of 15-100 consecutive nucleotides, or both. In some embodiments, the nucleic acid has a length of 10-15, 15-20, 20-25, 25-30, 30-24, 35-40 nucleotides. In some embodiments, the nucleic acid is bound, e.g., covalently bound, to a detectable label, e.g., a fluorescent label. In some embodiments, the nucleic acid comprises 10-15, 15-20, 20-25, 25-30, 30-24, 35-40, 40-50, 50-60, 60-70, 70-80, 80-90, or 90-100 consecutive nucleotides from within the D23 genome. In some embodiments, the nucleic acid comprises at least about 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 consecutive nucleotides from within the D23 genome. In some embodiments, the nucleic acid is DNA.
In some aspects, the disclosure provides a composition or a kit comprising a first nucleic acid and a second nucleic acid. In some embodiments, the first nucleic acid comprises consecutive nucleotides (e.g., 15-100) from within SEQ ID NO: 1, SEQ ID NO: 66, a gene of FIGS. 6-8 , or a gene of Table 1, or a reverse complement thereof. In some embodiments, the second nucleic acid comprises consecutive nucleotides (e.g., 15-100) from within SEQ ID NO: 1, SEQ ID NO: 66, a gene of FIGS. 6-8 , or a gene of Table 1, or a reverse complement thereof. In some embodiments, the nucleic acid has a non-naturally occurring sequence, e.g., a sequence not found in N. eutropha strain C91. In some embodiments, the first nucleic acid and the second nucleic acid define an amplicon in a gene of Table 1, e.g., a sequence of SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, or 33) or a reverse complement thereof.
In some embodiments, the first nucleic acid has a sequence that corresponds to a first region of SEQ ID NO: 1, and the reverse complement of the second nucleic acid has a sequence that corresponds to a second region of SEQ ID NO: 1, and the first and second regions are separated by a distance suitable for PCR. In some embodiments, the reverse complement of the first nucleic acid has a sequence that corresponds to a first region of SEQ ID NO: 1, and the second nucleic acid has a sequence that corresponds to a second region of SEQ ID NO: 1, and the first and second regions are separated by a distance suitable for PCR. In an embodiment, the distance suitable for PCR is no more than 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 nucleotides of SEQ ID NO: 1. In some embodiments, the first nucleic acid and second nucleic acid delineate an amplicon in SEQ ID NO: 1. In some embodiments, the first nucleic acid and second nucleic acid each has a melting temperature (Tm) suitable for PCR, e.g., about 55-65° or about 60-65° C. In some embodiments, the Tm of the first nucleic acid is within 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1° C. of the Tm of the second nucleic acid.
In some embodiments, the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid further comprises a heterologous sequence 5′ to the sequence of consecutive nucleotides. Alternatively or in combination, in some embodiments, the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid further comprises a heterologous sequence 3′ to the sequence of consecutive nucleotides from within SEQ ID NO: 1 or SEQ ID NO: 66. In some embodiments, the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid has a length of 15-20, 20-25, 25-30, 30-24, or 35-40 nucleotides. In some embodiments, the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid is bound, e.g., covalently bound, to a detectable label, e.g., a fluorescent label. In some embodiments, the first nucleic acid comprises, or consists of, a sequence of SEQ ID NO: 64. In some embodiments, the second nucleic acid comprises, or consists of, a sequence of SEQ ID NO: 65. In some embodiments, the first nucleic acid, the second nucleic acid, or both, are DNA.
In some embodiments, the composition or kit comprises at least two (e.g., 3, 4, 5, 6, 7, 8, 9, or 10) pairs of primers, each pair recognizing an amplicon in a gene of Table 1 (e.g., a sequence of SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, or 33) or a reverse complement thereof. In some embodiments, a first pair of primers recognizes an amplicon in an Amo gene (e.g., AmoA1, AmoA2, AmoB1, AmoB2, AmoC1, AmoC2, or AmoC3) and the second pair of primers recognizes an amplicon in an Amo gene (e.g., AmoA1, AmoA2, AmoB1, AmoB2, AmoC1, AmoC2, or AmoC3). In some embodiments, a first pair of primers recognizes an amplicon in an AmoA gene (e.g., AmoA1 or AmoA2). In some embodiments, a second pair of primers recognizes an amplicon in an AmoB gene (e.g., AmoB1 or AmoB2). In some embodiments, a third pair of primers recognizes an amplicon in an AmoC gene (e.g., AmoC1, AmoC2, or AmoC3).
In some embodiments, the kit comprises a first container in which the first nucleic acid is disposed and a second container in which the second nucleic acid is disposed. The kit may comprise additional containers, e.g., for a third, fourth, fifth, or sixth nucleic acid. In some embodiments, a pair of primers recognizing an amplicon is stored in a single container.
The present disclosure also provides, in some aspects, a nucleic acid comprising, or consisting of, the sequence of SEQ ID NO: 64. The present disclosure also provides, in some aspects, a nucleic acid comprising, or consisting of, the sequence of SEQ ID NO: 65. The present disclosure also provides, in some aspects, the present disclosure provides a molecule comprising a nucleic acid described herein and a detectable label, e.g., a fluorescent label. The nucleic acid may consist of a sequence of SEQ ID NO: 64 or SEQ ID NO: 65, for example.
The present disclosure provides, in some aspects, a composition comprising a first molecule and a second molecule. In some embodiments, the first molecule comprises a nucleic acid described herein, e.g., a nucleic acid consisting of the sequence of SEQ ID NO: 64, and optionally comprises a detectable label, e.g., a fluorescent label. In some embodiments, the second molecule comprises a nucleic acid described herein, e.g., a nucleic acid consisting of the sequence of SEQ ID NO: 65, and optionally comprises a detectable label, e.g., a fluorescent label.
In some embodiments, the kit comprises a first container in which the first molecule is disposed and a second container in which the second molecule is disposed.
In some embodiments, a kit described herein further comprises one or more of a buffer, an enzyme (e.g., a polymerase such as a thermostable polymerase such as Taq), nucleotides (e.g., dNTPs), and chain-terminating nucleotides (e.g., dideoxy nucleotides) which are optionally dye-labeled; these components may be provided separately or as part of a single composition.
In certain aspects, this disclosure provides a method of detecting whether a D23 N. eutropha nucleic acid is present in a sample, comprising: performing a polymerase chain reaction (PCR) on the sample using primers specific to D23 N. eutropha , and determining whether a PCR product is produced, wherein the presence of a PCR product indicates that the D23 N. eutropha nucleic acid was present in the sample. In embodiments, at least two PCR reactions are performed, e.g., 3, 4, 5, 6, 7, 8, 9 or 10 PCR reactions. In embodiments, the PCR reactions are performed in separate reaction volumes. In embodiments, two or more PCR reactions are performed in multiplex.
In some embodiments, the primers specific to D23 N. eutropha are a first nucleic acid and second nucleic acid described herein, e.g., a first and second nucleic acid from a composition or kit described herein. In some embodiments, the first primer comprises or consists of a sequence of SEQ ID NO: 65, and the second primer comprises or consists of a sequence of SEQ ID NO: 66.
In some embodiments, the PCR reaction is a quantitative or real-time PCR reaction. In some embodiments, the PCR reaction comprises a TaqMan reaction. In some embodiments, the PCR reaction comprises cycling the temperature of a reaction mixture between a denaturing temperature (e.g., about 95° C.), an annealing temperature (e.g., 45-68, 55-65, or 60-65° C.), and an elongation temperature (e.g., about 68° C.) for a number of cycles sufficient to produce a detectable PCR product, e.g., about 10, 15, 20, 25, or 30 cycles. In some embodiments, detecting the PCR product comprises detecting fluorescence from the PCR product. In some embodiments, a positive control is performed, e.g., using a known D23 N. eutropha nucleic acid as a template. In some embodiments, a negative control is used, e.g., using no template or using another bacterial nucleic acid as a template.
In certain aspects, the disclosure provides a method of detecting whether a D23 N. eutropha nucleic acid is present in a sample, comprising detecting binding of a nucleic acid described herein to a sample, wherein the presence of binding indicates that the D23 N. eutropha nucleic acid was present in the sample. In some embodiments, binding is detected by primer extension or RNase protection.
In some embodiments of the methods herein, the sample comprises at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 strains of bacteria. In some embodiments, the sample is from the skin of a subject, e.g., a human subject. In some embodiments, the methods herein comprise detecting one or more additional types of bacterium in the sample, e.g., Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes , or Acinetobacter baumannii.
The disclosure contemplates all combinations of any one or more of the foregoing aspects and/or embodiments, as well as combinations with any one or more of the embodiments set forth in the detailed description and examples.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the growth of a mixed culture of bacteria comprising N. eutropha strain D23. The optical density at a 600 nm wavelength is plotted relative to time.
FIG. 2A shows the nitrite production of a mixed culture of bacteria comprising N. eutropha strain D23. The nitrite concentration is plotted relative to time.
FIG. 2B-I shows the nitrite production kinetics by N. eutropha D23 in batch culture. The nitrite concentration is plotted relative to time.
FIG. 2B -II shows the nitrite production kinetics by N. eutropha D23 in vitro. The nitrite concentration is plotted relative to time.
FIG. 2C shows N. eutropha D23 stability upon storage at 4° C. The nitrite concentration is plotted relative to time.
FIG. 3A shows the N. eutropha D23's ability to inhibit the growth of P. aeruginosa (left panel) and S. aureus (right panel) in co-culture experiments. The amount of each type of undesirable bacteria (in CFU/ml) is plotted relative to time. In this figure, “AOB” refers to strain D23.
FIG. 3B shows the N. eutropha D23's ability to inhibit the growth of Streptococcus pyogenes (left panel) and Acinetobacter baumannii (right panel) in co-culture experiments. The amount of each type of undesirable bacteria (in CFU/ml) is plotted relative to time. In this figure, “AOB” refers to strain D23.
FIG. 3C shows the N. eutropha D23's ability to inhibit the growth of Propionibacterium acnes in co-culture experiments. The amount of each type of undesirable bacteria (in CFU/ml) is plotted relative to time. In this figure, “AOB” refers to strain D23.
FIG. 4A (top panel) plots the NO 2 − concentration over time in a co-culture experiment. The bottom panel plots pH over time in a co-culture experiment.
FIG. 4B (top panels) plots the CFU/ml of the indicated bacteria over time in a co-culture experiment. The center panels plot the NO 2 − concentration over time in a co-culture experiment.
The bottom panels plot pH over time in a co-culture experiment.
FIG. 4C plots the microbicidal activity of D23 against skin pathogens.
FIG. 4D plots the microbicidal activity of D23 against skin pathogens.
FIG. 4E shows an alternative plot of microbicidal activity of D23 against skin pathogens.
FIG. 5A plots the percent wound closure over time in an experiment testing D23's ability to improve wound healing.
FIG. 5B plots CT 50 for various D23 treatments.
FIG. 5C plots the percent wound closure over time in an experiment testing D23's ability to improve wound healing.
FIG. 5D plots the percent wound closure over time in an experiment testing D23's ability to improve wound healing.
FIG. 5E plots CT 50 for various D23 treatments.
FIG. 5F shows images of D23 enhanced wound healing in diabetic mice at Day 1, Day 11, and Day 15.
FIG. 5G shows blood glucose measurements for various concentrations of D23.
FIG. 5H shows body weight of test subjects over the course of testing.
FIG. 5I shows body weight of test subjects over the course of testing.
FIG. 5J shows PCR scores for a scalp test of subjects. AOB refers to D23 in this Figure.
FIG. 5K shows a schematic of a human volunteer study for an evaluation of a Nitrosomonas -containing topical suspension (AOB-001).
FIG. 5L (left panel) shows PCR analyses of scalp swabs collected during the study. Percent-positive samples for AOB-specific three-gene signature (amoA, amoB, amoC). The right panel shows PCR analyses of scalp swabs collected during the study. Composite PCR scores for a total of six samples collected from each of 23 volunteers. The scoring scheme used for the positive samples collected at each of six sampling points is indicated.
FIG. 5M shows genus-level bacterial diversity as determined by 16S rDNA sequencing in skin swab samples collected before and after topical application of AOB-001. The percentage of the total sequence reads representing each of twelve bacterial genera in samples collected at baseline prior to application (Day 0) and immediately after the one week application (Day 8), or one week after stopping topical application (Day 14), are shown. The proportions of Acinetobacter, Burkholderia, Enterobacter, Escherichia Shigella, Klebsiella, Nitrosomonas, Pantoea, Propionibacterium, Pseudomonas, Serratia, Staphylococcus , and Stenotrophomonas are shown.
FIG. 5N-A shows changes in abundance of Nitrosomonas and other species in skin samples collected before and after AOB-001 application. The percentages of the total 16S rDNA sequence reads representing Nitrosomonas prior to application (Day 0), immediately after the one-week application (Day 8), or one week after terminating application (Day 14) are shown.
FIG. 5N-B shows changes in abundance of Nitrosomonas and other species in skin samples collected before and after AOB-001 application. Changed patterns in abundance of species were detected by 16S rDNA sequencing in Day 0 versus Day 8 samples collected from AOB users.
FIG. 5O shows user evaluation of AOB-001. Assessment of AOB-001 cosmetic effects as provided by 23 volunteers upon completion of the one week application to their scalp and face. Subjects were plotted in order of increasing composite PCT scores. (2=agree strongly; 0=no change; −2=disagree strongly).
FIG. 6 is a table displaying unique D23 genes that have either an assigned open reading frame (ORF) number and a function based on sequence analysis, or a hypothetical gene above 200 base pairs in length. The column headers signify as follows: Feature.ID=a unique identifier for the gene; Type=type of gene, where CDS indicates a protein-coding DNA sequence; Start=starting position of gene in the genome sequence of SEQ ID NO: 1; Stop=end of gene in the genome sequence of SEQ ID NO: 1; Frame=reading frame; Length=length of gene in base pairs; Function=gene or protein function based on sequence analysis; Subsystem=category of gene function; D23GbkId=a gene identifier.
FIG. 7 is a table displaying unique D23 genes below 200 base pairs that have an assigned ORF number. Column headers are as described in FIG. 6 .
FIG. 8 is a table displaying unique D23 genes with no assigned ORF number. Column headers are as described in FIG. 6 .
FIG. 9 lists unique C91 genes that do not have a homolog in D23.
FIG. 10 is a sequence alignment between the AmoA1 and AmoA2 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 10 discloses SEQ ID NOS 6, 12, 36 and 42, respectively, in order of appearance.
FIG. 11 is a sequence alignment between the AmoB1 and AmoB2 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 11 discloses SEQ ID NOS 8, 14, 38 and 44, respectively, in order of appearance.
FIG. 12 is a sequence alignment between the AmoC1 and AmoC2 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 12 discloses SEQ ID NOS 34, 40, 10 and 4, respectively, in order of appearance.
FIG. 13 is a sequence alignment between the AmoC3 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 13 discloses SEQ ID NOS 46 and 16, respectively, in order of appearance.
FIG. 14 A and FIG. 14 B show a sequence alignment between the Hao1, Hao2, and Hao3 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 14 discloses SEQ ID NOS 20, 22, 18, 50, 52 and 48, respectively, in order of appearance.
FIG. 15 is a sequence alignment between the cycA1, cycA2, and cycA3 genes in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 15 discloses SEQ ID NOS 26, 28, 24, 58, 56 and 54, respectively, in order of appearance.
FIG. 16 is a sequence alignment between the cycB1 and cycB2 genes in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 16 discloses SEQ ID NOS 30, 32, 60 and 62, respectively, in order of appearance.
FIG. 17 shows a bar graph of proportion of bacteria, by genus versus day.
FIG. 18 shows a bar graph of proportion of bacteria, by genus versus bacteria genus, for day 0, day 1, day 8, day 14, and day 16.



Supplementary Table 1 displays the genome annotation of 2,777 genes identified in strain D23 using sequence analysis. Column headers are as described in FIG. 6 . “C91 Alias” refers to a homolog in strain C91. Supplementary Table 1 is appended to the end of the Detailed Description and Examples.
Supplementary Table 2 displays the sequences of selected proteins genes identified in strain D23. Supplementary Table 2 is appended to the end of the Detailed Description and Examples.
DETAILED DESCRIPTION
Ammonia-oxidizing bacteria (AOB) of the genus Nitrosomonas are Gram-negative obligate autotrophic bacteria with a unique capacity to generate nitrite and nitric oxide exclusively from ammonia as an energy source. They are widely present both in soil and water environments and are essential components of environmental nitrification processes. Due to the roles of nitrite and nitric oxide on human skin as important components of several physiological functions, such as vasodilation, skin inflammation and wound healing, these bacteria may have beneficial properties for both healthy and immunopathological skin conditions. These bacteria may be safe for use in humans because they are slow-growing, cannot grow on organic carbon sources, may be sensitive to soaps and antibiotics, and have never been associated with any disease or infection in animals or humans.
1. DEFINITIONS
An ammonia oxidizing bacterium refers to a bacterium capable of oxidizing ammonia or ammonium to nitrite at a rate, e.g., a substantial rate, e.g., a pre-determined rate, e.g., at least the rate depicted in any one of FIG. 2A, 2B, 2C, 4A, 4B , or 5 or at least 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, or 10% of that rate. In some embodiments, the substantial rate refers to the conversion of ammonium ions (NH 4 + )(e.g., at about 200 mM) to nitrite (NO 2 − ) at a rate of at least 50, 75, 125, or 150 micromoles NO 2 − per minute, e.g., about 100-150, 75-175, 75-125, 100-125, 125-150, or 125-175 micromoles/minute, e.g., about 125 micromoles NO 2 − per minute. Examples of ammonia oxidizing bacteria include N. eutropha strains D23 and C91, and other bacteria in the genera Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosocystis, Nitrosolobus , and Nitrosovibrio . D23 Nitrosomonas eutropha strain refers to the strain, designated AOB D23-100, deposited with the American Tissue Culture Collection (ATCC) on Apr. 8, 2014 having accession number PTA-121157. The D23 Nitrosomonas eutropha of accession number PTA-121157 has a genome sequence as set out in SEQ ID NO: 1 herein. The nucleic acid sequence(s), e.g., genome sequence, of accession number PTA-121157 are hereby incorporated by reference in their entireties.
Optimized Nitrosomonas eutropha ( N. eutropha ), as that term is used herein, refers to an N. eutropha having an optimized growth rate; an optimized NH 4 + oxidation rate; or optimized resistance to NH 4 + . In an embodiment it differs from naturally occurring N. eutropha by at least one nucleotide, e.g., a nucleotide in a gene selected from ammonia monooxygenase, hydroxylamine oxidoreductase, cytochrome c554, and cytochrome c M 552. The difference can arise, e.g., through selection of spontaneously arising mutation, induced mutation, or directed genetic engineering, of the N. eutropha . In an embodiment it differs from a naturally occurring N. eutropha in that it has a constellation of alleles, not present together in nature. These differences may provide for one or more of a treatment or prevention of a skin disorder, a treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, and a treatment to inhibit microbial growth.
As used herein, “axenic” refers to a composition comprising an organism that is substantially free of other organisms. For example, an axenic culture of ammonia oxidizing bacteria is a culture that is substantially free of organisms other than ammonia oxidizing bacteria. For example, an axenic culture of N. eutropha is a culture that is substantially free of organisms other than N. eutropha . In some embodiments, “substantially free” denotes undetectable by a method used to detect other organisms, e.g., plating the culture and examining colony morphology, or PCR for a conserved gene such as 16S RNA. An axenic composition may comprise elements that are not organisms, e.g., it may comprise nutrients or excipients. Any embodiment, preparation, composition, or formulation of ammonia oxidizing bacteria discussed herein may comprise, consist essentially of, or consist of optionally axenic ammonia oxidizing bacteria.
Throughout this disclosure, formulation may refer to a composition or preparation.
As used herein, an “autotroph”, e.g., an autotrophic bacterium, is any organism capable of self-nourishment by using inorganic materials as a source of nutrients and using photosynthesis or chemosynthesis as a source of energy. Autotrophic bacteria may synthesize organic compounds from carbon dioxide and ATP derived from other sources, oxidation of ammonia to nitrite, oxidation of hydrogen sulfide, and oxidation of Fe 2+ to Fe 3+ Autotrophic bacteria of the present disclosure are incapable of causing infection.
Administered “in combination,” as used herein, means that two (or more) different treatments are delivered to the subject during the course of the subject's affliction with the disorder, e.g., the two or more treatments are delivered after the subject has been diagnosed with the disorder and before the disorder has been cured or eliminated. In some embodiments, the delivery of one treatment is still occurring when the delivery of the second begins, so that there is overlap. This is sometimes referred to herein as “simultaneous” or “concomitant” or “concurrent delivery”. In other embodiments, the delivery of one treatment ends before the delivery of the other treatment begins. This is sometimes referred to herein as “successive” or “sequential delivery.” In embodiments of either case, the treatment is more effective because of combined administration. For example, the second treatment is a more effective, e.g., an equivalent effect is seen with less of the second treatment, or the second treatment reduces symptoms to a greater extent, than would be seen if the second treatment were administered in the absence of the first treatment, or the analogous situation is seen with the first treatment. In some embodiments, delivery is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with one treatment delivered in the absence of the other. The effect of the two treatments can be partially additive, wholly additive, or greater than additive (i.e., synergistic). The delivery can be such that an effect of the first treatment delivered is still detectable when the second is delivered.
Complete N. europaea medium refers to the N. europaea growth medium described in Ensign et al., “In vitro activation of ammonia monooxygenase from Nitrosomonas europaea by copper.” J Bacteriol. 1993 April; 175(7):1971-80.
To “culture” refers to a process of placing an amount of a desired bacterium under conditions that promote its growth, i.e., promoting cell division. The conditions can involve a specified culture medium, a set temperature range, and/or an agitation rate. Bacteria can be cultured in a liquid culture or on plates, e.g., agar plates.
The term “isolated,” as used herein, refers to material that is removed from its original or native environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated by human intervention from some or all of the co-existing materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition, and still be isolated in that such vector or composition is not part of the environment in which it is found in nature.
The terms “nucleic acid,” “nucleic acid sequence,” “nucleotide sequence,” or “polynucleotide sequence,” and “polynucleotide” are used interchangeably. They refer to a polymeric form of nucleotides of any length, e.g., deoxyribonucleotides or ribonucleotides, or analogs thereof. The polynucleotide may be either single-stranded or double-stranded, and if single-stranded may be the coding strand or non-coding (antisense) strand. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.
The nucleic acid may be a recombinant polynucleotide, or a polynucleotide of genomic, cDNA, semisynthetic, or synthetic origin which either does not occur in nature or is linked to another polynucleotide in a nonnatural arrangement.
As used herein, the term “optimized growth rate” refers to one or more of: a doubling time of less than about 4, 5, 6, 7, 8, 9, or 10 hours when cultured under batch conditions as described herein in Example 2; a doubling time of less than about 16, 18, 20, 22, 24, or 26 hours, when grown under chemostat conditions as described herein in Example 2; or growing from an OD600 of about 0.15 to at least about 0.3, 0.4, 0.5, 0.6, 0.7, or 0.8 over about 1 or 2 days. In an embodiment, optimized growth rate is one having a doubling time that it is at least 10, 20, 30, 40, or 50% shorter than that of a naturally occurring N. eutropha.
As used herein, “optimized NH 4 + oxidation rate” refers to a rate of at least about 50, 75, 125, or 150 micromoles per minute of converting NH 3 or NH 4 + into NO 2 − . For instance, the rate may be at least about 50, 75, 125, or 150 micromoles per minute of converting NH 4 + (e.g., at about 200 mM) to NO 2 − . In an embodiment, an optimized NH 4 + oxidation rate is one in which NH 3 or NH 4 + is converted into NO 2 − ′ at least 10, 20, 30, 40, or 50% more rapidly than is seen with a naturally occurring N. eutropha.
Percent (%) amino acid sequence identity, with respect to the amino acid sequences here (e.g., proteins expressed by N. eutropha D23) is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference sequence, which may be a naturally-occurring N. eutropha sequence or an N. eutropha D23 sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the means of those skilled in the art, for instance, using publicly available computer software such as BLAST, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For instance, the WU-BLAST-2 software may be used to determine amino acid sequence identity (Altschul et al, Methods in Enzymology 266, 460-480 (1996); http://blast.wustl/edu/blast/README.html). WU-BLAST-2 uses several search parameters, most of which are set to the default values. The adjustable parameters are set with the following values: overlap span=1, overlap fraction=0.125, world threshold (T)=I 1. HSP score (S) and HSP S2 parameters are dynamic values and are established by the program itself, depending upon the composition of the particular sequence, however, the minimum values may be adjusted as appropriate.
Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements. Typical but not limiting conservative substitutions are the replacements, for one another, among the aliphatic amino acids Ala, Val, Leu and Ile; interchange of Ser and Thr containing hydroxy residues, interchange of the acidic residues Asp and Glu, interchange between the amide-containing residues Asn and Gln, interchange of the basic residues Lys and Arg, interchange of the aromatic residues Phe and Tyr, and interchange of the small-sized amino acids Ala, Ser, Thr, Met and Gly. Additional conservative substitutions include the replacement of an amino acid by another of similar spatial or steric configuration, for example the interchange of Asn for Asp, or Gln for Glu. Amino acid substitutions can also be the result of replacing one amino acid with another amino acid having dis-similar structural and/or chemical properties, i.e., non-conservative amino acid replacements. Insertions or deletions may optionally be in the range of 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity in the in vivo or in vitro assays for, e.g., metabolizing urea or ammonia.
Percent (%) sequence identity with respect to the nucleic acid sequences here (e.g., the N. eutropha D23 genome and portions thereof) is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the reference sequence, which may be a naturally-occurring N. eutropha sequence or an N. eutropha D23 sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleotide sequence identity can be achieved in various ways that are within the means of those skilled in the art, for instance, using publicly available computer software such as BLAST. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
The terms “polypeptide”, “peptide” and “protein” (if single chain) are used interchangeably herein to refer to amino acid polymers. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. The polypeptide can be isolated from natural sources, can be a produced by recombinant techniques from a eukaryotic or prokaryotic host, or can be a product of synthetic procedures.
As used herein, “optimized resistance to NH 4 + ” refers to an ability to grow in conditions of greater than 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, or 300 mM NH 3 or NH 4 + for at least about 24 or 48 hours. In an embodiment, an optimized resistance to NH 4 + refers to the ability to grow at least 10, 20, 30, 40, or 50% more rapidly, or at least 10, 20, 30, 40, or 50% longer, in the presence of a selected concentration of NH 3 or NH 4 + than can a naturally occurring N. eutropha.
As used herein with respect to a comparison between nucleic acid or protein sequences, “similar” means having homology. A similar gene or protein may comprise, e.g., substitutions (such as conservative or non-conservative substitutions), insertions (e.g., of at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30 amino acids, and for example up to 2, 3, 4, 5, 10, 15, 20, 25, 30, or 50 amino acids, or any positive combination thereof, or the number of nucleotides necessary to encode said amino acids), or deletions (e.g., of at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30 amino acids, and for example up to 2, 3, 4, 5, 10, 15, 20, 25, 30, or 50 amino acids, or any positive combination thereof, or the number of nucleotides necessary to encode said amino acids), or any combination thereof. Each of substitutions, insertions, and deletions may be positioned at the N-terminus, C-terminus, or a central region of the protein or gene. In embodiments, a conservative substitution is one that does not alter the charge and/or polarity and/or approximate size and/or geometry at the substituted position.
As used herein, “transgenic” means comprising one or more exogenous portions of DNA. The exogenous DNA is derived from another organism, e.g., another bacterium, a bacteriophage, an animal, or a plant.
As used herein, treatment of a disease or condition refers to reducing the severity or frequency of at least one symptom of that disease or condition, compared to a similar but untreated patient. Treatment can also refer to halting, slowing, or reversing the progression of a disease or condition, compared to a similar but untreated patient. Treatment may comprise addressing the root cause of the disease and/or one or more symptoms.
As used herein a therapeutically effective amount refers to a dose sufficient to prevent advancement, or to cause regression of a disease or condition, or which is capable of relieving a symptom of a disease or condition, or which is capable of achieving a desired result. A therapeutically effective dose can be measured, for example, as a number of bacteria or number of viable bacteria (e.g., in CFUs) or a mass of bacteria (e.g., in milligrams, grams, or kilograms), or a volume of bacteria (e.g., in mm 3 ).
As used herein, the term “viability” refers to the autotrophic bacteria's, e.g., ammonia oxidizing bacteria's, ability to oxidize ammonia, ammonium, or urea to nitrite at a pre-determined rate. In some embodiments, the rate refers to the conversion of ammonium ions (NH 4 + ) (e.g., at about 200 mM) to nitrite (NO 2 − ) at a rate of at least 50, 75, 125, or 150 micromoles NO 2 − per minute, e.g., about 100-150, 75-175, 75-125, 100-125, 125-150, or 125-175 micromoles/minute, e.g., about 125 micromoles NO 2 − per minute.
“Growth media” or “AOB media,” as referred to herein comprises the following components of Table 3 or Table 4 herein.
In some embodiments, the states most relevant to the present disclosure are the state of growth, e.g., maximal growth, characterized by a pH of at least about 7.6, ammonia, trace minerals, oxygen and carbon dioxide. Another state may be characterized by a pH of about 7.4 or less and characterized by an absence of carbon dioxide. Under low carbon dioxide conditions, ammonia oxidizing bacteria, e.g., Nitrosomonas , continues to oxidize ammonia into nitrite and generates ATP, but lacking carbon dioxide, e.g., lacking sufficient carbon dioxide, to fix and generate protein, it instead generates polyphosphate, which it uses as an energy storage medium. This may allow the ammonia oxidizing bacteria to remain in a “storage state” for a period of time, e.g., a pre-determined period of time, for example, at least 1, 2, 3, 4, 5, 6, 7, days, 1, 2, 3, 4 weeks, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months, 1, 2, 3, 4, or 5 years. In some embodiments, the ammonia oxidizing bacteria may remain in a storage state for at least about 6 months to about 1 year.
As used herein, “growth state” refers to autotrophic bacteria, e.g., ammonia oxidizing bacteria, in a state or in an environment, e.g., a media, e.g., a culture media, e.g., a growth media, that may have a pH of at least about 7.6. Levels of at least one of ammonia, ammonium ions, and urea may be between about 1 micromolar and 1000 millimolar. Levels of trace materials are between about 0.01 micromolar iron and 200 micromolar iron. Levels of oxygen are between about 5% and 100% oxygen saturation (e.g., of media). Levels of carbon dioxide are between about 20 ppm and 10% saturation (e.g., of media). In certain aspects, levels of at least one of ammonia, ammonium ions, and urea may be between about 10 micromolar and 100 millimolar. Levels of trace materials are between about 0.1 micromolar iron and 20 micromolar iron. Levels of oxygen are between about 5% and 100% oxygen saturation. Levels of carbon dioxide are between about 200 ppm and 5% saturation (e.g., of media).
As used herein, “polyphosphate loading state” refers to autotrophic bacteria, e.g., ammonia oxidizing bacteria, in a state or in an environment, e.g., a media, e.g., a culture media, e.g., a growth media, that may have a pH of about 7.4, or less. Levels of at least one of ammonia, ammonium ions, and urea are between about 1 micromolar and 2000 millimolar. Levels of trace materials are between 0.01 micromolar iron and 200 micromolar iron. Levels of oxygen are between about 0% and 100% 02 saturation (e.g., of media). Levels of carbon dioxide are between/less than about zero and 400 ppm, and phosphate levels greater than about 1 micromolar. In certain aspects, levels of at least one of ammonia, ammonium ions, and urea are between about 10 micromolar and 200 millimolar. Levels of trace materials are between 0.1 micromolar iron and 20 micromolar iron. Levels of oxygen are between about 5% and 100% 02 saturation. Levels of carbon dioxide are between/less than about zero and 200 ppm, and phosphate levels greater than about 10 micromolar.
The polyphosphate loading state may be induced for a period of time, e.g., a pre-determined period of time. The pre-determined period of time may the time period that allows sufficient polyphosphate accumulation in the ammonia oxidizing bacteria. This pre-determined period of time is the period of time suitable to provide for sufficient polyphosphate loading to allow for the ammonia oxidizing bacteria to be stored for an extended period of time. The pre-determined period of time may be at least partially based on a period of time of about 0.2-10 times, 0.3-5 times, 0.5-3 times, 0.5-1.5 times, or 0.5 to 1 times the doubling time for the ammonia oxidizing bacteria. The pre-determined period of time may be at least partially based on a period of time of about one doubling time for the ammonia oxidizing bacteria. In some embodiments, the pre-determined period of time is between about 8 hours and 12 hours. In some embodiments, the pre-determined period of time is about 10 hours. In some embodiments, the pre-determined period of time is about 24 hours.
A purpose of the polyphosphate loading state may be to provide AOB with sufficient ammonia, ammonium ions, and/or urea, and O 2 such that ATP can be produced, but to deny them CO 2 and carbonate such that they are unable to use that ATP to fix CO 2 and instead use that ATP to generate polyphosphate which may be stored by the bacteria.
As used herein, the term “storage state” refers to autotrophic bacteria, e.g., ammonia oxidizing bacteria, in a state or in an environment, e.g., a media, e.g., a culture media, e.g., a growth media, having a pH of about 7.4 or less (in some embodiments, the pH may be 7.6 or less). Levels of at least one of ammonia, ammonium ions, and urea are between about _1 and 1000 micromolar. Levels of trace materials are between about 0.1 and 100 micromolar. Levels of oxygen are between about 0 and 100% saturation (e.g., of media). Levels of carbon dioxide are between about 0 and 800 ppm. In certain aspects, levels of at least one of ammonia, ammonium ions, and urea are between about _10 and 100 micromolar. Levels of trace materials are between about 1 and 10 micromolar. Levels of oxygen are between about 0 and 100% saturation (e.g., of media). Levels of carbon dioxide are between about 0 and 400 ppm.
AOB are produced according to some embodiments of the present disclosure by generating AOB biomass during a growth state, then exposing the AOB to a polyphosphate loading state and then removing the media and resuspending the AOB in a buffer, e.g., a storage buffer (i.e., the storage state).
The ammonia oxidizing bacteria may remain in a “storage state” for a period of time, e.g., a pre-determined period of time, for example, at least 1, 2, 3, 4, 5, 6, 7, days, 1, 2, 3, 4 weeks, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months, 1, 2, 3, 4, or 5 years. In some embodiments, the ammonia oxidizing bacteria may remain in a storage state for at least about 6 months to about 1 year. Upon revival, the viability of the ammonia oxidizing bacteria is at least about 50%, 60%, 70%, 80%, 90%, or 100% of the viability as of the ammonia oxidizing bacteria prior to storage e.g., in a growth state). In some embodiments, the preparation of ammonia oxidizing bacteria may be prepared, such that no more than 10%, 20%, 30%, 40%, 50%, 60%, or 70% of the ability to oxidize NH 4 + is lost upon storage at selected conditions.
The time that it takes to revive the ammonia oxidizing bacteria from a storage state (or a polyphosphate loading state) may be a pre-determined period of time. For example, the pre-determined period of time may be less than about 75 hours, or less than about 72 hours. The pre-determined period of time may at least partially based on a period time of about 0.2-10 times, 0.3-5 times, 0.5-3 times, 0.5-1.5 times, or 0.5 to 1 times the doubling time for the ammonia oxidizing bacteria. The pre-determined period of time may be at least partially based on a period of time of about one doubling time for the ammonia oxidizing bacteria. The pre-determined period of time may be between about 8 hours and 12 hours. The pre-determined period of time may be about 10 hours. The pre-determined time may be less than about 75 hours, 72 hours, 70 hours, 68 hours, 65 hours, 60 hours, 55 hours, 50 hours, 45 hours, 40 hours, 35 hours, 30 hours, 25 hours, 20 hours, 15 hours, 10 hours, 5 hours, 4 hours, 3, hours, 2 hours, or 1 hour. The pre-determined period of time may be between about 5 minutes and 5 hours. The pre-determined period of time may be about 5-10 minutes, 10-15 minutes, 15-20 minutes, 20-25 minutes, 25-30 minutes, 30-45 minutes, 45-60 minutes, 60 minutes-1.5 hours, 1.5 hours-2 hours, 2 hours-2.5 hours, 2.5 hours-3 hours, 3 hours-3.5 hours, 3.5 hours-4 hours, 4 hours-4.5 hours, 4.5 hours-5 hours. In some embodiments, the pre-determined period of time may be about 2 hours. The pre-determined period of time, e.g., may be the time it may take to achieve revival of the ammonia oxidizing bacteria, e.g., achieve viability of the ammonia oxidizing bacteria as compared to the viability of the bacteria prior to storage (e.g., in a growth state), e.g., at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, or 100% viability.
2. AMMONIA OXIDIZING BACTERIA (AOBS), N. EUTROPHA STRAIN D23 AND SIMILAR BACTERIA
Autotrophic ammonia oxidizing bacteria, which may be referred to herein as AOBs or AOB, are obligate autotrophic bacteria as noted by Alan B. Hooper and A. Krummel at al. Alan B. Hooper, Biochemical Basis of Obligate Autotrophy in Nitrosomonas europaea , Journal of Bacteriology, February 1969, p. 776-779. Antje Krummel et al., Effect of Organic Matter on Growth and Cell Yield of Ammonia-Oxidizing Bacteria, Arch Microbiol (1982) 133: 50-54. These bacteria derive all metabolic energy only from the oxidation of ammonia to nitrite with nitric oxide (NO) as an intermediate product in their respiration chain and derive virtually all carbon by fixing carbon dioxide. They are incapable of utilizing carbon sources other than a few simple molecules.
Ammonia oxidizing bacteria (AOB) are widely found in the environment, and in the presence of ammonia, oxygen and trace metals will fix carbon dioxide and proliferate. AOB may be slow growing and toxic levels of ammonia may kill fish and other organisms before AOB can proliferate and reduce ammonia to non-toxic levels. Slow growth of AOB also may delay the health benefits of the NO and nitrite the AOB produce when applied to the skin.
Supplementing the aquarium, skin, or process with sufficient viable AOB grown and stored for that purpose is desired. AOB do not form spores, so storage in the dry state with high viability is difficult, and storage in the wet state leaves them metabolically active. Decay of nitrifying capacity during storage of AOB for wastewater treatment has been studied, as for example (Munz G, Lubello C, Oleszkiewicz J A. Modeling the decay of ammonium oxidizing bacteria. Water Res. 2011 January; 45(2): 557-64. Oi: 10.1016/j.watres.2010.09.022.)
Growth, prolonged storage, and restoration of activity of Nitrosomonas is discussed by Cassidy et al. (U.S. Pat. No. 5,314,542) where they disclose growing Nitrosomonas , removing toxic waste products, storing in sterile water of appropriate salinity for periods of time up to one year, and then reviving by adding buffer (CaCO 3 ) and 200 ppm, of ammonium, which reviving takes 72 hours.
As obligate autotrophs, AOB synthesize protein via the fixing of CO 2 using the energy and reducing equivalents generated by the oxidation of ammonia to nitrite. Growth requires ammonia, oxygen, minerals and carbon dioxide.
Nitrosomonas may exist in several metabolic states, according to “Polyphosphate and Orthophosphate Content of Nitrosomonas europaea as a Function of Growth” by K. R. Terry and A. B. Hooper, Journal of Bacteriology, July 1970, p. 199-206, Vol. 103, No. I.
In certain embodiments of the disclosure, the ammonia oxidizing bacteria may be axenic. The preparation (formulation or composition) of ammonia oxidizing bacteria may comprise, consist essentially of, or consist of axenic ammonia oxidizing bacteria. The ammonia oxidizing bacteria may be from a genus selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio , and combinations thereof.
This disclosure provides, inter alia, N. eutropha strain D23, a unique, e.g., optimized strain of ammonia oxidizing bacteria that can increase production of nitric oxide and nitric oxide precursors on the surface of a subject, e.g., a human subject. This disclosure also provides methods of using the bacteria and articles comprising the bacteria.
In embodiments, the N. eutropha is non-naturally occurring. For instance, it may have accumulated desirable mutations during a period of selection. In other embodiments, desirable mutations may be introduced by an experimenter. In some embodiments, the N. eutropha may be a purified preparation, and may be an optimized N. eutropha.
In preferred embodiments, the N. eutropha strain is autotrophic and so incapable of causing infection. A preferred strain utilizes urea as well as ammonia, so that hydrolysis of the urea in sweat would not be necessary prior to absorption and utilization by the bacteria. Also, in order to grow at low pH, the bacteria may either absorb NH 4 + ions or urea. The selected strain should also be capable of living on the external skin of a subject, e.g., a human, and be tolerant of conditions there.
Although this disclosure refers to N. eutropha strain D23 in detail, the preparations, methods, compositions, treatments, wearable articles, and articles of clothing may be used with one or more of: one or more other strains of N. eutropha , one or more other species of Nitrosomonas , and one or more other ammonia oxidizing bacteria. Autotrophic AOBs are obligate autotrophic bacteria as noted by Alan B. Hooper and A. Krummel at al. Alan B. Hooper, Biochemical Basis of Obligate Autotrophy in Nitrosomonas europaea , Journal of Bacteriology, February 1969, p. 776-779. Antje Krummel et al., Effect of Organic Matter on Growth and Cell Yield of Ammonia-Oxidizing Bacteria, Arch Microbiol (1982) 133: 50-54. These bacteria derive all metabolic energy only from the oxidation of ammonia to nitrite with nitric oxide (NO) as an intermediate product in their respiration chain and derive virtually all carbon by fixing carbon dioxide. They are incapable of utilizing carbon sources other than a few simple molecules.
In certain embodiments, the N. eutropha is the strain deposited with the American Tissue Culture Collection (ATCC) on Apr. 8, 2014, designated AOB D23-100 (25 vials) under accession number PTA-121157.
In certain embodiments, the N. eutropha comprises a chromosome having a sequence at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO: 1 (the strain D23 whole-genome sequence).
In certain embodiments, a bacterium with the above-mentioned sequence characteristics has one or more of (1) an optimized growth rate as measured by doubling time, (2) an optimized growth rate as measured by OD600, (3) an optimized NH 4 + oxidation rate, (4) an optimized resistance to NH 4 + , and (4) an optimized resistance to NO 2 − . Particular sub-combinations of these properties are specified in the following paragraph.
In some embodiments, the N. eutropha described herein has one or more of: (1) an optimized growth rate as measured by doubling time, (2) an optimized growth rate as measured by OD600, (3) an optimized NH 4 + oxidation rate, (4) an optimized resistance to, NH 4 + , and (4) an optimized resistance to, NO 2 − . For instance, the bacterium may have properties (1) and (2); (2) and (3); (3) and (4); or (4) and (5) from the list at the beginning of this paragraph. As another example, the bacterium may have properties (1), (2), and (3); (1), (2), and (4); (1), (2), and (5); (1), (3), and (4); (1), (3), and (5); (1), (4), and (5); (2), (3), and (4); (2), (3), and (5), or (3), (4), and (5) from the list at the beginning of this paragraph. As a further example, the bacterium may have properties (1), (2), (3), and (4); (1), (2), (3), and (5); (1), (2), (4), and (5); (1), (3), (4), and (5); or (2), (3), (4), and (5) from the list at the beginning of this paragraph. In some embodiments, the bacterium has properties (1), (2), (3), (4), and (5) from the list at the beginning of this paragraph.
This disclosure also provides an axenic composition of N. eutropha having one or more of: (1) an optimized growth rate as measured by doubling time, (2) an optimized growth rate as measured by OD600, (3) an optimized NH 4 + oxidation rate, (4) an optimized resistance to, NH 4 + , and (4) an optimized resistance to, NO 2 − . For instance, the axenic N. eutropha composition may have properties (1) and (2); (2) and (3); (3) and (4); or (4) and (5) from the list at the beginning of this paragraph. As another example, the axenic N. eutropha composition may have properties (1), (2), and (3); (1), (2), and (4); (1), (2), and (5); (1), (3), and (4); (1), (3), and (5); (1), (4), and (5); (2), (3), and (4); (2), (3), and (5), or (3), (4), and (5) from the list at the beginning of this paragraph. As a further example, the axenic N. eutropha composition may have properties (1), (2), (3), and (4); (1), (2), (3), and (5); (1), (2), (4), and (5); (1), (3), (4), and (5); or (2), (3), (4), and (5) from the list at the beginning of this paragraph. In some embodiments, the axenic N. eutropha composition has properties (1), (2), (3), (4), and (5) from the list at the beginning of this paragraph.
N. eutropha strain D23, as deposited in the form of 25 vials on Apr. 8, 2014, in the ATCC patent depository, designated AOB D23-100, under accession number PTA-121157, comprises a circular genome having SEQ ID NO: 1 or its complement. Accordingly, in some embodiments, an N. eutropha strain described herein comprises a nucleic acid sequence, e.g., a genome, that is similar to SEQ ID NO: 1 or its complement.
For instance, the N. eutropha may comprise a nucleic acid sequence having a 1,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 1,000 base pair portion of SEQ ID NO: 1 or its complement. The 1,000 base pair portion may span, e.g., nucleotides (n*1,000)+1 to (n+1)*1,000, where n=0, 1, 2, 3 . . . 2538, e.g., nucleotides 1-1,000, 1,001-2,000, and so on through the end of SEQ ID NO: 1.
In embodiments, the N. eutropha comprises a nucleic acid sequence having a 2,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 2,000 base pair portion of SEQ ID NO: 1 or its complement. The 2,000 base pair portion may span, e.g., nucleotides (n*2,000)+1 to (n+1)*2,000, where n=0, 1, 2, 3 . . . 1269, e.g., nucleotides 1-2,000, 2,001-4,000, and so on through the end of SEQ ID NO: 1.
In embodiments, the N. eutropha comprises a nucleic acid sequence having a 5,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 5,000 base pair portion of SEQ ID NO: 1 or its complement. The 5,000 base pair portion may span, e.g., nucleotides (n*5,000)+1 to (n+1)*5,000, where n=0, 1, 2, 3 . . . 508, e.g., nucleotides 1-5,000, 5,001-10,000, and so on through the end of SEQ ID NO: 1.
In embodiments, the N. eutropha comprises a nucleic acid sequence having a 10,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 10,000 base pair portion of SEQ ID NO: 1 or its complement. The 10,000 base pair portion may span, e.g., nucleotides (n*10,000)+1 to (n+1)*10,000, where n=0, 1, 2, 3 . . . 254, e.g., nucleotides 1-10,000, 10,001-20,000, and so on through the end of SEQ ID NO: 1.
In embodiments, the N. eutropha comprises a nucleic acid sequence having a 20,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 20,000 base pair portion of SEQ ID NO: 1 or its complement. The 20,000 base pair portion may span, e.g., nucleotides (n*20,000)+1 to (n+1)*20,000, where n=0, 1, 2, 3 . . . 127, e.g., nucleotides 1-20,000, 20,001-40,000, and so on through the end of SEQ ID NO: 1.
In embodiments, the N. eutropha comprises a nucleic acid sequence having a 50,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 50,000 base pair portion of SEQ ID NO: 1 or its complement. The 50,000 base pair portion may span, e.g., nucleotides (n*50,000)+1 to (n+1)*50,000, where n=0, 1, 2, 3 . . . 51, e.g., nucleotides 1-50,000, 50,001-100,000, and so on through the end of SEQ ID NO: 1.
In embodiments, the N. eutropha comprises a nucleic acid sequence having a 100,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 100,000 base pair portion of SEQ ID NO: 1 or its complement. The 100,000 base pair portion may span, e.g., nucleotides (n*100,000)+1 to (n+1)*100,000, where n=0, 1, 2, 3 . . . 26, e.g., nucleotides 1-100,000, 100,001-20,000, and so on through the end of SEQ ID NO: 1.
In some aspects, the present disclosure provides a composition of N. eutropha comprising a chromosome at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO: 1. In some aspects, the present disclosure provides an axenic composition of N. eutropha comprising a chromosome at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO: 1.
In certain embodiments, the N. eutropha strain comprises a nucleic acid sequence, e.g., a genome, that hybridizes to SEQ ID NO: 1, or to the genome of the D23 strain deposited in the form of 25 vials with the ATCC patent depository on Apr. 8, 2014, designated AOB D23-100, under accession number PTA-121157, or their complements, under low stringency, medium stringency, high stringency, or very high stringency, or other hybridization condition described herein. As used herein, the term “hybridizes under low stringency, medium stringency, high stringency, or very high stringency conditions” describes conditions for hybridization and washing. Guidance for performing hybridization reactions can be found in Current Protocols in Molecular Biology , John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6, which is incorporated by reference. Aqueous and nonaqueous methods are described in that reference and either can be used. Specific hybridization conditions referred to herein are as follows: 1) low stringency hybridization conditions in 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by two washes in 0.2×SSC, 0.1% SDS at least at 50° C. (the temperature of the washes can be increased to 55° C. for low stringency conditions); 2) medium stringency hybridization conditions in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 60° C.; 3) high stringency hybridization conditions in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 65° C.; 4) very high stringency hybridization conditions are 0.5M sodium phosphate, 7% SDS at 65° C., followed by one or more washes at 0.2×SSC, 1% SDS at 65° C. Very high stringency conditions (4) are suitable conditions and the ones that should be used unless otherwise specified.
The genome of strain D23 (SEQ ID NO: 1) was compared with the genome of N. eutropha C91. An annotation of the D23 genome is shown in Supplementary Table 1, which lists the positions of 2,777 genes in SEQ ID NO: 1 as identified by sequence analysis. In certain embodiments, the N. eutropha described herein comprises one or more genes or proteins listed in Supplementary Table 1, or a gene or protein similar to one of said genes or proteins.
Accordingly, in some embodiments, the N. eutropha comprises a gene of Supplementary Table 1, or a protein encoded by said gene. In certain embodiments, the N. eutropha comprises a gene that is similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to a gene of Supplementary Table 1, or a protein encoded by said gene. In embodiments, the N. eutropha comprises genes or proteins that are identical or similar to at least 2, 3, 4, 5, 10, 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 1000, 1500, 2000, 2500, or all the genes of Supplementary Table 1, or a protein encoded by said genes.
In some embodiments, the N. eutropha described herein (e.g., strain D23) comprises one or more genes or proteins that are absent from strain C91, or a gene or protein similar to one of said genes or proteins. Examples of these genes are set out in FIG. 6-8 and are described in more detail in Example 4 herein.
Accordingly, with respect to FIG. 6 , in some embodiments, the N. eutropha comprises genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the genes in FIG. 6 . In some embodiments, the N. eutropha comprises proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the proteins encoded by the genes listed in FIG. 6 .
With respect to FIG. 7 , in some embodiments, the N. eutropha comprises genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the genes in FIG. 7 . In some embodiments, the N. eutropha comprises proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the proteins encoded by the genes listed in FIG. 7 .
With respect to FIG. 8 , in some embodiments, the N. eutropha comprises genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, or all of the genes in FIG. 8 . In some embodiments, the N. eutropha comprises proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, or all of the proteins encoded by the genes listed in FIG. 8 .
With respect to FIGS. 6-8 collectively, in some embodiments, the N. eutropha comprises genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or all of the genes in FIGS. 6-8 . In some embodiments, the N. eutropha comprises proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or all of the proteins encoded by genes listed in FIGS. 6-8 .
In some embodiments, the N. eutropha described herein (e.g., strain D23) lacks one or more genes or proteins that are unique to strain C91, or a gene or protein similar to one of said genes or proteins. Examples of these genes are set out in FIG. 9 and are described in more detail in Example 4 herein. Accordingly, in some embodiments, the N. eutropha described herein lacks at least 1, 2, 3, 4, 5, 10, 20, 50, 100, 150, 200, 250, or all of the genes of FIG. 9 . In some embodiments, the N. eutropha described herein lacks up to 2, 3, 4, 5, 10, 20, 50, 100, 150, 200, 250, or all of the genes of FIG. 9 . In embodiments, the N. eutropha described herein lacks about 1-5, 5-10, 10-20, 20-50, 50-100, 100-150, 150-200, 200-250, or 250-all of the genes of FIG. 9 .
Sequencing of the D23 genome revealed several genes of potential interest, including genes involved in ammonia metabolism (e.g., ammonia monooxygenase, hydroxylamine oxidoreductase, cytochrome c554, and cytochrome c M 552). All of these genes are present in multiple copies, and in general the copies are not identical to each other. One set of genes of interest is the ammonia monooxygenase synthesis operon amoCAB, which is present in two copies, along with a third copy of amoC. The operons have homologs in C91, i.e., Neut_2078/7/6 and Neut_2319/8/7. Another set of genes of interest is hydroxylamine oxidoreductase (hao), which is present in three copies. The hao homologs in C91 are designated Neut_1672, 1793, and 2335. A third set of genes of interest is the cytochrome c554 gene encoded by cycA, which is present in three copies. The corresponding C91 genes are designated Neut_1670, 1791, and 2333. A fourth set of genes of interest is the cytochrome c M 552 genes encoded by cycB, which are present in two copies. The homologous C91 genes are designated Neut_1790 and 2332. Each group of genes is summarized in Table 1 and is discussed in more detail below.





TABLE 1



Sequences of ammonia metabolism genes in N . eutropha

strain D23.








SEQ ID in
SEQ ID in




strain D23
strain C91
Type
Gene name






1. ammonia monooxygenase








4
34
Protein
amoC1


5
35
DNA
amoC1


6
36
Protein
amoA1


7
37
DNA
amoA1


8
38
Protein
amoB1


9
39
DNA
amoB1


10
40
Protein
amoC2


11
41
DNA
amoC2


12
42
Protein
amoA2


13
43
DNA
amoA2


14
44
Protein
amoB2


15
45
DNA
amoB2


16
46
Protein
amoC3


17
47
DNA
amoC3



2. hydroxylamine oxidoreductase








18
48
Protein
hao1


19
49
DNA
hao1


20
50
Protein
hao2


21
51
DNA
hao2


22
52
Protein
hao3


23
53
DNA
hao3



3. cytochrome c554








24
54
Protein
c554 cycA1


25
55
DNA
c554 cycA1


26
56
Protein
c554 cycA2


27
57
DNA
c554 cycA2


28
58
Protein
c554 cycA3


29
59
DNA
c554 cycA3



4. cytochrome c M 552








30
60
Protein
c M 552 cycB1


31
61
DNA
c M 552 cycB1


32
62
Protein
c M 552 cycB2


33
63
DNA
c M 552 cycB2

















































































In some aspects, the N. eutropha described herein comprises genes identical to or similar to the genes and proteins of Table 1.
More particularly, in certain aspects, this disclosure provides a composition of N. eutropha , e.g., a purified preparation of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to an ammonia monooxygenase sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a hydroxylamine oxidoreductase sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a cytochrome c554 sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising nucleic acid sequences at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a cytochrome c M 552 sequence of Table 1.
In certain aspects, this disclosure provides a composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.2%, 99.3%, 99.4%, 99.5%, or 99.6% identical to an ammonia monooxygenase sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.4%, 99.5%, 99.6%, or 99.7% identical to hydroxylamine oxidoreductase sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.5%, 99.6%, or 99.7% identical to a cytochrome c554 sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising amino acid sequences at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 97.1%, 97.2%, 97.5%, 98%, 98.5%, 98.6%, 98.7%, 98.8%, 99%, or 99.5% identical to a cytochrome c M 552 sequence of Table 1.
In some embodiments, the N. eutropha are present in an axenic composition, and e.g., in the form of a purified preparation of optimized N. eutropha.
More particularly, in certain aspects, this disclosure provides an axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 98.5%, 98.8%, 98.9%, 99%, 99.2%, 99.3%, 99.4%, 99.5%, or 99.6% identical to an ammonia monooxygenase sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a hydroxylamine oxidoreductase sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a cytochrome c554 sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising nucleic acid sequences at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a cytochrome c M 552 sequence of Table 1.
In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 98.5%, 98.8%, 98.9%, 99%, 99.2%, 99.3%, 99.4%, 99.5%, or 99.6% identical to an ammonia monooxygenase sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.4%, 99.5%, 99.6%, or 99.7% identical to hydroxylamine oxidoreductase sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.5%, 99.6%, or 99.7% identical to a cytochrome c554 sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising amino acid sequences at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 97.1%, 97.2%, 97.5%, 98%, 98.5%, 98.6%, 98.7%, 98.8%, 99%, or 99.5% identical to a cytochrome c M 552 sequence of Table 1.
In some embodiments, the N. eutropha comprises a gene or protein comprising a sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a strain D23 sequence of Table 1, e.g., any of SEQ IDs 4-33. Substitutions may be conservative or non-conservative; also, insertions and deletions are contemplated. In some embodiments, the N. eutropha comprises a gene or protein comprising a sequence of Table 1, e.g., any of SEQ IDs 4-33. In some embodiments, the protein has an N-terminal and/or C-terminal extension or deletion of up to about 1, 2, 3, 4, 5, 6, 8, 10, 15, 20, 25, 50, or 100 amino acids.
Alignment of the nucleic acid sequences of Table 1 shows the percent identity between homologs in C91 and D23. The following paragraphs discuss this percent identity and describe various genes having homology to the D23 genes of Table 1.
More specifically, the amoA1 genes are about 98.8% identical (i.e., at 821/831 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.8%, 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoA1 gene.
The amoA2 genes are about 98.8% identical (i.e., at 821/831 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.8%, 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoA2 gene.
The amoB1 genes are about 99.1% identical (i.e., at 1255/1266 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.1%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoB1 gene.
The amoB2 genes are about 99.1% identical (i.e., at 1254/1266 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.1%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoB2 gene.
The amoC1 genes are about 99.8% identical (i.e., at 814/816 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.8%, 99.9%, or 100% identical to the D23 amoC1 gene.
The amoC2 genes are about 99.8% identical (i.e., at 814/816 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.8%, 99.9%, or 100% identical to the D23 amoC2 gene.
The amoC3 genes are about 98.9% identical (i.e., at 816/825 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoC3 gene.
The hao1 genes are about 99.0% identical (i.e., at 1696/1713 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao1 gene.
The hao2 genes are about 99.4% identical (i.e., at 1702/1713 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao2 gene.
The hao3 genes are about 99.2% identical (i.e., at 1700/1713 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao3 gene.
The cycA1 genes are about 98.0% identical (i.e., at 694/708 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.0%, 98.2%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA1 gene.
The cycA2 genes are about 98.7% identical (i.e., at 699/708 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.7%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA2 gene.
The cycA3 genes are about 99.3% identical (i.e., at 703/708 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.3%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA3 gene.
The cycB1 genes are about 96.7% identical (i.e., at 696/720 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 96.7%, 96.8%, 97.0%, 97.2%, 97.4%, 97.6%, 97.8%, 98.0%, 98.2%, 98.4%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycB1 gene.
The cycB2 genes are about 97.1% identical (i.e., at 702/723 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 97.1%, 97.2%, 97.4%, 97.6%, 97.8%, 98.0%, 98.2%, 98.4%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycB2 gene.
The following four paragraphs describe genes and proteins of Table 1 in more detail.
Ammonia monooxygenase is an enzyme involved in ammonia oxidation, that catalyzes the reaction NH 3 +O 2 +2e − +2H + NH 2 OH+H 2 O (Ensign et al., 1993). In N. eutropha strain D23, the ammonia monooxygenase operon comprises three genes designated amoA, amoB, and amoC. Strain D23 comprises two copies of the entire operon, and a third copy of amoC. These genes and the corresponding proteins are listed in Table 1 above. In certain embodiments, the N. eutropha described herein comprise 1 or 2 ammonia monooxygenase subunit A genes and/or protein of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. In some embodiments, the N. eutropha described herein comprise 1 or 2 ammonia monooxygenase subunit B genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. In certain embodiments, the N. eutropha described herein comprise 1, 2, or 3 ammonia monooxygenase subunit C genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. In some embodiments, the N. eutropha described herein comprise at least one or two each of (a) an ammonia monooxygenase subunit A gene and/or protein of Table 1 (e.g., the D23 sequences of Table 1), (b) an ammonia monooxygenase subunit B gene and/or protein of Table 1 (e.g., the D23 sequences of Table 1), and (c) an ammonia monooxygenase subunit C gene and/or protein of Table 1 (e.g., the D23 sequences of Table 1). For instance, the N. eutropha may comprise all of the ammonia monooxygenase genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. Even more specifically, in some embodiments, the N. eutropha comprises all of the D23 ammonia monooxygenase genes of Table 1. In some embodiments, the N. eutropha comprises all of the D23 ammonia monooxygenase proteins of Table 1. Hydroxylamine oxidoreductases catalyze the general reaction NH 2 OH+O 2 NO 2 − +H 2 O. They typically use heme as a cofactor. N. eutropha strain D23 comprises three hydroxylamine oxidoreductases, designated hao1, hao2, and hao3. These genes and the corresponding proteins are listed in Table 1 above. In some embodiments, the N. eutropha described herein comprise 1, 2, or 3 hydroxylamine oxidoreductase genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. For instance, the N. eutropha may comprise all of the hydroxylamine oxidoreductase genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. Even more specifically, in some embodiments, the N. eutropha comprises all of the D23 hydroxylamine oxidoreductase genes of Table 1. In some embodiments, the N. eutropha comprises all of the D23 hydroxylamine oxidoreductase proteins of Table 1.
The capacity of D23 to aerobically catabolize ammonia as the sole source of energy and reductant requires two specialized protein complexes, Amo and Hao as well as the cytochromes c554 and c m 552, which relay the electrons to the quinone pool. The NO reductase activity of c554 is important during ammonia oxidation at low oxygen concentrations. N. eutropha strain D23 comprises three cytochrome c554 genes, designated cycA1, cycA2, and cycA3. These genes and the corresponding proteins are listed in Table 1 above. In some embodiments, the N. eutropha described herein comprise 1, 2, or 3 cytochrome c554 genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. For instance, the N. eutropha may comprise all of the cytochrome c554 genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. Even more specifically, in some embodiments, the N. eutropha comprises all of the D23 cytochrome c554 genes of Table 1. In some embodiments, the N. eutropha comprises all of the D23 cytochrome c554 proteins of Table 1.
The capacity of D23 to aerobically catabolize ammonia as the sole source of energy and reductant requires two specialized protein complexes, Amo and Hao as well as the Cytochromes c554 and c M 552, which relay the electrons to the quinone pool. Cytochrome c M 552 reduces quinones, with electrons originating from Hao. N. eutropha strain D23 comprises two cytochrome c M 552 genes, designated cycB1 and cycB2. These genes and the corresponding proteins are listed in Table 1 above. In some embodiments, the N. eutropha described herein comprise 1 or 2 cytochrome c M 552 genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. For instance, the N. eutropha may comprise both of the cytochrome c M 552 genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. Even more specifically, in some embodiments, the N. eutropha comprises both of the D23 cytochrome c M 552 genes of Table 1. In some embodiments, the N. eutropha comprises both of the D23 Cytochrome c M 552 proteins of Table 1.
In some embodiments, the N. eutropha described herein comprises a combination of genes and/or proteins selected from Table 1. This combination may comprise, for instance, genes and/or proteins listed in the preceding four paragraphs. For instance, the combination may comprise genes and/or proteins from two classes within Table 1. Accordingly, in some embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more hydroxylamine oxidoreductase genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs. In embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more cytochrome c554 genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs. In embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more cytochrome c M 552 genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs. In embodiments, the N. eutropha comprises one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c554 genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs. In embodiments, the N. eutropha comprises one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c M 552 genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs.
The combination may also comprise genes and/or proteins from three classes within Table 1. Accordingly, in some embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c554 genes and/or proteins as described in Table 1, or as described in the aforementioned four paragraphs. In embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c M 552 genes and/or proteins as described in Table 1, or as described in the aforementioned four paragraphs. In embodiments, the N. eutropha comprises one or more one or more ammonia monooxygenase genes and/or proteins and one or more cytochrome c554 genes and/or proteins and/or one or more cytochrome c M 552 genes and/or proteins as described in Table 1, or as described in the aforementioned four paragraphs. In embodiments, the N. eutropha comprises one or more one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c554 genes and/or proteins and/or one or more cytochrome c M 552 genes and/or proteins as described in Table 1, or as described in the aforementioned four paragraphs.
The combination may comprise genes and/or proteins from all four classes within Table 1. Accordingly, in some embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c554 genes and/or proteins and/or one or more cytochrome c M 552 genes as described in Table 1, or as described in the aforementioned four paragraphs.
Table 2 (below) lists sequence differences between the D23 and C91 proteins of Table 1. For example, AmoA1 has M at position 1 in C91 but V at position 1 in D23, and this difference is abbreviated as M1V in Table 2. As another example, the D23 CycB1 has an insertion of DDD between residues 194 and 195 of the C91 protein, so that the added residues are residues number 195, 196, and 197 of the D23 protein and this difference is abbreviated as 195insD, 196insD, and 197insD respectively in Table 2. The sequence alignments that form the basis for Table 2 are shown in FIGS. 10-16 .





TABLE 2



Amino acid sequence differences between N . eutropha

strains D23 and C91




Protein
Sequence characteristics of D23 compared to C91





1. ammonia monooxygenase




AmoA1
M1V, M160L, P167A

AmoA2
M1V, M160L, P167A

AmoB1
I33V, V165I

AmoB2
I33V, V165I

AmoC1
N/A

AmoC2
N/A

AmoC3
V79A, I271V



2. hydroxylamine oxidoreductase




Hao1
N85S, V163A, G312E

Hao2
N85S, G312E

Hao3
N85S, G312E



3. cytochrome c554




c554 CycA1
A65T, A186T

c554 CycA2
A65T

c554 CycA3
A65T



4. cytochrome c M 552




c M 552 CycB1
I63V, S189P, D194G, 195insD, 196insD,


197insD, 206insE, 207insE

c M 552 CycB2
I63V, S189P, 206insE, 207insE

































































Accordingly, the N. eutropha described herein may comprise one or more of the sequence characteristics listed in Table 2. For instance, the N. eutropha may comprise at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, or all of the sequence characteristics of Table 2. In some embodiments, the N. eutropha comprises no more than 2, 3, 4, 5, 10, 15, 20, 25, 30, or all of the sequence characteristics of Table 2. In embodiments, the N. eutropha comprises 1-5, 5-10, 10-15, 15-20, 20-25, 25-30, or all of the sequence characteristics of Table 2. The N. eutropha may also comprise fragments of said proteins.
As to individual categories of genes or proteins, in some embodiments, the N. eutropha comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the sequence characteristics of Table 2, Section 1 (which describes ammonia monooxygenases). In embodiments, the N. eutropha comprises 1-5, 3-7, 4-8, or 5-10 of the sequence characteristics of Table 2, Section 1. For instance, in some embodiments, the N. eutropha comprises at least 1, 2, or 3 sequence characteristics of an amoA gene or protein as listed in Table 2, and/or no more than 2 or 3 of these characteristics. The N. eutropha may also comprise at least 1 or 2 sequence characteristics of an amoB gene or protein as listed in Table 2. In addition, the N. eutropha may comprise at least 1 or 2 sequence characteristics of the amoC3 gene as listed in Table 2. The N. eutropha may also comprise fragments of said proteins.
With respect to hao genes and proteins, the N. eutropha may comprise at least 1, 2, 3, 4, 5, 6, 7, 8, or all of the sequence characteristics of Table 2, Section 2 (which describes hydroxylamine oxidoreductases). In embodiments, the N. eutropha comprises 1-4, 2-5, 3-6, or 4-8 of the sequence characteristics of Table 2, Section 2. The N. eutropha may also comprise at least 1, 2 or 3 sequence characteristics of Hao1 as listed in Table 1, and/or no more than 2 or 3 of these characteristics. The N. eutropha may also comprise at least 1 or 2 sequence characteristics of Hao2 or Hao3 as listed in Table 2. The N. eutropha may also comprise fragments of said proteins.
Turning now to cytochrome c554, the N. eutropha may comprise at least 1, 2, 3, 4, or all of the sequence characteristics of Table 2, Section 3 (which describes cytochrome c554). In embodiments, the N. eutropha comprises at most 2, 3, 4, or all of the sequence characteristics of Table 2 Section 3. In embodiments, the N. eutropha comprises at least 1 or 2 sequence characteristics of cytochrome c554 CycA1 as listed in Table 2. The N. eutropha may also comprise at least 1 sequence characteristic of c554 CycA2 or c554 CycA3 as listed in Table 2. The N. eutropha may also comprise fragments of said proteins.
With respect to the c M 552 genes and proteins, the N. eutropha may comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the sequence characteristics of Table 2, Section 4 (which describes cytochrome c M 552). In embodiments, the N. eutropha comprises at most 2, 3, 4, 5, 6, 7, 8, 9, 10, or all the sequence characteristics of Table 2, Section 4. For instance, in embodiments the N. eutropha comprises 1-5, 2-7, 3-8, or 5-10 sequence characteristics of Table 2, Section 4. In embodiments, at least 1, 2, 3, 4, 5, 6, or 7 sequence characteristics of c M 552 CycB1 as listed in Table 2, and/or no more than 2, 3, 4, 5, 6, or 7 of these characteristics. The N. eutropha may also comprise at least 1, 2, or 3 sequence characteristics of c M 552 CycB2 as listed in Table 2, and/or no more than 2 or 3 of these characteristics. The N. eutropha may also comprise fragments of said proteins.
It is understood that the paragraphs above, which refer to sequence characteristics of various N. eutropha proteins, also describe the sequences of nucleic acids that encode these proteins.
The sequencing analysis described herein revealed that strain D23 lacks plasmids. Consequently, in some embodiments, the N. eutropha bacterium lacks plasmids, i.e., all of its DNA is contained in the chromosome. In some embodiments, the N. eutropha bacterium lacks endogenous plasmids, but carries one or more transgenic plasmids.
This D23 strain is not believed to be a product of nature, but rather has acquired certain mutations and characteristics during an extended period of culture and selection in the laboratory. For instance, D23 has an ability to grow in conditions of greater than about 200 or 250 mM NH 4 + for more than 24 hours.
In some embodiments, the N. eutropha disclosed herein differ from naturally occurring bacteria in the abundance of siderophores. For instance, the N. eutropha may have elevated or reduced levels of siderophores compared to N. eutropha C91. Generally, siderophores are secreted iron-chelating compounds that help bacteria scavenge iron from their environment. Some siderophores are peptides, and others are small organic molecules.
The AOBs, for example, N. eutropha contemplated in this disclosure may comprise mutations relative to wild-type N. eutropha and/or the N. eutropha sequences disclosed herein. These mutations may, e.g., occur spontaneously, be introduced by random mutagenesis, or be introduced by targeted mutagenesis. For instance, the N. eutropha may lack one or more genes or regulatory DNA sequences that wild-type N. eutropha typically comprises. The N. eutropha may also comprise point mutations, substitutions, insertions, deletions, and/or rearrangements relative to the sequenced strain or a wild-type strain. The N. eutropha may be a purified preparation of optimized N. eutropha.
In certain embodiments, the N. eutropha is transgenic. For instance, it may comprise one or more genes or regulatory DNA sequences that wild-type N. eutropha D23 lacks. More particularly, the N. eutropha may comprise, for instance, a reporter gene, a selective marker, a gene encoding an enzyme, or a promoter (including an inducible or repressible promoter). In some embodiments the additional gene or regulatory DNA sequence is integrated into the bacterial chromosome; in some embodiments the additional gene or regulatory DNA sequence is situated on a plasmid, for instance a plasmid related to a plasmid found in N. eutropha N91.
In some preferred embodiments, the N. eutropha differs by at least one nucleotide from naturally occurring bacteria. For instance, the N. eutropha may differ from naturally occurring bacteria in a gene or protein that is part of a relevant pathway, e.g., an ammonia metabolism pathway, a urea metabolism pathway, or a pathway for producing nitric oxide or nitric oxide precursors. More particularly, the N. eutropha may comprise a mutation that elevates activity of the pathway, e.g., by increasing levels or activity of an element of that pathway.
The above-mentioned mutations can be introduced using any suitable technique. Numerous methods are known for introducing mutations into a given position. For instance, one could use site-directed mutagenesis, oligonucleotide-directed mutagenesis, or site-specific mutagenesis. Non-limiting examples of specific mutagenesis protocols are described in, e.g., Mutagenesis, pp. 13.1-13.105 (Sambrook and Russell, eds., Molecular Cloning A Laboratory Manual, Vol. 3, 3.sup.rd ed. 2001). In addition, non-limiting examples of well-characterized mutagenesis protocols available from commercial vendors include, without limitation, Altered Sites® II in vitro Mutagenesis Systems (Promega Corp., Madison, Wis.); Erase-a-Base® System (Promega, Madison, Wis.); GeneTailor™ Site-Directed Mutagenesis System (Invitrogen, Inc., Carlsbad, Calif.); QuikChange® II Site-Directed Mutagenesis Kits (Stratagene, La Jolla, Calif.); and Transformer™ Site-Directed Mutagenesis Kit (BD-Clontech, Mountain View, Calif.).
In some embodiments, the preparation of ammonia oxidizing bacteria may comprise a concentration or amount of ammonia oxidizing bacteria in order to at least partially treat a condition or disease. The preparation of ammonia oxidizing bacteria may comprise a concentration or amount of ammonia oxidizing bacteria in order to alter, e.g., reduce or increase, an amount, concentration or proportion of a bacterium, or genus of bacteria, on a surface, e.g., a skin surface. The bacteria may be non-pathogenic or pathogenic, or potentially pathogenic.
In some embodiments, the preparation of ammonia oxidizing bacteria may comprise between about 10 8 to about 10 14 CFU/L. The preparation may comprise at least 10 8 , 10 9 , 10 10 , 10 11 , 2×10 11 , 5×10 11 , 10 12 , 2×10 12 , 5×10 12 , 10 13 , 2×10 13 , 5×10 13 , or 10 14 ; or about 10 8 -10 9 , 10 9 -10 10 , 10 11 -10 11 , 10 11 -10 12 , 10 12 -10 13 , or 10 13 -10 14 CFU/L. In certain aspects, the preparation may comprise between about 1×10 9 CFU/L to about 10×10 9 CFU/L. In certain aspects, the preparation may comprise between about 1×10 9 CFU to about 10×10 9 CFU.
In some embodiments, the preparation of ammonia oxidizing bacteria may comprise between about 0.1 milligrams (mg) and about 1000 mg of ammonia oxidizing bacteria. In certain aspects, the preparation may comprise between about 50 mg and about 1000 mg of ammonia oxidizing bacteria. The preparation may comprise between about 0.1-0.5 mg, 0.2-0.7 mg, 0.5-1.0 mg, 0.5-2 mg, 0.5-5 mg, 2.5-5 mg, 2.5-7.0 mg, 5.0-10 mg, 7.5-15 mg, 10-15 mg, 15-20 mg, 15-25 mg, 20-30 mg, 25-50 mg, 25-75 mg, 50-75 mg, 50-100 mg, 75-100 mg, 100-200 mg, 200-300 mg, 300-400 mg, 400-500 mg, 500-600 mg, 600-700 mg, 700-800 mg, 800-900 mg, 900-1000 mg, 100-250 mg, 250-500 mg, 100-500 mg, 500-750 mg, 750-1000 mg, or 500-1000 mg.
In some embodiments, the preparation of ammonia oxidizing bacteria may comprise a mass ratio of ammonia oxidizing bacteria to an excipient, e.g., a pharmaceutically acceptable excipient or a cosmetically acceptable excipient in a range of about 0.1 grams per liter to about 1 gram per liter. The preparation may comprise a mass ratio of ammonia oxidizing bacteria to an excipient in a range of about 0.1-0.2, 0.2-0.3, 0.1-0.5, 0.2-0.7, 0.5-1.0, or 0.7-1.0 grams per liter.
In some embodiments, the preparation of ammonia oxidizing bacteria may be in a growth state. A growth state may be provided by exposing ammonia oxidizing bacteria to an environment that may promote growth. The growth state may be a state, e.g., ammonia oxidizing bacteria in an environment that allows immediate availability of ammonia oxidizing bacteria to convert ammonium ions (NH 4 + ) to nitrite (NO 2 − ). The growth state may comprise providing ammonia oxidizing bacteria in an environment having a pH of greater than about 7.6. The growth state may also comprise providing ammonia oxidizing bacteria in an environment having ammonia, ammonium salts, and/or urea, trace minerals and sufficient oxygen and carbon dioxide, as described above in Section 1.
In some embodiments, the preparation of ammonia oxidizing bacteria may be in a polyphosphate loading state, wherein the state or the environment, e.g., a media, e.g., a culture media, e.g., a growth media, may have a pH of less than about 7.4. Levels of at least one of ammonia, ammonium ions, and urea may be between about 10 micromolar and 200 millimolar. Levels of trace materials may be between 0.1 micromolar iron and 20 micromolar iron. Levels of oxygen may be between about 5% and 100% oxygen saturation. Levels of carbon dioxide may be between/less than about zero and 200 ppm, and phosphate levels greater than about 10 micromolar. The purpose of the polyphosphate loading state is to provide AOB with ammonia and oxygen such that ATP can be produced, but to deny them carbon dioxide and carbonate such that they are unable to use that ATP to fix carbon dioxide and instead use that ATP to generate polyphosphate which may be stored.
In some embodiments, the preparation of ammonia oxidizing bacteria may be in a storage state. A storage state may be defined as ammonia oxidizing bacteria in an environment in which they may be stored to be later revived. The storage state may be a state, e.g., ammonia oxidizing bacteria in an environment that allows availability of ammonia oxidizing bacteria after being revived, e.g., after being place in an environment promoting a growth state for a pre-determined period of time.
The storage state may comprise providing ammonia oxidizing bacteria in an environment having a pH of less than about 7.4. The storage state may also comprise providing ammonia oxidizing bacteria in an environment having ammonia, ammonia salts, and/or urea, trace minerals, oxygen, and low concentrations of carbon dioxide, as described above in Section 1.
Storage may also be accomplished by storing at 4° C. for up to several months. The storage buffer in some embodiments may comprise 50 mM Na 2 HPO 4 -2 mM MgCl 2 (pH 7.6).
In some embodiments, ammonia oxidizing bacteria may be cyropreserved. A 1.25 ml of ammonia oxidizing bacteria mid-log culture may be added to a 2 ml cryotube and 0.75 ml of sterile 80% glycerol. Tubes may be shaken gently, and incubate at room temperature for 15 min to enable uptake of the cryoprotective agents by the cells. The tubes may be directly stored in a −80° C. freezer for freezing and storage.
For resuscitation of cultures, frozen stocks may be thawed on ice for 10-20 minutes, and then centrifuged at 8,000×g for 3 minutes at 4° C. The pellet may be washed by suspending it in 2 ml AOB medium followed by another centrifugation at 8,000×g for 3 minutes at 4° C. to reduce potential toxicity of the cryoprotective agents. The pellet may be resuspended in 2 ml of AOB medium, inoculated into 50 ml of AOB medium containing 50 mM NH 4 + , and incubated in dark at 30° C. by shaking at 200 rpm.
In some embodiments, the preparation of ammonia oxidizing bacteria may comprise ammonia oxidizing bacteria in a storage state and/or ammonia oxidizing bacteria in a polyphosphate loading state and/or ammonia oxidizing bacteria in a growth state.
Without wishing to be bound by theory, by maintaining ammonia oxidizing bacteria under conditions or in an environment of low carbon dioxide, with sufficient oxygen and ammonia, they may accumulate polyphosphate for a pre-determined period, e.g., for a period of about one doubling time, e.g., for about 8-12 hours, e.g., for about 10 hours. The ammonia oxidizing bacteria may accumulate sufficient polyphosphate to extend their storage viability, storage time, and accelerate their revival. This may occur with or without the addition of buffer and ammonia.
The presence of sufficient stored polyphosphate may allow the ammonia oxidizing bacteria the ATP resources to maintain metabolic activity even in the absence of ammonia and oxygen, and to survive insults that would otherwise be fatal.
The process of oxidation of ammonia to generate ATP has two steps. The first step is the oxidation of ammonia to hydroxylamine by ammonia monoxoygenase (Amo), followed by the conversion of hydroxylamine to nitrite by hydroxylamine oxidoreductase (Hao). Electrons from the second step (conversion of hydroxylamine to nitrite) are used to power the first step (oxidation of ammonia to hydroxylamine).
If an ammonia oxidizing bacteria does not have hydroxylamine to generate electrons for Amo, then hydroxylamine is not available for Hao. For example, acetylene irreversibly inhibits the enzyme crucial for the first step in the oxidation of ammonia to nitrite, the oxidation of ammonia to hydroxylamine. Once AOB are exposed to acetylene, Amo is irreversibly inhibited and new enzyme must be synthesized before hydroxylamine can be generated. In a normal consortium biofilm habitat, AOB may share and receive hydroxylamine form other AOB (even different strains with different susceptibilities to inhibitors) and so the biofilm tends to be more resistant to inhibitors such as acetylene than an individual organism. AOB can use stored polyphosphate to synthesize new Amo, even in the absence of hydroxylamine.
Any embodiment, preparation, composition, or formulation of ammonia oxidizing bacteria discussed herein may comprise, consist essentially of, or consist of optionally axenic ammonia oxidizing bacteria.
3. METHODS OF PRODUCING N. EUTROPHA
Methods of culturing various Nitrosomonas species are known in the art. N. eutropha may be cultured, for example, using N. europaea medium as described in Example 2 below. Ammonia oxidizing bacteria may be cultured, for example, using the media described in Table 3 or Table 4, above.
N. eutropha may be grown, for example, in a liquid culture or on plates. Suitable plates include 1.2% R2A agar, 1.2% agar, 1.2% agarose, and 1.2% agarose with 0.3 g/L pyruvate.
In some embodiments, ammonia oxidizing bacteria, such as N. eutropha is cultured in organic free media. One advantage of using organic free media is that it lacks substrate for heterotrophic bacteria to metabolize except for that produced by the autotrophic bacteria. Another advantage of using the as-grown culture is that substantial nitrite accumulates in the culture media, and this nitrite is also inhibitory of heterotrophic bacteria and so acts as a preservative during storage.
In some embodiments, ammonia oxidizing bacteria such as an N. eutropha strain with improved, e.g. optimized, properties is produced by an iterative process of propagation and selecting for desired properties. In some embodiments, the selection and propagation are carried out simultaneously. In some embodiments, the selection is carried out in a reaction medium (e.g., complete N. europaea medium) comprising 50 mM, 75 mM, 100 mM, 125 mM, 150 mM, 175 mM, 200 mM, 225 mM, 250 mM, 275 mM, or 300 mM NH 4 + , e.g., at least 200 mM NH 4 + . In some embodiments, the period of propagation and/or selection is at least 1, 2, 3, or 6 months. In embodiments, the period of propagation and/or selection is at least 1, 2, 4, 6, 8, or 10 years.
In some aspects, the ammonia oxidizing bacteria, such as the N. eutropha are manufactured on a commercial scale. In some embodiments, commercial scale refers to a liquid culturing method with a culture medium volume of at least 10,000, 20,000, 30,000, 50,000, or 100,000 liters (L). In some embodiments, the bacteria are produced in a bioreactor. The bioreactor may maintain the bacteria at a constant temperature, e.g., about 26-30 degrees Celsius using, for example a thermal jacket for insulation, a temperature sensor, and a heating or cooling element. The bioreactor may have an apparatus for stirring the culture to improve distribution of nutrients like ammonia, urea, oxygen, carbon dioxide, and various minerals. The bioreactor may also have an inlet tube for addition of new medium, and an outlet tube for collection of cells. The bioreactor may also have an aerator for distributing oxygen and/or carbon dioxide to the culture. The bioreactor may be, e.g., a batch reactor, a fed batch reactor, or a continuous reactor. In some embodiments, commercial scale production of N. eutropha yields a batch of 1,000 to 100,000 L per day at about 10 12 CFU/liter and 1,000 to 100,000. The commercial scale production may yield e.g., a batch of 1,000-5,000, 5,000-10,000, 10,000-50,000, or 50,000-100,000 L/day. The commercial scale production may yield e.g., a batch of 1,000-5,000, 5,000-10,000, 10,000-50,000, or 50,000-100,000 L per batch. In some embodiments, the yield is at a concentration of at least 10 10 , 10 11 , 2×10 11 , 5×10 11 , or 10 12 , or about 10 10 -10 11 , 10 11 -10 12 , 10 12 -10 13 , or 10 13 -10 14 CFU/L
In some embodiments, typically including commercial scale production, quality control (QC) testing steps are carried out. The general steps of QC typically comprise, 1) culturing N. eutropha, 2) performing a testing step on the culture or an aliquot thereof, and 3) obtaining a value from the testing step, and optionally: 4) comparing the obtained value to a reference value or range of acceptable values, and 5) if the obtained value meets the acceptable reference value or range, then classifying the culture as acceptable, and if the obtained value does not meet the acceptable reference value or range, then classifying the culture as unacceptable. If the culture is classified as acceptable, the culture may, e.g., be allowed to continue growing and/or may be harvested and added to a commercial product. If the culture is classified as unacceptable, the culture may, e.g., be safely disposed of or the defect may be remedied.
The testing step may comprise measuring the optical density (OD) of the culture. OD is measured in a spectrophotometer, and provides information on the amount of light transmitted through the sample as distinguished from light absorbed or scattered. In some embodiments, the OD600 (e.g., optical density of light with a wavelength of 600 nm) may be determined. This measurement typically indicates the concentration of cells in the medium, where a higher optical density corresponds to a higher cell density.
The testing step may comprise measuring the pH of the culture. The pH of an N. eutropha culture indicates the rate of nitrogen oxidation, and can also indicate whether the culture comprises a contaminating organism. pH may be measured using, e.g., a pH-sensing device comprising a electrode (such as a hydrogen electrode, quinhydron-Electrode, antimony electrode, glass electrode), a pH-sensing device comprising a semiconductor, or a color indicator reagent such as pH paper.
In certain embodiments, producing the ammonia oxidizing bacteria such as N. eutropha comprises carrying out various quality control steps. For instance, one may test the medium in which the N. eutropha is grown, e.g., to determine whether it has an appropriate pH, whether it has a sufficiently low level of waste products, and/or whether it has a sufficiently high level or nutrients. One may also test for the presence of contaminating organisms. A contaminating organism is typically an organism other than an ammonia oxidizing bacteria such as N. eutropha , for instance an organism selected Microbacterium sp., Alcaligenaceae bacterium, Caulobacter sp., Burkodelia multivorans, Escherichia coli, Klebsiella pneumoniae , and Staphylococcus aureus . One may test for contaminants by, e.g., extracting DNA, amplifying it, and sequencing a conserved gene such as 16S rRNA. One may also test for contaminants by plating culture on agar plates and observing colony morphology. N. eutropha typically forms red colonies, so non-red colonies are often indicative of contaminating organisms.
4. COMPOSITIONS COMPRISING AMMONIA OXIDIZING BACTERIA; COMPOSITIONS COMPRISING N. EUTROPHA
The present disclosure provides, inter alia, compositions comprising ammonia oxidizing bacteria, e.g., a preparation of ammonia oxidizing bacteria, or a purified preparation of ammonia oxidizing bacteria e.g., a natural product, or a fortified natural product. The compositions comprising ammonia oxidizing bacteria, e.g., a preparation of ammonia oxidizing bacteria, or a purified preparation of ammonia oxidizing bacteria may be provided in a cosmetic product or a therapeutic product. The preparation may comprise, inter alia, at least one of ammonia, ammonium salts, and urea.
The present disclosure provides, inter alia, compositions comprising N. eutropha , e.g., a purified preparation of an optimized N. eutropha . In some embodiments, the N. eutropha in the compositions has at least one property selected from an optimized growth rate, an optimized NH 4 + oxidation rate, and an optimized resistance to NH 4 + .
In some aspects, the present disclosure provides compositions with a defined number of species. For instance, this disclosure provides a composition having N. eutropha and one other type of organism, and no other types of organism. In other examples, the composition has N. eutropha and 2, 3, 4, 5, 6, 7, 8, 9, or 10 other types of organism, and no other types of organism. The other type of organism in this composition may be, for instance, a bacterium, such as an ammonia-oxidizing bacterium. Suitable ammonia-oxidizing bacteria for this purpose include those in the genera Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosocystis, Nitrosolobus , or Nitrosovibrio.
In some embodiments, the composition comprising N. eutropha provides conditions that support N. eutropha viability. For instance, the composition may promote N. eutropha growth and metabolism or may promote a dormant state (e.g., freezing) from which viable N. eutropha can be recovered. When the composition promotes growth or metabolism, it may contain water and/or nutrients that N. eutropha consumes, e.g., as ammonium, ammonia, urea, oxygen, carbon dioxide, or trace minerals. In some embodiments, the composition comprising ammonia oxidizing bacteria provides conditions that support ammonia oxidizing bacteria viability. For instance, the composition may promote ammonia oxidizing bacteria growth and metabolism or may promote a dormant state (e.g., freezing) or storage state as described herein, from which viable ammonia oxidizing bacteria can be recovered. When the composition promotes growth or metabolism, it may contain water and/or nutrients that ammonia oxidizing bacteria consumes, e.g., as ammonium ions, ammonia, urea, oxygen, carbon dioxide, or trace minerals.
In some embodiments, one or more other organisms besides ammonia oxidizing bacteria may be included in the preparation of ammonia oxidizing bacteria. For example, an organism of the genus selected from the group consisting of Lactobacillus, Streptococcus, Bifidobacter , and combinations thereof, may be provided in the preparation of ammonia oxidizing bacteria. In some embodiments, the preparation may be substantially free of other organisms.
Preparations of ammonia oxidizing bacteria may comprise between about between about 10 8 to about 10 14 CFU/L. The preparation may comprise at least about 10 8 , 10 9 , 10 10 , 10 11 , 2×10 11 , 5×10 11 , 10 12 , 2×10 12 , 5×10 12 , 10 13 , 2×10 13 , 5×10 13 , or 10 14 ; or about 10 8 -10 9 , 10 9 -10 10 , 10 10 -10 11 , 10 11 -10 12 , 10 12 -10 13 , or 10 13 -10 14 CFU/L.
In some embodiments, the preparation may comprise at least 10 8 , 10 9 , 10 10 , 10 11 , 2×10 11 , 5×10 11 , 10 12 , 2×10 12 , 5×10 12 , 10 13 , 2×10 13 , 5×10 13 , or 10 14 ; or about 10 8 -10 9 , 10 9 -10 10 , 10 10 -10 11 , 10 11 -10 12 , 10 12 -10 13 , or 10 13 -10 14 CFU/ml.
In some embodiments, the preparation may comprise between about 1×10 9 to about 10×10 9 CFU/L. In some embodiments, the preparation may comprise about 3×10 10 CFU, e.g., 3×10 10 CFU per day. In some embodiments, the preparation may comprise about 1×10 9 to about 10×10 9 CFU, e.g., about 1×10 9 to about 10×10 9 CFU per day.
In some embodiments, the preparation of ammonia oxidizing bacteria may comprise between about 0.1 milligrams (mg) and about 1000 mg of ammonia oxidizing bacteria. In certain aspects, the preparation may comprise between about 50 mg and about 1000 mg of ammonia oxidizing bacteria. The preparation may comprise between about 0.1-0.5 mg, 0.2-0.7 mg, 0.5-1.0 mg, 0.5-2 mg, 0.5-5 mg, 2.5-5 mg, 2.5-7.0 mg, 5.0-10 mg, 7.5-15 mg, 10-15 mg, 15-20 mg, 15-25 mg, 20-30 mg, 25-50 mg, 25-75 mg, 50-75 mg, 50-100 mg, 75-100 mg, 100-200 mg, 200-300 mg, 300-400 mg, 400-500 mg, 500-600 mg, 600-700 mg, 700-800 mg, 800-900 mg, 900-1000 mg, 100-250 mg, 250-500 mg, 100-500 mg, 500-750 mg, 750-1000 mg, or 500-1000 mg.
In some embodiments, the preparation of ammonia oxidizing bacteria my comprise a mass ratio of ammonia oxidizing bacteria to an excipient, e.g., a pharmaceutically acceptable excipient or a cosmetically acceptable excipient in a range of about 0.1 grams per liter to about 1 gram per liter. The preparation may comprise a mass ratio of ammonia oxidizing bacteria to an excipient in a range of about 0.1-0.2, 0.2-0.3, 0.1-0.5, 0.2-0.7, 0.5-1.0, or 0.7-1.0 grams per liter.
Advantageously, a formulation may have a pH that promotes AOB, e.g., N. eutropha viability, e.g., metabolic activity. Urea would hydrolyze to ammonia and would raise the pH to 7 to 8. AOB are very active at this pH range and would lower the pH to about 6 where the NH3 converts to ammonium and is unavailable. Lower pH levels, e.g. about pH 4, are also acceptable. The ammonia oxidizing bacteria, e.g., N. eutropha may be combined with one or more pharmaceutically or cosmetically acceptable excipients. In some embodiments, “pharmaceutically acceptable excipient” refers to a pharmaceutically-acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, solvent, or encapsulating material. In some embodiments, each excipient is “pharmaceutically acceptable” in the sense of being compatible with the other ingredients of a pharmaceutical formulation, and suitable for use in contact with the tissue or organ of humans and animals without excessive toxicity, irritation, allergic response, immunogenicity, or other problems or complications, commensurate with a reasonable benefit/risk ratio. See, Remington: The Science and Practice of Pharmacy, 21st ed.; Lippincott Williams & Wilkins: Philadelphia, Pa., 2005; Handbook of Pharmaceutical Excipients, 6th ed.; Rowe et al., Eds.; The Pharmaceutical Press and the American Pharmaceutical Association: 2009; Handbook of Pharmaceutical Additives, 3rd ed.; Ash and Ash Eds.; Gower Publishing Company: 2007; Pharmaceutical Preformulation and Formulation, 2nd ed.; Gibson Ed.; CRC Press LLC: Boca Raton, Fla., 2009.
In some embodiments, a cosmetically acceptable excipient refers to a cosmetically acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, solvent, or encapsulating material. In some embodiments, each excipient is cosmetically acceptable in the sense of being compatible with the other ingredients of a cosmetic formulation, and suitable for use in contact with the tissue or organ of humans and animals without excessive toxicity, irritation, allergic response, immunogenicity, or other problems or complications, commensurate with a reasonable benefit/risk ratio.
While it is possible for the active ingredient, e.g., ammonia oxidizing bacteria, e.g., N. eutropha , to be administered alone, in many embodiments it present in a pharmaceutical formulation or composition. Accordingly, this disclosure provides a pharmaceutical formulation comprising ammonia oxidizing bacteria, for example, N. eutropha and a pharmaceutically acceptable excipient. Pharmaceutical compositions may take the form of a pharmaceutical formulation as described below.
The pharmaceutical formulations described herein include those suitable for oral, parenteral (including subcutaneous, intradermal, intramuscular, intravenous, and intraarticular), inhalation (including fine particle dusts or mists which may be generated by means of various types of metered doses, pressurized aerosols, nebulizers or insufflators, and including intranasally or via the lungs), rectal and topical (including dermal, transdermal, transmucosal, buccal, sublingual, and intraocular) administration, although the most suitable route may depend upon, for example, the condition and disorder of the recipient.
The formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods known in the art of pharmacy. Typically, methods include the step of bringing the active ingredient (e.g., ammonia oxidizing bacteria, e.g., N. eutropha ) into association with a pharmaceutical carrier which constitutes one or more accessory ingredients. In general the formulations are prepared by uniformly and intimately bringing into association the active ingredient with liquid carriers or finely divided solid carriers or both and then, if necessary, shaping the product into the desired formulation.
Formulations may be presented as discrete units such as capsules, cachets or tablets, each containing a predetermined amount of, e.g., N. eutropha ; as a powder or granules; as a solution or a suspension in an aqueous liquid or a non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion. The active ingredient may also be presented as a bolus, electuary or paste. Various pharmaceutically acceptable carriers and their formulation are described in standard formulation treatises, e.g., Remington's Pharmaceutical Sciences by E. W. Martin. See also Wang, Y. J. and Hanson, M. A., Journal of Parenteral Science and Technology, Technical Report No. 10, Supp. 42:2 S, 1988.
The ammonia oxidizing bacteria, e.g., N. eutropha compositions can, for example, be administered in a form suitable for immediate release or extended release. Suitable examples of sustained-release systems include suitable polymeric materials, for example semi-permeable polymer matrices in the form of shaped articles, e.g., films, or microcapsules; suitable hydrophobic materials, for example as an emulsion in an acceptable oil; or ion exchange resins. Sustained-release systems may be administered orally; rectally; parenterally; intracisternally; intravaginally; intraperitoneally; topically, for example as a powder, ointment, gel, drop or transdermal patch; bucally; or as a spray.
Preparations for administration can be suitably formulated to give controlled release of ammonia oxidizing bacteria, e.g., N. eutropha . For example, the pharmaceutical compositions may be in the form of particles comprising one or more of biodegradable polymers, polysaccharide jellifying and/or bioadhesive polymers, or amphiphilic polymers. These compositions exhibit certain biocompatibility features which allow a controlled release of an active substance. See U.S. Pat. No. 5,700,486.
Exemplary compositions include suspensions which can contain, for example, microcrystalline cellulose for imparting bulk, alginic acid or sodium alginate as a suspending agent, methylcellulose as a viscosity enhancer, dicalcium phosphate, starch, magnesium stearate and/or lactose and/or other excipients, binders, extenders, disintegrants, diluents and lubricants, mannitol, lactose, sucrose and/or cyclodextrins. Also included in such formulations may be high molecular weight excipients such as celluloses (avicel) or polyethylene glycols (PEG). Such formulations can also include an excipient to aid mucosal adhesion such as hydroxy propyl cellulose (HPC), hydroxy propyl methyl cellulose (HPMC), sodium carboxy methyl cellulose (SCMC), maleic anhydride copolymer (e.g., Gantrez), and agents to control release such as polyacrylic copolymer (e.g. Carbopol 934). Lubricants, glidants, flavors, coloring agents and stabilizers may also be added for ease of fabrication and use. The surfactant may be a zwitterionic surfactant, a non-ionic surfactant, or an anionic surfactant.
Excipients, such as surfactants that may be used with embodiments of the present disclosure may include one or more of cocamidopropyl betaine (ColaTeric COAB), polyethylene sorbitol ester (e.g., Tween 80), ethoxylated lauryl alcohol (RhodaSurf 6 NAT), sodium laureth sulfate/lauryl glucoside/cocamidopropyl betaine (Plantapon 611 L UP), sodium laureth sulfate (e.g., RhodaPex ESB 70 NAT), alkyl polyglucoside (e.g., Plantaren 2000 N UP), sodium laureth sulfate (Plantaren 200), Dr. Bronner's Castile soap, Dr. Bronner's Castile baby soap, Lauramine oxide (ColaLux Lo), sodium dodecyl sulfate (SDS), polysulfonate alkyl polyglucoside (PolySufanate 160 P), sodium lauryl sulfate (Stepanol-WA Extra K). and combinations thereof. Dr. Bronner's Castile soap and Dr. Bronner's baby soap comprises water, organic coconut oil, potassium hydroxide, organic olive oil, organic fair deal hemp oil, organic jojoba oil, citric acid, and tocopherol.
In some embodiments, surfactants may be used with ammonia oxidizing bacteria in amounts that allow nitrite production to occur. In some embodiments, the preparation may have less than about 0.0001% to about 10% of surfactant. In some embodiments, the preparation may have between about 0.1% and about 10% surfactant. In some embodiments, the concentration of surfactant used may be between about 0.0001% and about 10%. In some embodiments, the preparation may be substantially free of surfactant.
In some embodiments, the formulation, e.g., preparation, may include other components that may enhance effectiveness of ammonia oxidizing bacteria, or enhance a treatment or indication.
In some embodiments, a chelator may be included in the preparation. A chelator may be a compound that may bind with another compound, e.g., a metal. The chelator may provide assistance in removing an unwanted compound from an environment, or may act in a protective manner to reduce or eliminate contact of a particular compound with an environment, e.g., ammonia oxidizing bacteria, e.g. a preparation of ammonia oxidizing bacteria, e.g., an excipient. In some embodiments, the preparation may be substantially free of chelator.
Formulations may also contain anti-oxidants, buffers, bacteriostats that prevent the growth of undesired bacteria, solutes, and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilised) condition requiring only the addition of a sterile liquid carrier, for example saline or water-for-injection, immediately prior to use. Extemporaneous solutions and suspensions may be prepared from powders, granules and tablets of the kind previously described. Exemplary compositions include solutions or suspensions which can contain, for example, suitable non-toxic, pharmaceutically acceptable diluents or solvents, such as mannitol, 1,3-butanediol, water, Ringer's solution, an isotonic sodium chloride solution, or other suitable dispersing or wetting and suspending agents, including synthetic mono- or diglycerides, and fatty acids, including oleic acid, or Cremaphor. An aqueous carrier may be, for example, an isotonic buffer solution at a pH of from about 3.0 to about 8.0, a pH of from about 3.5 to about 7.4, for example from 3.5 to 6.0, for example from 3.5 to about 5.0. Useful buffers include sodium citrate-citric acid and sodium phosphate-phosphoric acid, and sodium acetate/acetic acid buffers. The composition in some embodiments does not include oxidizing agents.
Excipients that can be included are, for instance, proteins, such as human serum albumin or plasma preparations. If desired, the pharmaceutical composition may also contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate. In some embodiments, excipients, e.g., a pharmaceutically acceptable excipient or a cosmetically acceptable excipient, may comprise an anti-adherent, binder, coat, disintegrant, filler, flavor, color, lubricant, glidant, sorbent, preservative, or sweetener. In some embodiments, the preparation may be substantially free of excipients.
In some embodiments, the preparation may be substantially free of one or more of the compounds or substances listed in the disclosure.
Exemplary compositions for aerosol administration include solutions in saline, which can contain, for example, benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, and/or other solubilizing or dispersing agents. Conveniently in compositions for aerosol administration the ammonia oxidizing bacteria, e.g., N. eutropha is delivered in the form of an aerosol spray presentation from a pressurized pack or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoro-methane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g., gelatin can be formulated to contain a powder mix of the N. eutropha and a suitable powder base, for example lactose or starch. In certain embodiments, N. eutropha is administered as an aerosol from a metered dose valve, through an aerosol adapter also known as an actuator. Optionally, a stabilizer is also included, and/or porous particles for deep lung delivery are included (e.g., see U.S. Pat. No. 6,447,743).
Formulations may be presented with carriers such as cocoa butter, synthetic glyceride esters or polyethylene glycol. Such carriers are typically solid at ordinary temperatures, but liquefy and/or dissolve at body temperature to release the ammonia oxidizing bacteria, e.g., N. eutropha.
Exemplary compositions for topical administration include a topical carrier such as Plastibase (mineral oil gelled with polyethylene). In some aspects, the composition and/or excipient may be in the form of one or more of a liquid, a solid, or a gel. For example, liquid suspensions may include, but are not limited to, water, saline, phosphate-buffered saline, or an ammonia oxidizing storage buffer. Gel formulations may include, but are not limited to agar, silica, polyacrylic acid (for example Carbopol®), carboxymethyl cellulose, starch, guar gum, alginate or chitosan. In some embodiments, the formulation may be supplemented with an ammonia source including, but not limited to ammonium chloride or ammonium sulfate.
In some embodiments, an ammonia oxidizing bacteria, e.g., N. eutropha composition is formulated to improve NO penetration into the skin. A gel-forming material such as KY jelly or various hair gels would present a diffusion barrier to NO loss to ambient air, and so improve the skin's absorption of NO. The NO level in the skin will generally not greatly exceed 20 nM/L because that level activates GC and would cause local vasodilatation and oxidative destruction of excess NO.
It should be understood that in addition to the ingredients particularly mentioned above, the formulations as described herein may include other agents conventional in the art having regard to the type of formulation in question.
The formulation, e.g., preparation, e.g., composition may be provided in a container, delivery system, or delivery device, having a weight, including or not including the contents of the container, that may be less than about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 grams.
Suitable unit dosage formulations are those containing an effective dose, as hereinbefore recited, or an appropriate fraction thereof, of ammonia oxidizing bacteria, e.g., N. eutropha.
A therapeutically effective amount of ammonia oxidizing bacteria, e.g., N. eutropha may be administered as a single pulse dose, as a bolus dose, or as pulse doses administered over time. Thus, in pulse doses, a bolus administration of ammonia oxidizing bacteria, e.g., N. eutropha is provided, followed by a time period wherein ammonia oxidizing bacteria, e.g., N. eutropha is administered to the subject, followed by a second bolus administration. In specific, non-limiting examples, pulse doses are administered during the course of a day, during the course of a week, or during the course of a month.
In some embodiments, a preparation of ammonia oxidizing bacteria, e.g., a formulation, e.g., a composition, may be applied for a pre-determined number of days. This may be based, for example, at least in part, on the severity of the condition or disease, the response to the treatment, the dosage applied and the frequency of the dose. For example, the preparation may be applied for about 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, 84-91 days, for about 1 month, for about 2 months, for about 3 months. In some embodiments, the ammonia oxidizing bacteria is administered for an indefinite period of time, e.g., greater than one year, greater than 5 years, greater than 10 years, greater than 15 years, greater than 30 years, greater than 50 years, greater than 75 years. In certain aspects, the preparation may be applied for about 16 days.
In some embodiments, a preparation of ammonia oxidizing bacteria, e.g., a formulation, e.g., a composition, may be applied a pre-determined number of times per day. This may be based, for example, at least in part, on the severity of the condition or disease, the response to the treatment, the dosage applied and the frequency of the dose. For example, the preparation may be applied 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 times per day.
In some embodiments, the preparation may be applied one time per day. In other embodiments, the preparation may be applied two times per day. In some embodiments, the preparation may be applied a first pre-determined amount for a certain number of days, and a second pre-determined amount for a certain subsequent number of days. In some embodiments, the preparation may be applied for about 16 days.
Consumer Products
Ammonia oxidizing bacteria, e.g., N. eutropha may be associated with a variety of consumer products, and examples of such products are set out below. In some embodiments, the ammonia oxidizing bacteria, e.g., N. eutropha associated with a product is admixed with the product, for example, spread evenly throughout the product, and in some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha associated with a product is layered on the product.
In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with a powder. Powders are typically small particulate solids that are not attached to each other and that can flow freely when tilted. Exemplary powders for consumer use include talcum powder and some cosmetics (e.g., powder foundation).
In some embodiments, the ammonia oxidizing bacteria is associated with a cosmetic. The cosmetic may be a substance for topical application intended to alter a person's appearance, e.g., a liquid foundation, a powder foundation, blush, or lipstick. The cosmetic may be any substance recited in the Food and Drug Administration regulations, e.g., under 21 C.F.R. §720.4.
The cosmetic may be at least one of a baby product, e.g., a baby shampoo, a baby lotion, a baby oil, a baby powder, a baby cream; a bath preparation, e.g., a bath oil, a tablet, a salt, a bubble bath, a bath capsule; an eye makeup preparation, e.g., an eyebrow pencil, an eyeliner, an eye shadow, an eye lotion, an eye makeup remover, a mascara; a fragrance preparation, e.g., a colognes, a toilet water, a perfume, a powder (dusting and talcum), a sachet; hair preparations, e.g., hair conditioners, hair sprays, hair straighteners, permanent waves, rinses, shampoos, tonics, dressings, hair grooming aids, wave sets; hair coloring preparations, e.g., hair dyes and colors, hair tints, coloring hair rinses, coloring hair shampoos, hair lighteners with color, hair bleaches; makeup preparations, e.g., face powders, foundations, leg and body paints, lipstick, makeup bases, rouges, makeup fixatives; manicuring preparations, e.g., basecoats and undercoats, cuticle softeners, nail creams and lotions, nail extenders, nail polish and enamel, nail polish and enamel removers; oral hygiene products, e.g., dentrifices, mouthwashes and breath fresheners; bath soaps and detergents, deodorants, douches, feminine hygiene deodorants; shaving preparations, e.g., aftershave lotions, beard softeners, talcum, preshave lotions, shaving cream, shaving soap; skin care preparations, e.g., cleansing, depilatories, face and neck, body and hand, foot powders and sprays, moisturizing, night preparations, paste masks, skin fresheners; and suntan preparations, e.g., gels, creams, and liquids, and indoor tanning preparations.
In some embodiments, the formulations, compositions, or preparations described herein, may comprise, be provided as, or disposed in at least one of a baby product, e.g., a baby shampoo, a baby lotion, a baby oil, a baby powder, a baby cream; a bath preparation, e.g., a bath oil, a tablet, a salt, a bubble bath, a bath capsule; a powder (dusting and talcum), a sachet; hair preparations, e.g., hair conditioners, rinses, shampoos, tonics, face powders, cuticle softeners, nail creams and lotions, oral hygiene products, mouthwashes, bath soaps, douches, feminine hygiene deodorants; shaving preparations, e.g., aftershave lotions, skin care preparations, e.g., cleansing, face and neck, body and hand, foot powders and sprays, moisturizing, night preparations, paste masks, skin fresheners; and suntan preparations, e.g., gels, creams, and liquids.
In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with a cosmetic. The cosmetic may be a substance for topical application intended to alter a person's appearance, e.g., a liquid foundation, a powder foundation, blush, or lipstick. Other components may be added to these cosmetic preparations as selected by one skilled in the art of cosmetic formulation such as, for example, water, mineral oil, coloring agent, perfume, aloe, glycerin, sodium chloride, sodium bicarbonate, pH buffers, UV blocking agents, silicone oil, natural oils, vitamin E, herbal concentrates, lactic acid, citric acid, talc, clay, calcium carbonate, magnesium carbonate, zinc oxide, starch, urea, and erythorbic acid, or any other excipient known by one of skill in the art, including those disclosed herein.
In some embodiments, the preparation may be disposed in, or provided as, a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage.
In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with a cream. The cream may be a fluid comprising a thickening agent, and generally has a consistency that allows it to be spread evenly on the skin. Exemplary creams include moisturizing lotion, face cream, and body lotion.
In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is associated with a stick. A stick is typically a solid that, when placed in contact with a surface, transfers some of the stick contents to the surface. Exemplary sticks include deodorant stick, lipstick, lip balm in stick form, and sunscreen applicator sticks.
In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is associated with an aerosol. An aerosol is typically a colloid of fine solid particles or fine liquid droplets, in a gas such as air. Aerosols may be created by placing the N. eutropha (and optionally carriers) in a vessel under pressure, and then opening a valve to release the contents. The container may be designed to only exert levels of pressure that are compatible with N. eutropha viability. For instance, the high pressure may be exerted for only a short time, and/or the pressure may be low enough not to impair viability. Examples of consumer uses of aerosols include for sunscreen, deodorant, perfume, hairspray, and insect repellant.
In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is associated with a salve. A salve may be a topically applied agent with a liquid or cream-like consistency, intended to protect the skin or promote healing. Examples of salves include burn ointments and skin moisturizers.
In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is associated with a wipe. A wipe may be a flexible material suitable for topically applying a liquid or cream onto skin. The wipe may be, e.g., paper-based or cloth based. Exemplary wipes include tissues and wet wipes.
The compositions comprising ammonia oxidizing bacteria, e.g., N. eutropha may also comprise one or more of a moisturizing agent, deodorizing agent, scent, colorant, insect repellant, cleansing agent, or UV-blocking agent.
For instance, the moisturizing agent may be an agent that reduces or prevents skin dryness. Exemplary moisturizing agents include humectants (e.g., urea, glycerin, alpha hydroxy acids and dimethicone) and emollients (e.g., lanolin, mineral oil and petrolatum). Moisturizing agents may be included, e.g., in ammonia oxidizing bacteria, e.g., N. eutropha -containing creams, balms, lotions, or sunscreen.
A deodorizing agent may be an agent that reduces unwanted odors. A deodorizing agent may work by directly neutralizing odors, preventing perspiration, or preventing the growth of odor-producing bacteria. Exemplary deodorizing agents include aluminum salts (e.g., aluminum chloride or aluminum chlorohydrate), cyclomethicone, talc, baking soda, essential oils, mineral salts, hops, and witch hazel. Deodorizing agents are typically present in spray or stick deodorants, and can also be found in some soaps and clothing.
An insect repellant may be an agent that can be applied to surfaces (e.g., skin) that discourage insects and other arthropods from lighting on the surface. Insect repellants include DEET (N,N-diethyl-m-toluamide), p-menthane-3,8-diol (PMD), icaridin, nepetalactone, citronella oil, neem oil, bog myrtle, dimethyl carbate, Tricyclodecenyl allyl ether, and IR3535 (3-[N-Butyl-N-acetyl]-aminopropionic acid, ethyl ester).
A cleansing agent may be an agent that removes dirt or unwanted bacteria from a surface like skin. Exemplary cleansing agents include bar soaps, liquid soaps, and shampoos.
A UV-blocking agent may be an agent that can be applied to a surface to reduce the amount of ultraviolet light the surface receives. A UV-blocking agent may block UV-A and/or UV-B rays. A UV blocking agent can function by absorbing, reflecting, or scattering UV. Exemplary UV-blocking agents include absorbers, e.g., homosalate, octisalate (also called octyl salicylate), octinoxate (also called octyl methoxycinnamate or OMC), octocrylene, oxybenzone, and avobenzone, and reflectors (e.g., titanium dioxide and zinc oxide). UV-blocking agents are typically presents in sunscreens, and can also be found in skin creams and some cosmetics.
In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with a conditioner. Conditioner generally refers to a substance with cream-like consistency that can be applied to hair to improve its appearance, strength, or manageability.
In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with cloth. Cloth generally refers to a flexible material suitable to be made into clothing, e.g., having enough material strength to withstand everyday motion by a wearer. Cloth can be fibrous, woven, or knit; it can be made of a naturally occurring material or a synthetic material. Exemplary cloth materials include cotton, flax, wool, ramie, silk, denim, leather, nylon, polyester, and spandex, and blends thereof.
In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with yarn. Yarn generally refers to a long, thin spun flexible material that is suitable for knitting or weaving. Yarn can be made of, e.g., wool, cotton, polyester, and blends thereof.
In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with thread. Thread generally refers to a long, thin spun flexible material that is suitable for sewing. Thread generally has a thinner diameter than yarn. Thread can be made of, e.g., cotton, polyester, nylon, silk, and blends thereof.
Articles of clothing such as, for example, shoes, shoe inserts, pajamas, sneakers, belts, hats, shirts, underwear, athletic garments, helmets, towels, gloves, socks, bandages, and the like, may also be treated with ammonia oxidizing bacteria, e.g., N. eutropha . Bedding, including sheets, pillows, pillow cases, and blankets may also be treated with ammonia oxidizing bacteria, e.g., N. eutropha . In some embodiments, areas of skin that cannot be washed for a period of time may also be contacted with ammonia oxidizing bacteria, e.g., N. eutropha . For example, skin enclosed in orthopedic casts which immobilize injured limbs during the healing process, and areas in proximity to injuries that must be kept dry for proper healing such as stitched wounds may benefit from contact with the ammonia oxidizing bacteria, e.g., N. eutropha.
In some aspects, the present disclosure provides a wearable article comprising an N. eutropha strain as described herein. A wearable article may be a light article that can be closely associated with a user's body, in a way that does not impede ambulation. Examples of wearable articles include a wristwatch, wristband, headband, hair elastic, hair nets, shower caps, hats, hairpieces, and jewelry. The wearable article comprising an ammonia oxidizing bacteria, e.g., N. eutropha strain described herein may provide, e.g., at a concentration that provides one or more of a treatment or prevention of a skin disorder, a treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, or a treatment to inhibit microbial growth.
In some embodiments, the ammonia oxidizing bacteria, e.g., N. eutropha is associated with a product intended to contact the hair, for example, a brush, comb, shampoo, conditioner, headband, hair elastic, hair nets, shower caps, hats, and hairpieces. Nitric oxide formed on the hair, away from the skin surface, may be captured in a hat, scarf or face mask and directed into inhaled air.
Articles contacting the surface of a human subject, such as a diaper, may be associated with ammonia oxidizing bacteria, e.g., N. eutropha . Because diapers are designed to hold and contain urine and feces produced by incontinent individuals, the urea in urine and feces can be hydrolyzed by skin and fecal bacteria to form free ammonia which is irritating and may cause diaper rash. Incorporation of bacteria that metabolize urea into nitrite or nitrate, such as ammonia oxidizing bacteria, e.g., N. eutropha , may avoid the release of free ammonia and may release nitrite and ultimately NO which may aid in the maintenance of healthy skin for both children and incontinent adults. The release of nitric oxide in diapers may also have anti-microbial effects on disease causing organisms present in human feces. This effect may continue even after disposable diapers are disposed of as waste and may reduce the incidence of transmission of disease through contact with soiled disposable diapers
In some embodiments, the product comprising ammonia oxidizing bacteria, e.g., N. eutropha is packaged. The packaging may serve to compact the product or protect it from damage, dirt, or degradation. The packaging may comprise, e.g., plastic, paper, cardboard, or wood. In some embodiments the packaging is impermeable to bacteria. In some embodiments the packaging is permeable to oxygen and/or carbon dioxide.
5. METHODS OF TREATMENT WITH N. EUTROPHA
The present disclosure provides various methods of treating diseases and conditions using ammonia oxidizing bacteria, e.g., N. eutropha . The ammonia oxidizing bacteria, e.g., N. eutropha that may be used to treat diseases and conditions include all the ammonia oxidizing bacteria, e.g., N. eutropha compositions described in this application, e.g. a purified preparation of optimized ammonia oxidizing bacteria, e.g., N. eutropha , e.g. those in Section 2 above, for instance strain D23.
For instance, the disclosure provides uses, for treating a condition or disease (e.g., inhibiting microbial growth on a subject's skin), an optionally axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO: 1; an optionally axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to any one of the strain D23 nucleic acids of Table 1. In embodiments, the N. eutropha comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all of the strain D23 nucleic acids of Table 1. In embodiments, the N. eutropha comprises one or more nucleic acids of FIGS. 6-8 . As a further example, this disclosure provides uses, for treating a condition or disease, an optionally axenic composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to any one of the strain D23 protein sequences of Table 1. In embodiments, the N. eutropha comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all of the strain D23 protein sequences of Table 1. In embodiments, the N. eutropha comprises one or more proteins encoded by the nucleic acids of FIGS. 6-8 . The N. eutropha of this paragraph may be used to treat, e.g., diabetic ulcers, e.g., diabetic foot ulcers, chronic wounds, acne, rosacea, eczema, or psoriasis.
In certain embodiments, the disclosure provides uses, for treating a condition or disease (e.g., inhibiting microbial growth on a subject's skin), an optionally axenic composition of N. eutropha having one or more of: (1) an optimized growth rate, (2) an optimized NH 4 + oxidation rate, (3) an optimized resistance to NH 3 , (4) an optimized resistance to, NH 4 + , and (5) an optimized resistance to, NO 2 − . For instance, the axenic N. eutropha composition may have properties (1) and (2); (2) and (3); (3) and (4); or (4) and (5) from the list at the beginning of this paragraph. As another example, the axenic N. eutropha composition may have properties (1), (2), and (3); (1), (2), and (4); (1), (2), and (5); (1), (3), and (4); (1), (3), and (5); (1), (4), and (5); (2), (3), and (4); (2), (3), and (5), or (3), (4), and (5) from the list at the beginning of this paragraph. As a further example, the optionally axenic N. eutropha composition may have properties (1), (2), (3), and (4); (1), (2), (3), and (5); (1), (2), (4), and (5); (1), (3), (4), and (5); or (2), (3), (4), and (5) from the list at the beginning of this paragraph. In some embodiments, the axenic N. eutropha composition has properties (1), (2), (3), (4), and (5) from the list at the beginning of this paragraph. The N. eutropha of this paragraph may be used to treat, e.g., diabetic ulcers, e.g., diabetic foot ulcers, chronic wounds, acne, rosacea, eczema, or psoriasis.
In some embodiments, optionally axenic N. eutropha (e.g., strain D23) are used to treat a subject. Subjects may include an animal, a mammal, a human, a non-human animal, a livestock animal, or a companion animal.
In some embodiments, optionally axenic N. eutropha described herein (e.g., the N. eutropha described in this Section and in Section 2 above, e.g., strain D23) are used to inhibit the growth of other organisms. For instance, N. eutropha D23 is well-adapted for long-term colonization of human skin, and in some embodiments it out-competes other bacteria that are undesirable on the skin. Undesirable skin bacteria include, e.g., those that can infect wounds, raise the risk or severity of a disease, or produce odors. Certain undesirable skin bacteria include S. aureus, P. aeruginosa, S. pyogenes , and A. baumannii . The N. eutropha described herein may out-compete other organisms by, e.g., consuming scarce nutrients, or generating byproducts that are harmful to other organisms, e.g., changing the pH of the skin to a level that is not conducive to the undesirable organism's growth.
Accordingly, the present disclosure provides, inter alia, a method of inhibiting microbial growth on a subject's skin, comprising topically administering to a human in need thereof an effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23). Similarly, the present disclosure provides optionally axenic N. eutropha as described herein (e.g., strain D23) for use in inhibiting microbial growth on a subject's skin. Likewise, the present disclosure provides a use of optionally axenic N. eutropha (e.g., strain D23) in the manufacture of a medicament for inhibiting microbial growth on a subject's skin.
The present disclosure also provides a method of supplying nitric oxide to a subject, comprising positioning an effective dose of optionally axenic N. eutropha bacteria described herein (e.g., strain D23) in close proximity to the subject. Similarly, the present disclosure provides optionally axenic N. eutropha (e.g., strain D23) as described herein for use in supplying nitric oxide to a subject. Likewise, the present disclosure provides a use of optionally axenic N. eutropha (e.g., strain D23) in the manufacture of a medicament or composition suitable for position in close proximity to a subject.
The present disclosure also provides a method of reducing body odor, comprising topically administering to a subject in need thereof an effective dose of optionally axenic N. eutropha bacteria described herein (e.g., strain D23). Similarly, the present disclosure provides optionally axenic N. eutropha as described herein (e.g., strain D23) for use in reducing body odor in a subject. Likewise, the present disclosure provides a use of optionally axenic N. eutropha as described herein (e.g., strain D23) in the manufacture of a medicament or composition for reducing body odor.
The present disclosure also provides a method of treating or preventing a disease associated with low nitrite levels, comprising topically administering to a subject in need thereof a therapeutically effective dose of optionally axenic N. eutropha bacteria described herein (e.g., strain D23). Similarly, the present disclosure provides a topical formulation of optionally axenic N. eutropha as described herein (e.g., strain D23) for use in treating a disease associated with low nitrite levels. Likewise, the present disclosure provides a use of optionally axenic N. eutropha as described herein (e.g., strain D23) in the manufacture of a topical medicament for treating a disease associated with low nitrite levels.
The present disclosure also provides a method of treating or preventing a skin disorder or skin infection, comprising topically administering to a subject in need thereof a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23). Similarly, the present disclosure provides optionally axenic N. eutropha as described herein (e.g., strain D23) for use in treating a skin disorder in a subject. Likewise, the present disclosure provides a use of optionally axenic N. eutropha as described herein (e.g., strain D23) in the manufacture of a medicament for treating skin disorder. In embodiments, the skin disorder is acne, rosacea, eczema, psoriasis, or urticaria; the skin infection is impetigo.
While not wishing to be bound by theory, it is proposed that treatment of acne with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve the downregulation of inflammation due to NO generation; and/or limiting and/or inhibiting the spread and proliferation of Propionibacterium acnes associated with acne vulgaris through acidified nitrite and NO production.
For instance, the disclosure provides uses, for treating a condition or disease (e.g., inhibiting microbial growth on a subject's skin), a composition of ammonia oxidizing bacteria. In embodiments, the ammonia oxidizing bacteria may be used to treat, e.g., chronic wounds, acne, rosacea, eczema, psoriasis, uticaria, skin infections, or diabetic ulcers, e.g., diabetic foot ulcers.
The systems and methods of the present disclosure may provide for, or contain contents, to be useful for treating or preventing a skin disorder, treating or preventing a disease or condition associated with low nitrite levels, a treating or preventing body odor, treating to supply nitric oxide to a subject, or treating to inhibit microbial growth.
The systems and methods of the present disclosure may provide for reducing an amount of undesirable bacteria from an environment, e.g., a surface of a subject.
The systems and methods of the present disclosure may provide for, or contain contents, to be useful in a treatment of at least one of HIV dermatitis, infection in a diabetic foot ulcer, atopic dermatitis, acne, eczema, contact dermatitis, allergic reaction, psoriasis, uticaria, rosacea, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, pneumonia, primary immunodeficiency, epidermal lysis bulosa, or cancer.
The systems and methods of the present disclosure may provide for, or contain contents, to be useful in a treatment of at least one of acne, eczema, psoriasis, uticaria, rosacea, skin infections and wounds, e.g., an infected wound.
In some embodiments, ammonia oxidizing bacteria may be used to treat a subject. Subjects may include an animal, a mammal, a human, a non-human animal, a livestock animal, or a companion animal.
In some embodiments, ammonia oxidizing bacteria described herein are used to inhibit the growth of other organisms. For instance, ammonia oxidizing bacteria may be well-adapted for long-term colonization of human skin, and in some embodiments it out-competes other bacteria that are undesirable on the skin. Undesirable skin bacteria include, e.g., those that can infect wounds, raise the risk or severity of a disease, or produce odors. Undesirable bacteria may be referred to as pathogenic bacteria. Certain undesirable skin bacteria include Staphylococcus aureus ( S. aureus ), e.g., methicillin resistant Staphylococcus aureus Pseudomonas aeruginosa ( P. aeruginosa ), Streptococcus pyogenes ( S. pyogenes ), Acinetobacter baumannii ( A. baumannii ), Propionibacteria, and Stenotrophomonas . The ammonia oxidizing bacteria described herein may out-compete other organisms by, e.g., consuming scarce nutrients, or generating byproducts that are harmful to other organisms, e.g., changing the pH of the skin to a level that is not conducive to the undesirable organism's growth.
Accordingly, the present disclosure provides, inter alia, a method of inhibiting microbial growth on a subject's skin, comprising topically administering to a human in need thereof an effective dose of ammonia oxidizing bacteria as described herein. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in inhibiting microbial growth on a subject's skin. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria in the manufacture of a medicament for inhibiting microbial growth on a subject's skin.
The present disclosure provides, inter alia, a method of changing a composition of a skin microbiome, e.g., modulating a composition of a skin microbiome, e.g., modulating or changing the proportions of the skin microbiome, in an environment, e.g., a surface, e.g., a surface of a subject. The method may comprise administering, e.g., applying, a preparation comprising ammonia oxidizing bacteria to an environment, e.g., a surface, e.g., a surface of a subject. In some embodiments, the amount and frequency of administration, e.g., application, may be sufficient to reduce the proportion of pathogenic bacteria on the surface of the skin. In some embodiments, the subject may be selected on the basis of the subject being in need of a reduction in the proportion of pathogenic bacteria on the surface of the skin.
The present disclosure may further provide obtaining a sample from the surface of the skin, and isolating DNA of bacteria in the sample. Sequencing of the DNA of bacteria in the sample may also be performed to determine or monitor the amount or proportion of bacteria in a sample of a subject.
The present disclosure may also provide for increasing the proportion of non-pathogenic bacteria on the surface. In some embodiments, the non-pathogenic bacteria may be commensal non-pathogenic bacteria. In some embodiments, the non-pathogenic bacteria may be of the Staphylococcus genus. In some embodiments, the non-pathogenic bacteria may be Staphylococcus epidermidis . In some embodiments, the non-pathogenic bacteria that is increased in proportion may be of the Staphylococcus genus, comprising at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% Staphylococcus epidermidis.
The increase in the proportion of non-pathogenic bacteria may occur with a pre-determined period of time, e.g., in less than 1 day, 2 days, 3 days, 4 days, 5 days, 1 week, 2 weeks, 3 weeks, or 4 weeks, or in less than 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, 84-91 days.
The increase in the proportion of Staphylococcus bacteria, e.g., Staphylococcus epidermidis , may be observed in less than about 3 weeks, e.g., about 16 days, e.g., about 2 weeks.
The present disclosure may provide for decreasing the proportion of pathogenic bacteria, e.g., potentially pathogenic bacteria, e.g., disease-associated bacteria on the surface. In some embodiments, the pathogenic bacteria may be Propionibacteria. In some embodiments, the pathogenic bacteria may be Stenotrophomonas.
The decrease in the proportion of pathogenic bacteria may occur with a pre-determined period of time, e.g., in less than 1 day, 2 days, 3 days, 4 days, 5 days, 1 week, 2 weeks, 3 weeks, or 4 weeks, or in less than 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, 84-91 days.
The decrease in the proportion of Propionibacteria bacteria and/or Stenotrophomonas may be observed in less than about 3 weeks, e.g., about 16 days, e.g., about 2 weeks.
The present disclosure also provides a method of supplying nitric oxide to a subject, comprising positioning an effective dose of ammonia oxidizing bacteria described herein in close proximity to the subject. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in supplying nitric oxide to a subject. Likewise, the present disclosure provides a use of in the manufacture of a medicament or composition suitable for position in close proximity to a subject.
The present disclosure also provides a method of reducing body odor, comprising topically administering to a subject in need thereof an effective dose of ammonia oxidizing bacteria described herein. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in reducing body odor in a subject. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria as described herein in the manufacture of a medicament or composition for reducing body odor.
The present disclosure also provides a method of treating or preventing a disease associated with low nitrite levels, comprising topically administering to a subject in need thereof a therapeutically effective dose of ammonia oxidizing bacteria described herein. Similarly, the present disclosure provides a topical formulation of ammonia oxidizing bacteria as described herein for use in treating a disease associated with low nitrite levels. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria as described herein in the manufacture of a topical medicament for treating a disease associated with low nitrite levels.
The present disclosure also provides a method of treating or preventing a skin disorder or skin infection, comprising topically administering to a subject in need thereof a therapeutically effective dose of ammonia oxidizing bacteria as described herein. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in treating a skin disorder in a subject. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria as described herein in the manufacture of a medicament for treating skin disorder. In embodiments, the skin disorder is acne, rosacea, eczema, psoriasis, or urticaria; the skin infection is impetigo.
While not wishing to be bound by theory, it is proposed that treatment of rosacea with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve downregulation due to NO generation. This may be due to expression of Kazal-type KLK5/KLK7 inhibitor(s) that may reduce formation of the human cathelicidin peptide LL-37 from its precursor propeptide hCAP18.
While not wishing to be bound by theory, it is proposed that treatment of eczema and/or atopic dermatitis with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve downregulation of inflammation due to NO generation; and/or limiting and/or inhibiting the spread and proliferation of S. aureus and other skin pathogens often associated with very high colonization rates and skin loads in atopic dermatitis through acidified nitrite and NO production.
While not wishing to be bound by theory, it is proposed that treatment of psoriasis with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve downregulation of inflammation due to NO generation and reduction in formation of human cathelicidin peptide LL-37.
While not wishing to be bound by theory, it is proposed that treatment of psoriasis with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve downregulation of inflammation due to NO generation.
While not wishing to be bound by theory, it is proposed that treatment of impetigo or other skin and soft tissue infections with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve limiting and/or inhibiting the spread and proliferation of S. aureus and S. pyogenes.
The present disclosure also provides a method of promoting wound healing, comprising administering to a wound an effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23). Similarly, the present disclosure provides optionally axenic N. eutropha as described herein (e.g., strain D23) for use in treating a wound. Likewise, the present disclosure provides a use of optionally axenic N. eutropha as described herein (e.g., strain D23) in the manufacture of a medicament or a composition for treating a wound.
Optionally axenic N. eutropha as described herein (e.g., strain D23) may be used to promote wound healing in a patient that has an impaired healing ability, e.g., a diabetic patient.
In some embodiments, this disclosure provides methods of using optionally axenic N. eutropha as described herein (e.g., strain D23) to prevent a disease or disorder, e.g., a skin disorder. Prevention, in certain embodiments, means reducing the risk of a subject developing a disease, compared to a similar untreated subject. The risk need not be reduced to zero.
Individuals having a reduced bathing frequency, such as astronauts, submarine crew members, military personnel during a campaign, civilian workers in remote locations, refugees, bedridden individuals and many others may maintain healthier skin by maintaining N. eutropha on the skin. With regard to bedridden individuals, the N. eutropha in some embodiments reduces the frequency or severity of bed sores by augmenting inadequate circulation.
It is appreciated that many modern degenerative diseases may be caused by a lack of NO species, and that AOB on the external skin can supply those species by diffusion, and that application of AOB to the skin resolves long standing medical conditions. In certain embodiments, AOB are applied to a subject to offset modern bathing practices, especially with anionic detergents remove AOB from the external skin.
One suitable method of topical application to apply sufficient N. eutropha and then wear sufficient clothing so as to induce sweating. However, many people will want to derive the benefits of AOB while maintaining their current bathing habits, in which case, a culture of the bacteria can be applied along with sufficient substrate for them to produce NO. A nutrient solution approximating the inorganic composition of human sweat can be used for this purpose. Using bacteria adapted to media approximating human sweat minimizes the time for them to adapt when applied. Since sweat evaporates once excreted onto the skin surface, using a culture media that has a higher ionic strength is desirable. A concentration approximately twice that of human sweat is suitable, but other conditions are also contemplated. AOB's nutritional needs are typically met with NH 3 or urea, O 2 , CO 2 , and minerals. In some embodiments, the substrate comprises trace minerals including iron, copper, zinc, cobalt, molybdenum, manganese, sodium, potassium, calcium, magnesium, chloride, phosphate, sulfate, or any combination thereof.
In some embodiments, the present disclosure provides a method of treating a wound by applying a bandage comprising N. eutropha to the wound. Also provided are methods of producing such a bandage. The bandage may comprise, for example, an adhesive portion to affix the bandage to undamaged skin near the wound and a soft, flexible portion to cover or overlay the wound. In some embodiments, the bandage contains no other organisms but N. eutropha . The bandage may be made of a permeable material that allows gasses like oxygen and carbon dioxide to reach the N. eutropha when the bandage is applied to the wound. In certain embodiments, the bandage comprises nutrients for N. eutropha such as ammonium, ammonia, urea, or trace minerals. In certain embodiments, the bandage comprises an antibiotic to which the N. eutropha is resistant. The antibiotic resistance may arise from one or more endogenous resistance gene or from one or more transgenic.
In some embodiments, the N. eutropha is administered at a dose of about 10 8 -10 9 CFU, 10 9 -10 10 CFU, 10 10 -10 11 CFU, or 10 11 -10 12 CFU per application. In some embodiments, the N. eutropha is administered topically at a dose of about 10 10 -10 11 CFU, e.g., about 1×10 10 -5×10 10 , 1×10 10 -3×10 10 , or 1×10 10 -2×10 10 CFU.
In some embodiments, the N. eutropha is administered in a volume of about 1-2, 2-5, 5-10, 10-15, 12-18, 15-20, 20-25, or 25-50 ml per dose. In some embodiments, the solution is at a concentration of about 10 8 -10 9 , 10 9 -10 10 , or 10 10 -10 11 CFUs/ml. In some embodiments, the N. eutropha is administered as two 15 ml doses per day, where each dose is at a concentration of 10 9 CFU/ml.
In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is administered once, twice, three, or four times per day. In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is administered once, twice, three, four, five, or six times per week. In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is administered shortly after bathing. In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is administered shortly before sleep.
In certain aspects, the present disclosure provides combination therapies comprising ammonia oxidizing bacteria, e.g., a N. eutropha and a second therapeutic. For instance, the disclosure provides physical admixtures of the two (or more) therapies are physically admixed. In other embodiments, the two (or more) therapies are administered in combination as separate formulation. The second therapy may be, e.g., a pharmaceutical agent, surgery, or any other medical approach that treats the relevant disease or disorder. The following paragraphs describe combination therapies capable of treating diabetic ulcers, chronic wounds, acne, rosacea, eczema, and psoriasis.
For instance, in a combination therapy capable of treating diabetic ulcers, the second therapy may comprise, e.g., a wound dressing (e.g., absorptive fillers, hydrogel dressings, or hydrocolloids), angiotensin, angiotensin analogues, platelet-rich fibrin therapy, hyperbaric oxygen therapy, negative pressure wound therapy, debridement, drainage, arterial revascularization, hyperbaric oxygen therapy, low level laser therapy, and gastrocnemius recession. The combination therapy may comprise one or more of the above-mentioned treatments.
In a combination therapy capable of treating chronic wounds, the second therapy may comprise, e.g., an antibiotic (e.g., topical or systemic, and bacteriocidal or bacteriostatic) such as Penicillins, cephalosporins, polymyxins, rifamycins, lipiarmycins, quinolones, sulfonamides, macrolides, lincosamides, tetracyclines, cyclic lipopeptides, glycylcyclines, oxazolidinones, and lipiarmycins; angiotensin, angiotensin analogues; debridement; drainage; wound irrigation; negative pressure wound therapy; application of heat; arterial revascularization; hyperbaric oxygen therapy; antioxidants such as ascorbic acid, glutathione, lipoic acid, carotenes, α-tocopherol, or ubiquinol; low level laser therapy; gastrocnemius recession; growth factors such as vascular endothelial growth factor, insulin-like growth factor 1-2, platelet derived growth factor, transforming growth factor-β, or epidermal growth factor; application of autologous platelets such as those that secrete one or more growth factors such as vascular endothelial growth factor, insulin-like growth factor 1-2, platelet derived growth factor, transforming growth factor-β, or epidermal growth factor; implantation of cultured keratinocytes; allograft; collagen, for instance a dressing comprising collagen; or protease inhibitors such as SLPI. The combination therapy may comprise one or more of the above-mentioned treatments.
In a combination therapy capable of treating acne, the second therapy may comprise, e.g., a medication (e.g., systemic or topical) such as Benzoyl peroxide, antibiotics (such as erythromycin, clindamycin, or a tetracycline), Salicylic acid, hormones (e.g., comprising a progestin such as desogestrel, norgestimate or drospirenone), retinoids such as tretinoin, adapalene, tazarotene, or isotretinoin. The second therapy may also be a procedure such as comedo extraction, corticosteroid injection, or surgical lancing. The combination therapy may comprise one or more of the above-mentioned treatments.
In a combination therapy capable of treating rosacea, the second therapy may comprise, e.g., an antibiotic, e.g., an oral tetracycline antibiotic such as tetracycline, doxycycline, or minocycline, or a topical antibiotic such as metronidazole; azelaic acid; alpha-hydroxy acid; isotretinoin can be prescribed; sandalwood oil; clonidine; beta-blockers such as nadolol and propranolol; antihistamines (such as loratadine); mirtazapine; methylsulfonylmethane or silymarin, optionally in combination with each other; lasers such as dermatological vascular laser or CO 2 laser; or light therapies such as intense pulsed light, low-level light therapy or photorejuvenation. The combination therapy may comprise one or more of the above-mentioned treatments.
In a combination therapy capable of treating eczema, the second therapy may comprise, e.g., a corticosteroid such as hydrocortisone or clobetasol propionate, immunosuppressants (topical or systemic) such as pimecrolimus, tacrolimus, ciclosporin, azathioprine or methotrexate, or light therapy such as with ultraviolet light. The combination therapy may comprise one or more of the above-mentioned treatments.
In a combination therapy capable of treating psoriasis, the second therapy may comprise, e.g., a corticosteroid such as desoximetasone; a retinoid; coal tar; Vitamin D or an analogue thereof such as paricalcitol or calcipotriol; moisturizers and emollients such as mineral oil, vaseline, calcipotriol, decubal, or coconut oil; dithranol; or fluocinonide. The combination therapy may comprise one or more of the above-mentioned treatments.
While not wishing to be bound by theory, it is proposed that treatment of psoriasis with a therapeutically effective dose of ammonia oxidizing bacteria described herein may involve downregulation of inflammation due to NO generation and reduction in formation of human cathelicidin peptide LL-37.
While not wishing to be bound by theory, it is proposed that treatment of psoriasis with a therapeutically effective dose of ammonia oxidizing bacteria as described herein may involve downregulation of inflammation due to NO generation.
While not wishing to be bound by theory, it is proposed that treatment of impetigo or other skin and soft tissue infections with a therapeutically effective dose of ammonia oxidizing bacteria as described herein may involve limiting and/or inhibiting the spread and proliferation of Staphylococcus aureus ( S. aureus ), e.g., methicillin resistant Staphylococcus aureus, Pseudomonas aeruginosa ( P. aeruginosa ), Streptococcus pyogenes ( S. pyogenes ), Acinetobacter baumannii ( A. baumannii ), Propionibacteria, and Stenotrophomonas.
The present disclosure also provides a method of promoting wound healing, comprising administering to a wound an effective dose of ammonia oxidizing bacteria as described herein. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in treating a wound. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria as described herein in the manufacture of a medicament or a composition for treating a wound.
Ammonia oxidizing bacteria as described herein may be used to promote wound healing in a patient that has an impaired healing ability, e.g., a diabetic patient.
In some embodiments, this disclosure provides methods of using ammonia oxidizing bacteria as described herein to prevent a disease or disorder, e.g., a skin disorder. Prevention, in certain embodiments, means reducing the risk of a subject developing a disease, compared to a similar untreated subject. The risk need not be reduced to zero.
Individuals having a reduced bathing frequency, such as astronauts, submarine crew members, military personnel during a campaign, civilian workers in remote locations, refugees, bedridden individuals and many others may maintain healthier skin by maintaining ammonia oxidizing bacteria on the skin. With regard to bedridden individuals, the ammonia oxidizing bacteria in some embodiments reduces the frequency or severity of bed sores by augmenting inadequate circulation.
It is appreciated that many modern degenerative diseases may be caused by a lack of NO species, and that ammonia oxidizing bacteria on the external skin can supply those species by diffusion, and that application of ammonia oxidizing bacteria to the skin resolves long standing medical conditions. In certain embodiments, ammonia oxidizing bacteria are applied to a subject to offset modern bathing practices, especially with anionic detergents remove ammonia oxidizing bacteria from the external skin.
One suitable method of topical application to apply sufficient ammonia oxidizing bacteria and then wear sufficient clothing so as to induce sweating. However, many people will want to derive the benefits of ammonia oxidizing bacteria while maintaining their current bathing habits, in which case, a culture of the bacteria can be applied along with sufficient substrate for them to produce NO. A nutrient solution approximating the inorganic composition of human sweat can be used for this purpose. Using bacteria adapted to media approximating human sweat minimizes the time for them to adapt when applied. Since sweat evaporates once excreted onto the skin surface, using a culture media that has a higher ionic strength is desirable. A concentration approximately twice that of human sweat is suitable, but other conditions are also contemplated. Ammonia oxidizing bacteria's nutritional needs are typically met with NH 3 or urea, O 2 , CO 2 , and minerals. In some embodiments, the substrate comprises trace minerals including iron, copper, zinc, cobalt, molybdenum, manganese, sodium, potassium, calcium, magnesium, chloride, phosphate, sulfate, or any combination thereof.
In some embodiments, the present disclosure provides a method of treating a wound by applying a bandage comprising ammonia oxidizing bacteria to the wound. Also provided are methods of producing such a bandage. The bandage may comprise, for example, an adhesive portion to affix the bandage to undamaged skin near the wound and a soft, flexible portion to cover or overlay the wound. In some embodiments, the bandage contains no other organisms but ammonia oxidizing bacteria. The bandage may made of a permeable material that allows gasses like oxygen and carbon dioxide to reach the ammonia oxidizing bacteria when the bandage is applied to the wound. In certain embodiments, the bandage comprises nutrients for ammonia oxidizing bacteria such as ammonium, ammonia, urea, or trace minerals. In certain embodiments, the bandage comprises an antibiotic to which the ammonia oxidizing bacteria is resistant. The antibiotic resistance may arise from one or more endogenous resistance gene or from one or more transgenes.
In some embodiments, the ammonia oxidizing bacteria, e.g., a preparation of ammonia oxidizing bacteria, is administered at a dose of about 10 8 -10 9 CFU, 10 9 -10 10 CFU, 10 10 -10 11 CFU, or 10 11 -10 12 CFU per application or per day. In some embodiments, the ammonia oxidizing bacteria is administered topically at a dose of about 10 9 -10 10 CFU, e.g., about 1×10 9 -5×10 9 , 1×10 9 -3×10 9 , or 1×10 9 -10×10 9 CFU.
In some embodiments, the ammonia oxidizing bacteria is administered in a volume of about 1-2, 2-5, 5-10, 10-15, 12-18, 15-20, 20-25, or 25-50 ml per dose. In some embodiments, the solution is at a concentration of about 10 8 -10 9 , 10 9 -10 10 , or 10 10 -10 11 CFU/ml. In some embodiments, the ammonia oxidizing bacteria is administered as two 15 ml doses per day, where each dose is at a concentration of 10 9 CFU/ml.
In some embodiments, the ammonia oxidizing bacteria is administered once, twice, three, or four times per day. In some embodiments, the ammonia oxidizing bacteria is administered once, twice, three, four, five, or six times per week. In some embodiments, the ammonia oxidizing bacteria is administered shortly after bathing. In some embodiments, the ammonia oxidizing bacteria is administered shortly before sleep.
In some embodiments, the ammonia oxidizing bacteria is administered for about 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, 84-91 days, e.g., for about 1 month, for about 2 months, for about 3 months. In some embodiments, the ammonia oxidizing bacteria is administered for an indefinite period of time, e.g., greater than one year, greater than 5 years, greater than 10 years, greater than 15 years, greater than 30 years, greater than 50 years, greater than 75 years.
6. EXPERIMENTAL MODELS FOR REFINING D23 TREATMENTS
Treatments comprising ammonia oxidizing bacteria as described herein (optionally in combination with another therapy) can be refined using a number of model systems. These model systems can be used to determine suitable doses and timing of administration.
For instance, with respect to chronic wounds and diabetic ulcers, one may use the mouse skin puncture model. Other models for these disorders include controlled cutaneous ischemia in a guinea pig model, rabbit ear ulcer model, application of calcium to a wound, or topical application of doxorubicin.
With respect to acne, one may use (for example) the Mexican hairless dog model, the Rhino mouse model, or the rabbit ear assay. With respect to rosacea, one may use (for example) intradermal injection of LL-37 into mouse skin or the Syrian hamster model. With respect to eczema, one may use (for example) application of a crude extract of Dermatophagoides farina, application of dinitrochlorobenzene to the ears of sensitized guinea pigs, or NC/Nga mice. With respect to psoriasis, one may use (for example) xenograft models in which involved and uninvolved psoriatic skin are transplanted onto immunodeficient mice, application of an antibody directed against interleukin 15 to the skin of SCID mice, and the Sharpin cpdm /Sharpin cpdm mouse model.
Treatments comprising ammonia oxidizing bacteria, e.g., N. eutropha as described herein (e.g., strain D23) (optionally in combination with another therapy) can be refined using a number of model systems. These model systems can be used to determine suitable doses and timing of administration.
For instance, with respect to chronic wounds and diabetic ulcers, one may use the mouse skin puncture model described herein in Example 6. Other models for these disorders include controlled cutaneous ischemia in a guinea pig model, rabbit ear ulcer model, application of calcium to a wound, or topical application of doxorubicin.
With respect to acne, one may use (for example) the Mexican Hairless Dog model, the Rhino mouse model, or the rabbit ear assay. With respect to rosacea, one may use (for example) intradermal injection of LL-37 into mouse skin or the Syrian hamster model. With respect to eczema, one may use (for example) application of a crude extract of Dermatophagoides farina, application of dinitrochlorobenzene to the ears of sensitized guinea pigs, or NC/Nga mice. With respect to psoriasis, one may use (for example) xenograft models in which involved and uninvolved psoriatic skin are transplanted onto immunodeficient mice, application of an antibody directed against interleukin 15 to the skin of SCID mice, and the Sharpin cpdm /Sharpin cpdm mouse model.
7. MECHANISM OF THERAPEUTIC BENEFIT
While not wishing to be bound by theory, it is believed that one or more of the following mechanisms contributes to the beneficial effect of ammonia oxidizing bacteria, e.g., N. eutropha in treating the diseases and conditions discussed herein. Additional mechanistic details are found in International Application WO/2005/030147, which is herein incorporated by reference in its entirety.
In order to understand the beneficial aspects of these bacteria, it is helpful to understand angiogenesis. All body cells, except those within a few hundred microns of the external air, receive all metabolic oxygen from the blood supply. The oxygen is absorbed by the blood in the lung, is carried by red blood cells as oxygenated hemoglobin to the peripheral tissues, where it is exchanged for carbon dioxide, which is carried back and exhaled from the lung. Oxygen must diffuse from the erythrocyte, through the plasma, through the endothelium and through the various tissues until it reached the mitochondria in the cell which consumes it. The human body contains about 5 liters of blood, so the volume of the circulatory system is small compared to that of the body. Oxygen is not actively transported. It passively diffuses down a concentration gradient from the air to the erythrocyte, from the erythrocyte to the cell, and from the cell to cytochrome oxidase where it is consumed. The concentration of oxygen at the site of consumption is the lowest in the body, and the O 2 flux is determined by the diffusion resistance and the concentration gradient. Achieving sufficient oxygen supply to all the peripheral tissues requires exquisite control of capillary size and location. If the spacing between capillaries were increased, achieving the same flux of oxygen would require a larger concentration difference and hence a lower O 2 concentration at cytochrome oxidase. With more cells between capillaries, the O 2 demand would be greater. If the spacing between capillaries were decreased, there would be less space available for the cells that perform the metabolic function of the organ.
In certain aspects, it is appreciated that NO from ammonia oxidizing bacteria is readily absorbed by the outer skin and converted into S-nitrosothiols since the outer skin is free from hemoglobin. M. Stucker et al. have shown that the external skin receives all of its oxygen from the external air in “The cutaneous uptake of atmospheric oxygen contributes significantly to the oxygen supply of human dermis and epidermis. (Journal of Physiology (2002), 538.3, pp. 985-994.) This is readily apparent, because the external skin can be seen to be essentially erythrocyte free. There is circulation of plasma through these layers because they are living and do require the other nutrients in blood, just not the oxygen. S-nitrosothiols formed are stable, can diffuse throughout the body, and constitute a volume source of authentic NO and a source of NO to transnitrosate protein thiols.
In some aspects, it is appreciated that capillary rarefaction may be one of the first indications of insufficient levels of NO. F. T. Tarek et al. have shown that sparse capillaries, or capillary rarefaction, is commonly seen in people with essential hypertension. (Structural Skin Capillary Rarefaction in Essential Hypertension. Hypertension. 1999; 33:998-1001
A great many conditions are associated with the capillary density becoming sparser. Hypertension is one, and researchers reported that sparse capillaries are also seen in the children of people with essential hypertension, and also in people with diabetes. Significant complications of diabetes are hypertension, diabetic nephropathy, diabetic retinopathy, and diabetic neuropathy. R. Candido et al. have found that the last two conditions are characterized by a reduction in blood flow to the affected areas prior to observed symptoms. (Haemodynamics in microvascular complications in type 1 diabetes. Diabetes Metab Res Rev 2002; 18: 286-304.) Reduced capillary density is associated with obesity, and simple weight loss increases capillary density as shown by A Philip et al. in “Effect of Weight Loss on Muscle Fiber Type, Fiber Size, Capilarity, and Succinate Dehydrogenase Activity in Humans. The Journal of Clinical Endocrinology & Metabolism Vol. 84, No. 11 4185-4190, 1999.
Researchers have shown that in primary Raynaud's phenomena (PRP), the nailfold capillaries are sparser (slightly) than in normal controls, and more abundant than in patients that have progressed to systemic sclerosis (SSc). M. Bukhari, Increased Nailfold Capillary Dimensions In Primary Raynaud's Phenomenon And Systemic Sclerosis. British Journal of Rheumatology, Vol. 24 No 35: 1127-1131, 1996. They found that the capillary density decreased from 35 loops/mm 2 (normal controls) to 33 (PRP), to 17 (SSc). The average distance between capillary limbs was 18μ, 18μ, and 30μ for controls, PRP and SSc, respectively.
In certain aspects, it is appreciated that the mechanism that the body normally uses to sense “hypoxia” may affect the body's system that regulates capillary density. According to this aspect of the invention, a significant component of “hypoxia” is sensed, not by a decrease in O2 levels, but rather by an increase in NO levels. Lowering of basal NO levels interferes with this “hypoxia” sensing, and so affects many bodily functions regulated through “hypoxia.” For Example, anemia is commonly defined as “not enough hemoglobin,” and one consequence of not enough hemoglobin is “hypoxia”, which is defined as “not enough oxygen.” According to some aspects, these common definitions do not account for the nitric oxide mediated aspects of both conditions.
At rest, acute isovolemic anemia is well tolerated. A ⅔ reduction in hematocrit has minimal effect on venous return PvO2, indicating no reduction in either O 2 tension or delivery throughout the entire body. Weiskopf et al. Human cardiovascular and metabolic response to acute, severe isovolemic anemia. JAMA 1998, vol 279, No. 3, 217-221. At 50% reduction (from 140 to 70 g Hb/L), the average PvO2 (over 32 subjects) declined from about 77% to about 74% (of saturation). The reduction in O 2 capacity of the blood is compensated for by vasodilatation and tachycardia with the heart rate increasing from 63 to 85 bpm. That the compensation is effective is readily apparent, however, the mechanism is not. A typical explanation is that “hypoxia” sensors detected “hypoxia” and compensated with vasodilatation and tachycardia. However, there was no “hypoxia” to detect. There was a slight decrease in blood lactate (a marker for anaerobic respiration) from 0.77 to 0.62 mM/L indicating less anaerobic respiration and less “hypoxia.” The 3% reduction in venous return PvO2 is the same level of “hypoxia” one would get by ascending 300 meters in altitude (which typically does not produce tachycardia). With the O 2 concentration in the venous return staying the same, and the O 2 consumption staying the same, there is no place in the body where there is a reduction in O 2 concentration. Compensation during isovolemic anemia may not occur because of O 2 sensing.
Thus the vasodilatation that is observed in acute isovolemic anemia may be due to the increased NO concentration at the vessel wall. NO mediates dilatation of vessels in response to shear stress and other factors. No change in levels of NO metabolites would be observed, because the production rate of NO is unchanged and continues to equal the destruction rate. The observation of no “hypoxic” compensation with metHb substitution can be understood because metHb binds NO just as Hb does, so there is no NO concentration increase with metHb substitution as there is with Hb withdrawal.
Nitric oxide plays a role in many metabolic pathways. It has been suggested that a basal level of NO exerts a tonal inhibitory response, and that reduction of this basal level leads to a dis-inhibition of those pathways. Zanzinger et al. have reported that NO has been shown to inhibit basal sympathetic tone and attenuate excitatory reflexes. (Inhibition of basal and reflex-mediated sympathetic activity in the RVLM by nitric oxide. Am. J. Physiol. 268 (Regulatory Integrative Comp. Physiol. 37): R958-R962, 1995.)
In some aspects, it is appreciated that one component of a volume source of NO is low molecular weight S-nitrosothiols produced in the erythrocyte free skin from NO produced on the external skin by ammonia oxidizing bacteria. These low molecular weight S-nitrosothiols are stable for long periods, and can diffuse and circulate freely in the plasma. Various enzymes can cleave the NO from various S-nitrosothiols liberating NO at the enzyme site. It is the loss of this volume source of NO from AOB on the skin that leads to disruptions in normal physiology. The advantage to the body of using S-nitrosothiols to generate NO far from a capillary is that O 2 is not required for NO production from S-nitrosothiols. Production of NO from nitric oxide synthase (NOS) does require O 2 . With a sufficient background of S-nitrosothiols, NO can be generated even in anoxic regions. Free NO is not needed either since NO only exerts effects when attached to another molecule, such as the thiol of a cysteine residue or the iron in a heme, so the effects of NO can be mediated by transnitrosation reactions even in the absence of free NO provided that S-nitrosothiols and transnitrosation enzymes are present.
Frank et al. have shown that the angiogenesis that accompanies normal wound healing is produced in part by elevated VEGF which is induced by increased nitric oxide. (Nitric oxide triggers enhanced induction of vascular endothelial growth factor expression in cultured keratinocytes (HaCaT) and during cutaneous wound repair. FASEB J. 13, 2002-2014 (1999).)
NO has a role in the development of cancer, indicating that the bacteria described herein may be used in methods of cancer treatment and prevention. According to certain aspects, it is appreciated that the presence of NO during hypoxia may prevent cells from dividing while under hypoxic stress, when cells are at greater risk for errors in copying DNA. One relevant cell function is the regulation of the cell cycle. This is the regulatory program which controls how and when the cell replicates DNA, assembles it into duplicate chromosomes, and divides. The regulation of the cell cycle is extremely complex, and is not fully understood. However, it is known that there are many points along the path of the cell cycle where the cycle can be arrested and division halted until conditions for doing so have improved. The p53 tumor suppressor protein is a key protein in the regulation of the cell cycle, and it serves to initiate both cell arrest and apoptosis from diverse cell stress signals including DNA damage and p53 is mutated in over half of human cancers as reported by Ashcroft et al. in “Stress Signals Utilize Multiple Pathways To Stabilize p53.” (Molecular And Cellular Biology, May 2000, p. 3224-3233.) Hypoxia does initiate accumulation of p53, and while hypoxia is important in regulating the cell cycle, hypoxia alone fails to induce the downstream expression of p53 mRNA effector proteins and so fails to cause arrest of the cell cycle. Goda et al. have reported that hypoxic induction of cell arrest requires hypoxia-inducing factor-1 (HIF-1α). (Hypoxia-Inducible Factor 1α Is Essential for Cell Cycle Arrest during Hypoxia. Molecular And Cellular Biology, January 2003, p. 359-369.) Britta et al. have reported that NO is one of the main stimuli for HIF-1α. (Accumulation of HIF-1α under the influence of nitric oxide. Blood, 15 Feb. 2001, Volume 97, Number 4.) In contrast, NO does cause the accumulation of transcriptionally active p53 and does cause arrest of the cell cycle and does cause apoptosis. Wang et al., P53 Activation By Nitric Oxide Involves Down-Regulation Of Mdm2. THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 277, No. 18, Issue Of May 3, Pp. 15697-15702, 2002.
In certain aspect of the invention, it is appreciated that preventing the necrotic death of cells by preventing the capillary rarefaction that leads to their hypoxic death may prevent autoimmune disorders. When cells are exposed to chronic hypoxia, the production of reactive oxygen species (ROS) is increased, and there is increased damage to the cells metabolic machinery and ultimately to the cells' DNA. Decreased metabolic capacity will decrease capacity for repair of damage due to ROS and due to exogenous carcinogen exposure. Over time, the damage accumulates and increases the chance of three events: the cell will undergo deletion of cancer-preventing genes and the cell will become cancerous, the cell will die through necrosis, or the cell will die through apoptosis. When cells die, either through necrosis or apoptosis, the cell debris must be cleared from the site. Dead cells are phagocytosed by immune cells, including dendritic cells and macrophages. When these cells phagocytose a body, it is digested by various proteolytic enzymes into antigenic fragments, and then these antigens are attached to the major histocompatibility complex (MHC1, MHC2) and the antigen-MHC complex is moved to the surface of the cell where it can interact with T cells and activate the T cells in various ways. Any cell injury releases adjuvants which stimulate the immune system in various ways. In general, cells that undergo necrosis stimulate a greater immune response than cells that undergo apoptosis. Chronic exposure of immune cells to dead and dying cells is therefore likely to lead to autoimmune disorders.
In certain aspects, it is appreciated that low basal NO leads to fibrotic hypertrophy. Once a dead cell has been cleared, a new cell cannot easily take its place, because there is insufficient O 2 to support it. Any such new cell would suffer the same fate. The space can remain empty, in which case the organ shrinks, the capillaries draw closer together, new cells are now deprived of the VEGF formerly produced by the now-missing cell, so capillaries ablate and the hypoxic zone reforms. This could result in a general shrinkage of the affected tissues. In tissues that support fibrosis, relatively inert collagen fibers can fill the space. Since the metabolic requirements of the body for the particular organ in question are not reduced, the organ may attempt to grow larger, but now with a significant fibrous content. This may result in fibrotic hypertrophy, such as of the heart and liver. Some organs, such as the brain, cannot grow larger or smaller because the three-dimensional connectivity of nerves and blood vessels are important, and cannot be continuously and simultaneously mapped onto an asymmetrically shrinking brain. The space must be filled with something, and β-amyloid might be the (not so inert) space filler. The kidney cannot grow larger because of the renal capsule, so the number of living cells becomes smaller and they are replaced with fibrotic tissue. If the dead cells are cleared, the tissue shrinks, and the ratio of NO/O 2 goes down again, and the capillaries again become sparser. This may set up the vicious circle of end stage renal disease, congestive heart failure/cardiac hypertrophy, primary biliary cirrhosis, Alzheimer's disease, atherosclerosis, inflammatory bowel disease, hypertrophic scar formation, and the multiple connective tissue diseases starting with Raynaud's phenomena and ending with Systemic Sclerosis and primary Sjogren's syndrome where capillary rarefaction is also observed. Ferrini et al, have shown that a reduction in basal NO levels through chronic inhibition of NOS with L-NAME leads to generalized fibrosis of the heart and kidneys. (Antifibrotic Role of Inducible Nitric Oxide Synthase. Nitric Oxide: Biology and Chemistry Vol. 6, No. 3, pp. 283-294 (2002).) It may be that low basal NO leads to fibrotic hypertrophy.
In certain aspects, it is appreciated that capillary rarefaction affects a subject's ability to control their appetite. Capillary rarefaction is observed in the brains of aged humans and animals. Capillary rarefaction is associated with declines in circulating growth factors including insulin like growth factor-1. Neurogenesis in the adult brain is coordinated with angiogenesis. Since the brain regulates many homeostatic functions, increased diffusion lengths between capillaries to control elements of the brain might be “interpreted” as inadequate blood concentrations of those species. The flux of glucose in the brain is quite close to normal metabolic needs, where glucose flux is only 50 to 75% greater than glucose consumption and the glucose transporters across the blood brain barrier are saturable, stereospecific and independent of energy or ion gradients. A large part of the regulation of appetite is mediated through the brain, and capillary rarefaction may cause an adequate blood concentration of “nutrients” (or marker compounds proportional to “nutrients”) to be interpreted as insufficient. This may be one cause of obesity.
According to certain aspects, it is appreciated that capillary rarefaction may be a cause of non-insulin dependent diabetes. Non-insulin dependent diabetes (NIDDM) is also known as the Metabolic Syndrome or Diabetes type 2, and is characterized by insulin resistance. The sensitivity of the body to insulin is reduced, and insulin levels increase People with NIDDM have high blood glucose, high blood triglycerides, are typically obese, hypertensive, and typically have significant visceral fat.
Other symptoms accompany NIDDM, which may point to capillary rarefaction as the cause. In a study of 40 men, with and without NIDDM, obese (BMI 29) and lean (BMI 24) (10 of each), Konrad et al. report that blood lactate levels at rest were 1.78, 2.26, 2.42, and 2.76 (mM/L) for lean men without, obese men without, lean men with NIDDM, obese men with NIDDM respectively. (A-Lipoic acid treatment decreases serum lactate and pyruvate concentrations and improves glucose effectiveness in lean and obese patients with type 2 diabetes. Diabetes Care 22:280-287, 1999.) Lactate is a measure of anaerobic glycolysis. When O 2 is insufficient to generate ATP through oxidative phosphorylation, cells can produce ATP through anaerobic glycolysis. One of the products of anaerobic glycolysis is lactate, which must be exported from the cells, otherwise the pH drops and function is compromised. Blood lactate is commonly measured in exercise studies, where an increase indicates the work load at which maximum oxidative work can be done. Higher levels of lactate at rest would indicate increased anaerobic glycolysis at rest, which is consistent with capillary rarefaction.
Primary biliary cirrhosis is associated with Raynaud's phenomena, pruritus, sicca syndrome, osteoporosis, portal hypertension, neuropathy, and pancreatic insufficiency, and liver abnormalities are associated with rheumatic diseases. Elevated liver enzymes are a symptom of liver inflammation, and elevated liver enzymes are observed as an early symptom of “asymptomatic” primary biliary cirrhosis. Accordingly, the bacteria described herein may be used to treat liver inflammation.
Torre et al have reported that Alzheimer's disease (AD) is a microvascular disorder with neurological degeneration secondary to hypoperfusion, resulting in part from insufficient nitric oxide. (Review: Evidence that Alzheimer's disease is a microvascular disorder: the role of constitutive nitric oxide, Brain Research Reviews 34 (2000) 119-136.) Accordingly, the bacteria described herein may be used to treat AD.
Adverse health effects that are associated with hypertension may also be consequences of low basal NO. The decreased response to vasodilatation is also consistent with low basal NO. NO is a diffusible molecule that diffuses from a source to a sensor site where it has the signaling effect. With low NO levels, every NO source must produce more NO to generate an equivalent NO signal of a certain intensity a certain distance away. NO diffuses in three dimensions and the whole volume within that diffusion range must be raised to the level that will give the proper signal at the sensor location. This may result in higher NO levels at the source and between the source and the sensor. Adverse local effects of elevated NO near a source may then arise from too low a NO background. There is some evidence that this scenario actual occurs. In rat pancreatic islets, Henningsson et al have reported that inhibition of NOS with L-NAME increases total NO production through the induction of iNOS. (Chronic blockade of NO synthase paradoxically increases islet NO production and modulates islet hormone release. Am J Physiol Endocrinol Metab 279: E95-E107, 2000.) Increasing NO by increasing NOS activity will only work up to some limit. When NOS is activated but is not supplied with sufficient tetrahydrobiopterin (BH4) or L-arginine, it becomes “uncoupled” and generates superoxide (O2−) instead of NO. This O 2 − may then destroy NO. Attempting to produce NO at a rate that exceeds the supply of BH4 or L-arginine may instead decrease NO levels. This may result in positive feedback where low NO levels are made worse by stimulation of NOS, and uncoupled NOS generates significant O 2 − which causes local reactive oxygen species (ROS) damage such as is observed in atherosclerosis, end stage renal disease, Alzheimer's, and diabetes.
The bacteria described herein may also be used to delay the signs of aging. Caloric restriction extends lifespan, and Holloszy reported that restricting food intake to 70% of ad lib controls, prolongs life in sedentary rats from 858 to 1,051 days, almost 25%. (Mortality rate and longevity of food restricted exercising male rats: a reevaluation. J. Appl. Physiol. 82(2): 399-403, 1997.) The link between calorie restriction and prolonged life is well established, however, the causal mechanism is not. Lopez-Torres et al. reported that the examination of liver mitochondrial enzymes in rats indicates a reduction in H 2 O 2 production due to reduced complex I activity associated with calorie restriction. (Influence Of Aging And Long-Term Caloric Restriction On Oxygen Radical Generation And Oxidative DNA Damage In Rat Liver Mitochondria. Free Radical Biology & Medicine Vol. 32 No 9 pp 882-8899, 2002.) H 2 O 2 is produced by dismutation of O 2 − , which is a major ROS produced by the mitochondria during respiration. The main source of O 2 − has been suggested by Kushareva et al. and others to be complex I which catalyzes the NAD/NADH redox couple by reverse flow of electrons from complex III, the site of succinate reduction. The free radical theory, proposed by Beckman, of aging postulates, that free radical damage to cellular DNA, antioxidant systems and DNA repair systems accumulates with age and when critical systems are damaged beyond repair, death ensues. (The Free Radical Theory of Aging Matures. Physiol. Rev. 78: 547-581, 1998.)
As an additional mechanism, NO has been demonstrated by Vasa et al. to activate telomerase and to delay senescence of endothelial cells. (Nitric Oxide Activates Telomerase and Delays Endothelial Cell Senescence. Circ Res. 2000; 87:540-542.) Low basal NO will increase basal metabolic rate by disinhibition of cytochrome oxidase. Increased basal metabolism will also increase cell turn-over and growth rate. Capillary rarefaction, by inducing chronic hypoxia may increase free radical damage and may also increase cell turn-over, and so accelerate aging by both mechanisms.
In some aspects, it is appreciated that autotrophic ammonia-oxidizing bacteria may produce protective aspects for allergies and autoimmune disorders. The best known autoimmune disease is perhaps Diabetes Type 1, which results from the destruction of the insulin producing cells in the pancreas by the immune system. Recurrent pregnancy loss is also associated with autoimmune disorders where the number of positive autoimmune antibodies correlated positively with numbers recurrent pregnancy losses. Systemic Sclerosis, Primary Biliary Cirrhosis, autoimmune hepatitis, and the various rheumatic disorders are other examples of autoimmune disorders. Application of AOB was observed to reduce an allergy, hay fever, as described in WO/2005/030147.
One mechanism by which AOB may exert their protective effect on allergies and autoimmune disorders is through the production of nitric oxide, primarily through the regulatory inhibition of NF-κB and the prevention of activation of immune cells and the induction of inflammatory reactions. NF-κB is a transcription factor that up-regulates gene expression and many of these genes are associated with inflammation and the immune response including genes which cause the release of cytokines, chemokines, and various adhesion factors. These various immune factors cause the migration of immune cells to the site of their release resulting in the inflammation response. Constitutive NO production has been shown to inhibit NF-κB by stabilizing IκBα (an inhibitor of NF-κB) by preventing IκBα degradation.
Administration of an NO donor has been shown by Xu et al. to prevent the development of experimental allergic encephalomyelitis in rats. (SIN-1, a Nitric Oxide Donor, Ameliorates Experimental Allergic Encephalomyelitis in Lewis Rats in the Incipient Phase: The Importance of the Time Window. The Journal of Immunology, 2001, 166: 5810-5816.) In this study, it was demonstrated that administering an NO donor, reduced the infiltration of macrophages into the central nervous system, reduced the proliferation of blood mononuclear cells, and increased apoptosis of blood mononuclear cells. All of these results are expected to reduce the extent and severity of the induced autoimmune response.
Low basal NO may lead to autism via the mechanism that new connections in the brain are insufficiently formed as a result of insufficient basal nitric oxide. While not wishing to be bound in theory, in some embodiments, formation of neural connections is modulated by NO. In these cases, any condition that lowers the range of NO diffusion may decrease the volume size of brain elements that can undergo connections. A brain which developed under conditions of low basal NO levels may be arranged in smaller volume elements because the reduced effective range of NO.
Additional symptoms exhibited in autistic individuals may also point to low NO as a cause, including increased pitch discrimination, gut disturbances, immune system dysfunction, reduced cerebral blood flow, increased glucose consumption of the brain, increased plasma lactate, attachment disorders, and humming. Each of these symptoms may be attributed to a low basal NO level.
Takashi Ohnishi et al. have reported that autistic individuals show decreased blood flow. Takashi Ohnishi et al., Abnormal regional cerebral blood flow in childhood autism. Brain (2000), 123, 1838-1844. J. M. Rumsey et al. have reported that autistic individuals have increased glucose consumption. Rumsey J M, Duara R, Grady C, Rapoport J L, Margolin R A, Rapoport S I, Cutler N R. Brain metabolism in autism. Resting cerebral glucose utilization rates as measured with positron emission tomography. Arch Gen Psychiatry, 1985 May; 42(5):448-55 (abstract). D. C. Chugani has reported that autistic individuals have an increased plasma lactate levels. Chugani D C, et al., Evidence of altered energy metabolism in autistic children. Prog Neuropsychopharmacol Biol Psychiatry. 1999 May; 23(4):635-41. The occurrence of these effects may be a result of capillary rarefaction in the brain, which may reduce blood flow and O 2 supply, such that some of the metabolic load of the brain may be produced through glycolysis instead of oxidative phosphorylation.
Nitric oxide has been demonstrated by B. A. Klyachko et al. to increase the excitability of neurons by increasing the after hyperpolarization through cGMP modification of ion channels. Vitaly A. Klyachko et al., cGMP-mediated facilitation in nerve terminals by enhancement of the spike after hyperpolarization. Neuron, Vol. 31, 1015-1025, Sep. 27, 2001. C. Sandie et al. have shown that inhibition of NOS reduces startle. Carmen Sandi et al., Decreased spontaneous motor activity and startle response in nitric oxide synthase inhibitor-treated rats. European journal of pharmacology 277 (1995) 89-97. Attention-Deficit Hyperactivity Disorder (ADHD) has been modeled using the spontaneously hypertensive rat (SHR) and the Naples high-excitability (NHE) rat. Both of these models have been shown by Raffaele Aspide et al, to show increased attention deficits during periods of acute NOS inhibition. Raffaele Aspide et al., Non-selective attention and nitric oxide in putative animal models of attention-deficit hyperactivity disorder. Behavioral Brain Research 95 (1998) 123-133. Accordingly, the bacteria herein may be used in the treatment of ADHD.
Inhibition of NOS has also been shown by M. R. Dzoljic to inhibit sleep. M. R. Dzoljic, R. de Vries, R. van Leeuwen. Sleep and nitric oxide: effects of 7-nitro indazole, inhibitor of brain nitric oxide synthase. Brain Research 718 (1996) 145-150. G. Zoccoli has reported that a number of the physiological effects seen during sleep are altered when NOS is inhibited, including rapid eye movement and sleep-wake differences in cerebral circulation. G. Zoccoli, et al., Nitric oxide inhibition abolishes sleep-wake differences in cerebral circulation. Am. J. Physiol. Heart Circ Physiol 280: H2598-2606, 2001. NO donors have been shown by L. Kapas et al. to promote non-REM sleep, however, these increases persisted much longer than the persistence of the NO donor, suggesting perhaps a rebound effect. Levente Kapas et al. Nitric oxide donors SIN-1 and SNAP promote nonrapid-eye-movement sleep in rats. Brain Research Bullitin, vol 41, No 5, pp. 293-298, 1996. M. Rosaria et al., Central NO facilitates both penile erection and yawning. Maria Rosaria Melis and Antonio Argiolas. Role of central nitric oxide in the control of penile erection and yawning. Prog Neuro-Psychopharmacol & Biol. Phychiat. 1997, vol 21, pp 899-922. P. Tani et al, have reported that insomnia is a frequent finding in adults with Asperger's. Pekka Tani et al., Insomnia is a frequent finding in adults with Asperger's syndrome. BMC Psychiatry 2003, 3:12. Y. Hoshino has also observed sleep disturbances in autistic children. Hoshino Y, Watanabe H, Yashima Y, Kaneko M, Kumashiro H. An investigation on sleep disturbance of autistic children. Folia Psychiatr Neurol Jpn. 1984; 38(1):45-51. (abstract) K. A. Schreck et al. has observed that the severity of sleep disturbances correlates with severity of autistic symptoms. Schreck K A, et al., Sleep problems as possible predictors of intensified symptoms of autism. Res Dev Disabil. 2004 Jan.-Feb.; 25(1):57-66. (abstract). Accordingly, the bacteria herein may be used in the treatment of insomnia.
W. D. Ratnasooriya et al reported that inhibition of NOS in male rats reduces pre-coital activity, reduces libido, and reduces fertility. W. D. Ratnasooriya et al., Reduction in libido and fertility of male rats by administration of the nitric oxide (NO) synthase inhibitor N-nitro-L-arginine methyl ester. International journal of andrology, 23: 187-191 (2000).
It may be that a number of seemingly disparate disorders, characterized by ATP depletion and eventual organ failure are actually “caused” by nitropenia, caused by a global deficiency in basal nitric oxide. When this occurs in the heart, the result is dilative cardiomyopathy. When this occurs in the brain, the result is white matter hyperintensity, Alzheimer's, vascular depression, vascular dementia, Parkinson's, and the Lewy body dementias. When this occurs in the kidney, the result is end stage renal disease, when this occurs in the liver, the result is primary biliary cirrhosis. When this occurs in muscle, the consequence is fibromyaligia, Gulf War Syndrome, or chronic fatigue syndrome. When this occurs in the bowel, the consequence is ischemic bowel disease. When this occurs in the pancreas, the consequence is first type 2 diabetes, followed by chronic inflammation of the pancreas, followed by autoimmune attack of the pancreas (or pancreatic cancer), followed by type 1 diabetes. When this occurs in the connective tissue, the consequence is systemic sclerosis.
In the remnant kidney model of end stage renal disease, part of the kidney is removed, (either surgically or with a toxin) which increases the metabolic load on the remainder. Superoxide is generated to decrease NO and increase O 2 diffusion to the kidney mitochondria. Chronic overload results in progressive kidney capillary rarefaction and progressive kidney failure. In acute kidney failure, putting people in dialysis can give the kidney a “rest”, and allows it to recover. In acute renal failure induced by rhabdomyolysis (muscle damage which releases myoglobin into the blood stream) kidney damage is characterized by ischemic damage. Myoglobin scavenges NO, just as hemoglobin does, and would cause vasoconstriction in the kidney leading to ischemia. Myoglobin would also induce local nitropenia and the cascade of events leading to further ATP depletion.
In some aspects, low NO levels lead to reduced mitochondrial biogenesis. Producing the same ATP at a reduced mitochondria density will result in an increase in O 2 consumption, or an accelerated basal metabolic rate. An accelerated basal metabolic rate is observed in a number of conditions, including: Sickle cell anemia, Congestive heart failure, Diabetes, Liver Cirrhosis, Crohn's disease, Amyotrophic lateral sclerosis, Obesity, End stage renal disease, Alzheimer's, and chronic obstructive pulmonary disease.
While some increased O 2 consumption might be productively used, in many of these conditions uncoupling protein is also up-regulated, indicating that at least part of the increased metabolic rate is due to inefficiency. Conditions where uncoupling protein is known to be up-regulated include obesity and diabetes.
With fewer mitochondria consuming O 2 to a lower O 2 concentration, the O 2 gradient driving O 2 diffusion is greater, so the O 2 diffusion path length can increase resulting in capillary rarefaction, which is observed in dilative cardiomyopathy, hypertension, diabetes type 2, and renal hypertension.
Copper, either as Cu2+ or as ceruloplasmin (CP) (the main Cu containing serum protein which is present at 0.38 g/L in adult sera and which is 0.32% Cu and contains 94% of the serum copper) catalyzes the formation of S—NO-thiols from NO and thiol containing groups (RSH). The Cu content of plasma is variable and is increased under conditions of infection. Berger et al. reported that the Cu and Zn content of burn-wound exudates is considerable with patients with ⅓ of their skin burned, losing 20 to 40% of normal body Cu and 5 to 10% of Zn content in 7 days. (Cutaneous copper and zinc losses in burns. Burns. 1992 October; 18(5):373-80.) If the patients skin were colonized by AOB, wound exudates which contains urea and Fe, Cu, and Zn that AOB need, would be converted into NO and nitrite, greatly supplementing the local production of NO by iNOS, without consuming resources (such as O 2 and L-arginine) in the metabolically challenged wound. A high production of NO and nitrite by AOB on the surface of a wound would be expected to inhibit infection, especially by anaerobic bacteria such as the Clostridia which cause tetanus, gas gangrene, and botulism.
The practice of the present invention may employ, unless otherwise indicated, conventional methods of immunology, molecular biology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, et al. Molecular Cloning: A Laboratory Manual (Current Edition); and Current Protocols in Molecular Biology (F. M. Ausubel, et al. eds., current edition).
8. NUCLEIC ACIDS AND PROTEINS FROM N. EUTROPHA
This disclosure provides, among other things, proteins and nucleic acids (optionally, isolated proteins and nucleic acids) that are identical to or similar to those found in strain D23. While not wishing to be bound by theory, it is believed that the sequenced strain of D23 has non-naturally occurring protein and nucleic acid sequences due to an extended period of culture and selection in the laboratory.
These nucleic acids and proteins have numerous uses. For instance, the proteins may be used to generate antibodies or other binding molecules that detect strain D23 or related strains. The proteins may also be used to carry out reactions under high-NH 4 + conditions, because D23 is adapted for growth and metabolism under these conditions. As another example, the nucleic acids may be used to produce proteins for generating antibodies or carrying out reactions as described above. The nucleic acids may also be used to detect strain D23 or related strains, e.g., using a microarray or another hybridization-based assay.
The genome of strain D23 is provided as SEQ ID NO: 1. The genome annotation (including the position and orientation of genes within SEQ ID NO: 1) is provided as Supplementary Table 1. Accordingly, this disclosure provides genes and proteins identical or similar to the genes listed in Supplementary Table 1.
Accordingly, this disclosure provides a nucleic acid (e.g., an isolated nucleic acid) comprising a sequence of a gene of Supplementary Table 1, as well as a protein encoded by said gene. In certain embodiments, the nucleic acid comprises a sequence that is similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to a gene of Supplementary Table 1, or a protein encoded by said gene. The disclosure also provides a composition comprising a nucleic acid that is at least 1, 2, 3, 4, 5, 10, 15, 20, 50, 100, 200, 500, 1,000, 1,500, 2,000, 2,500, or all of the sequences of Supplementary Table 1, or a sequence that is similar thereto (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical), or one or more proteins encoded by said nucleic acids. Also provided are fragments of said nucleic acids and proteins.
The present disclosure also provides, inter alia, one or more genes or proteins that are present in strain D23 and absent from strain C91, or a gene or protein similar to one of said genes or proteins. Examples of these genes are set out in FIGS. 6-8 and are described in more detail in Example 4 herein. Examples of these genes and proteins, as well as genes and proteins similar thereto, are described below.
Accordingly, with respect to FIG. 6 , this application discloses nucleic acids that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the sequences in FIG. 6 . This application also discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the proteins encoded by the genes listed in FIG. 6 . Furthermore, the application discloses fragments of these genes and proteins, e.g., fragments of 0-20, 20-50, 50-100, 100-200, 200-500, 500-1000, or greater than 1000 nucleotides or amino acids. In some embodiments, a plurality of the above-mentioned genes or proteins are affixed to a solid support, e.g., to form a microarray.
With respect to FIG. 7 , this application discloses nucleic acids that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the sequences in FIG. 7 . This application also discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the proteins encoded by the genes listed in FIG. 7 . Furthermore, the application discloses fragments of these genes and proteins, e.g., fragments of 0-20, 20-50, 50-100, 100-200, 200-500, 500-1000, or greater than 1000 nucleotides or amino acids. In some embodiments, a plurality of the above-mentioned genes or proteins are affixed to a solid support, e.g., to form a microarray.
With respect to FIG. 8 , this application discloses nucleic acids that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, or all of the sequences in FIG. 8 . This application also discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, or all of the proteins encoded by the genes listed in FIG. 8 . Furthermore, the application discloses fragments of these genes and proteins, e.g., fragments of 0-20, 20-50, 50-100, 100-200, 200-500, 500-1000, or greater than 1000 nucleotides or amino acids. In some embodiments, a plurality of the above-mentioned genes or proteins are affixed to a solid support, e.g., to form a microarray.
With respect to FIGS. 6-8 collectively, this application discloses nucleic acids that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or all of the sequences in FIGS. 6-8 . This application discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or all of the proteins encoded by genes listed in FIGS. 6-8 . Furthermore, the application discloses fragments of these genes and proteins, e.g., fragments of 1-20, 20-50, 50-100, 100-200, 200-500, 500-1000, or greater than 1000 nucleotides or amino acids. In some embodiments, a plurality of the above-mentioned genes or proteins are affixed to a solid support, e.g., to form a microarray.
This disclosure also provides nucleic acid sequences that are fragments of SEQ ID NO: 1. The fragments may be, e.g., 1-20, 20-50, 50-100, 100-200, 200-500, 500-1000, 1,000-2,000, 2,000-5,000, or 10,000 or more nucleotides in length. The fragments may also be at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to the corresponding portion of SEQ ID NO: 1 or its complement. The fragment may also be a fragment that hybridizes to SEQ ID NO: 1, or to the genome of the D23 strain deposited with the ATCC patent depository on Apr. 8, 2014, designated AOB D23-100 with the ATCC under accession number PTA-121157, or their complements, under low stringency, medium stringency, high stringency, or very high stringency, or other hybridization condition described herein.
The disclosure also provides nucleic acid sequences set out in Table 1 (which describes genes involved in ammonia metabolism). Accordingly, in some aspects, this application discloses genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 97.5%, 98%, 98.2%, 98.4%, 98.6%, 98.8%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100% identical) to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all of the genes in Table 1. In embodiments, this application discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 97.5%, 98%, 98.2%, 98.4%, 98.6%, 98.8%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100% identical) to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all of the proteins in Table 1.
Alignment of the nucleic acid sequences of Table 1 shows the percent identity between homologs in C91 and D23. The following paragraphs discuss this percent identity and describe various nucleic acids having homology to the D23 genes of Table 1.
More specifically, the amoA1 genes are about 98.8% identical (i.e., at 821/831 positions). Accordingly, in some embodiments, the amoA1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoA1 nucleic acid comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoA1 nucleic acid comprises a sequence at least about 98.8%, 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoA1 gene.
The amoA2 genes are about 98.8% identical (i.e., at 821/831 positions). Accordingly, in some embodiments, the amoA2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoA2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoA2 nucleic acid comprises a sequence at least about 98.8%, 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoA2 gene.
The amoB1 genes are about 99.1% identical (i.e., at 1255/1266 positions). Accordingly, in some embodiments, the amoB1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoB1 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoB1 nucleic acid comprises a sequence at least about 99.1%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoB1 gene.
The amoB2 genes are about 99.1% identical (i.e., at 1254/1266 positions). Accordingly, in some embodiments, the amoB2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoB2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoB2 nucleic acid comprises a sequence at least about 99.1%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoB2 gene.
The amoC1 genes are about 99.8% identical (i.e., at 814/816 positions). Accordingly, in some embodiments, the amoC1 nucleic acid comprises D23 nucleotides at at least 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC1 nucleic acid comprises D23 nucleotides at at most 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC1 nucleic acid comprises a sequence at least about 99.8%, 99.9%, or 100% identical to the D23 amoC1 gene.
The amoC2 genes are about 99.8% identical (i.e., at 814/816 positions). Accordingly, in some embodiments, the amoC2 nucleic acid comprises D23 nucleotides at at least 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC2 nucleic acid comprises D23 nucleotides at at most 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC2 nucleic acid comprises a sequence at least about 99.8%, 99.9%, or 100% identical to the D23 amoC2 gene.
The amoC3 genes are about 98.9% identical (i.e., at 816/825 positions). Accordingly, in some embodiments, the amoC3 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC3 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC3 nucleic acid comprises a sequence at least about 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoC3 gene.
The hao1 genes are about 99.0% identical (i.e., at 1696/1713 positions). Accordingly, in some embodiments, the hao1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao1 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao1 nucleic acid comprises a sequence at least about 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao1 gene.
The hao2 genes are about 99.4% identical (i.e., at 1702/1713 positions). Accordingly, in some embodiments, the hao2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao2 nucleic acid comprises a sequence at least about 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao2 gene.
The hao3 genes are about 99.2% identical (i.e., at 1700/1713 positions). Accordingly, in some embodiments, the hao3 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao3 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao3 nucleic acid comprises a sequence at least about 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao3 gene.
The cycA1 genes are about 98.0% identical (i.e., at 694/708 positions). Accordingly, in some embodiments, the cycA1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA1 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA1 nucleic acid comprises a sequence at least about 98.0%, 98.2%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA1 gene.
The cycA2 genes are about 98.7% identical (i.e., at 699/708 positions). Accordingly, in some embodiments, the cycA2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA2 nucleic acid comprises a sequence at least about 98.7%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA2 gene.
The cycA3 genes are about 99.3% identical (i.e., at 703/708 positions). Accordingly, in some embodiments, the cycA3 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA3 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA3 nucleic acid comprises a sequence at least about 99.3%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA3 gene.
The cycB1 genes are about 96.7% identical (i.e., at 696/720 positions). Accordingly, in some embodiments, the cycB1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycB1 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycB1 nucleic acid comprises a sequence at least about 96.7%, 96.8%, 97.0%, 97.2%, 97.4%, 97.6%, 97.8%, 98.0%, 98.2%, 98.4%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycB1 gene.
The cycB2 genes are about 97.1% identical (i.e., at 702/723 positions). Accordingly, in some embodiments, the cycB2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycB2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycB2 nucleic acid comprises a sequence at least about 97.1%, 97.2%, 97.4%, 97.6%, 97.8%, 98.0%, 98.2%, 98.4%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycB2 gene.
Further provided herein are vectors comprising nucleotide sequences described herein. In some embodiments, the vectors comprise nucleotides encoding a protein described herein. The vectors include, but are not limited to, a virus, plasmid, cosmid, lambda phage or a yeast artificial chromosome (YAC). Such vectors may include a promoter, an open reading frame with or without introns, and a termination signal.
The present disclosure also provides host cells comprising a nucleic acid as described herein, or a nucleic acid encoding a protein as described herein.
In certain embodiments, the host cells are genetically engineered by using an expression cassette. The phrase “expression cassette,” refers to nucleotide sequences, which are capable of affecting expression of a gene in hosts compatible with such sequences. Such cassettes may include a promoter, an open reading frame with or without introns, and a termination signal. Additional factors necessary or helpful in effecting expression may also be used, such as, for example, an inducible promoter.
The disclosure also provides host cells comprising the vectors described herein.
The cell can be, but is not limited to, a eukaryotic cell, a bacterial cell, an insect cell, or a human cell. If the cell is a bacterial cell, it may be, e.g., E. coli or an ammonia-oxidizing bacterium such as Nitrosomonas (e.g., N. eutropha or N. europaea ), Nitrosococcus, Nitrosospira, Nitrosocystis, Nitrosolobus , and Nitrosovibrio.
9. ADJUSTING THE SKIN MICROBIOME WITH AMMONIA OXIDIZING BACTERIA
The present disclosure provides for systems and methods for changing the skin microbiome, e.g., the human skin microbiome. The systems and methods may provide treatment of infections or conditions, e.g., related to the skin, e.g., skin infections and/or skin conditions.
Ammonia-oxidizing bacteria (AOB) of the genus Nitrosomonas are Gram-negative obligate autotrophic bacteria with a unique capacity to generate nitrite and nitric oxide exclusively from ammonia as an energy source. They are widely present both in soil and water environments and are essential components of environmental nitrification processes. Due to the roles of nitrite and nitric oxide on human skin as important components of several physiological functions, such as vasodilation, skin inflammation and wound healing, these bacteria may have beneficial properties for both healthy and immunopathological skin conditions. These bacteria may be safe for use in humans because they are slow-growing, cannot grow on organic carbon sources, may be sensitive to soaps and antibiotics, and have never been associated with any disease or infection in animals or humans.
Topical application of ammonia oxidizing bacteria to a subject, e.g., a human subject may lead to unexpected changes in the skin microbiome, and more specifically it may lead to increases in the proportion of normal commensal non-pathogenic species and reductions in the proportion of potentially pathogenic, pathogenic, or disease causing organisms.
EXAMPLES
Example 1
Initial Culturing of N. eutropha
A soil-derived culture enriched in various ammonia oxidizing bacteria was applied to the skin of an adult male subject as described in WO/2003/057380. The period of growth on the human body selected for a strain with the capacity to colonize human skin for an extended period of time. After several months, the strain was re-isolated from the skin of the individual and cultured in laboratory conditions for a sustained period as described in the subsequent examples. While not wishing to be bound by theory, it is believed that the sustained laboratory culture selected for new mutations improving the strain properties, e.g., improved tolerance for high-ammonia conditions.
Example 2
Growing and Monitoring D23 or Mixtures of Strains that Comprise D23 Culture Conditions
D23 can be grown in batches or by continuous cultivation in a bioreactor. Batch preparation uses the medium of Table 3.





TABLE 3



Growth Medium for Batch culturing:






Weight/Volume
Final Concentration


(in~1.5 L)
(in~1.5 L)









(NH 4 ) 2 SO 4
4.95
g
50
mM NH 4 +

(MW 132.14)





KH 2 PO 4 (MW 136.1)
0.616
g
3.0
mM

1M MgSO 4
1.137
ml
0.76
mM

1M CaCl 2
0.3
ml
0.2
mM

30 mM FeCl 3 /50 mM
0.5
ml
10
μM/16.7 μM

EDTA





50 mM CuSO 4
30
μl
1.0
μM



Add 1400 ml ddH 2 O to flask. Autoclave. Store at room temperature.

After autoclaving add:







Phosphate Buffer
100
ml
32
mM KH 2 PO 4 /




2.7
mM NaH 2 PO 4 •H 2 O






5% Na 2 CO 3
12
ml
0.04%














































The medium of Table 3 is inoculated with ˜15 ml of a 3 day old culture of D23 (i.e. 1% volume). The cultures are incubated in the dark at 30° C. by shaking at 200 rpm.
Often, a N. eutropha D23 mixed culture is grown on complete N. europaea media. The culture medium is described below, and additional details on culturing ammonia-oxidizing bacteria are available on the World Wide Web at nitrificationnetwork.org/Nerecipe.php, Ensign et al., 1993, and Stein & Arp, 1998.
Step 1.
Add 900 ml of deionized water to a 2-liter Erlenmeyer flask.
Add in sequence:
3.3 g (NH 4 + ) 2 SO 4 (50 mM);
0.41 g KH 2 PO 4
0.75 ml 1 M MgSO 4 stock solution
0.2 ml 1 M CaCl 2 stock solution
0.33 ml 30 mM FeSO 4 /50 mM EDTA stock solution
0.01 ml 50 mM CuSO 4 stock solution
Sterilize the solution by autoclaving.
Step 2.
Add 400 ml of deionized water to a beaker. Add:
27.22 g KH 2 PO 4
2.4 g NaH 2 PO 4
Adjust the pH to 8.0 with 10 N NaOH, and bring the final volume to 500 ml with deionized water.
Sterilize 100 ml fractions of the solution by autoclaving in 250-500 ml Erlenmeyer flasks.
Step 3
Prepare 500 ml of 5% (w/v) Na 2 CO 3 (anhydrous)
Sterilize the solution by autoclaving.
Step 4
Add 1×100 ml aliquot of solution prepared in Step 2 to the flask prepared in Step 1.
Step 5
Add 8 ml of the solution prepared in Step 3 to the flask prepared in Step 1.
The D23 can also be cultured continuously in a bioreactor. Table 4 describes the appropriate media.





TABLE 4



Growth Medium for continuous culture:






Batch medium
Feeding solution


Weight/Volume (1 L)
Weight/Volume (1 L)


(Final concentration)
(Final concentration)









(NH 4 ) 2 SO 4 (MW 132.14)
3.3
g
13.2
g






(50 mM NH 4 + )
(200 mM NH 4 + )







KH 2 PO 4 (MW 136.1)
1.23
g
0.41
g






(9.0 mM)
(3.0 mM)







1M MgSO 4
0.758
ml
0.758
ml






(0.76 mM)
(0.76 mM)







1M CaCl 2
0.2
ml
0.2
ml






(0.2 mM)
(0.2 mM)







30 mM FeCl 3 /50 mM EDTA
0.333
ml
0.333
ml






(10 μM/16.7 μM)
(10 μM/16.7 μM)







50 mM CuSO 4
20
μl
20
μl






(1.0 μM)
(1.0 μM)

ddH 2 O
1000 ml
1000 ml



Autoclave each solution and store at room temperature.






































































The batch media, in a bioreactor vessel, is inoculated with ˜10 ml of a 3 day old N. eutropha D23 culture (i.e. 1% volume). The pH is adjusted to 7.6 using 7.5% Na 2 CO 3 The bioreactor is run in batch mode with below parameters: pH: 7.6 (lower limit: 7.45 & upper limit: 7.8), Temperature: 28° C. (lower limit: 25° C. & upper limit: 32° C.), DO (dissolved oxygen): 45% (lower limit: 10%, upper limit: 100%), Stirrer: 550 rpm.
The OD600 nm of the culture in the bioreactor reaches 0.15 to 0.18 in 3-4 days. At this point, the culture will consume most of the 50 mM NH 4 + present in the AOB growth media, and a user should start feeding the bioreactor with feeding solution at 0.59 ml/min (˜10%). The outflow pump should also be turned on at 0.59 ml/min (˜10%). The OD600 nm of the bioreactor reaches 0.5-0.6 in 1-2 days of continuous culture. The culture in the bioreactor is tested for heterotrophic contaminants by plating 1 ml of the bioreactor outflow on an LB plate.
Monitoring Growth of N. eutropha D23
Growth of N. eutropha D23 cells is monitored by measuring the OD600 nm of the culture. Typical growth in a batch culture as measured by OD600 nm is between 0.06 to 0.08.
The AOB growth medium contains NH 4 + that is stoichiometrically converted to NO 2 − by N. eutropha D23. Another way to monitor the growth of N. eutropha is to follow the release of nitrite (NO 2 −) in the growth medium. NO 2 − concentration is determined with Griess reagents, sulfanilamide and N-naphthylethylenediamine (also called NNEQ). Briefly, sulfanilamide and NNEQ are added to a sample and to known concentrations of sodium nitrite that make up a standard curve. Samples are incubated in the dark for 30 minutes. The absorbance is read at 540 nm.
Another way to follow nitrite production is by using a spectrophotometer by monitoring the optical density (OD) difference between 352 nm and 400 nm. The nitrite concentration is determined using a millimolar extinction coefficient of 0.0225 mM −1 . This assay can be performed directly by sampling the medium with the cells.
NO 2 − concentration (mM)=(OD 352 −OD 400 )/0.0225

The growth of a mixed culture comprising D23 was monitored by measuring optical density at 600 nm (OD600 nm) and by measuring Nitrite (NO 2 − ), and the growth rate is shown in FIGS. 1 and 2 . FIG. 1 shows that the optical density at a 600 nm wavelength plateaus slightly below 0.1, after 3 to 4 days. FIG. 2A shows that the amount of nitrite produced plateaus slightly below 25 mM after 3 to 4 days. NO 2 − concentrations in the cultures were determined colorimetrically by the Griess reagent (Hageman & Hucklesby, 1971), and is used as a second indicator for the growth rates and growth phases since the accumulation of NO 2 − is consistently proportional to the increase in cell mass during growth.
In FIG. 2B-I , increasing densities of D23 harvested from continuous culture were suspended in medium supplemented with 50 mM NH 4 + and grown shaking at 30° C. for 48 hours. Nitrite production was measured in supernatant samples using the Griess assay at the time points indicated. Results shown are mean values±SD from three independent experiments.
In FIG. 2B -II. Nitrite production by N. eutropha D23 in vitro is shown. Increasing densities of D23 were suspended in mineral salt medium supplemented with 50 mM NH 4 + and grown shaking at 30° C. for 24 hr. Nitrite production was measured in supernatant samples using the Griess assay at the time points indicated.
Storage Conditions
N. eutropha suspensions obtained from the continuous culture system showed remarkable stability upon storage at 4° C. for several months, as indicated by the highly consistent nitrite concentrations generated upon subculture under batch growth conditions. Protocols for storing and recovering N. eutropha are set out below.
Obtain 500 ml of a N. eutropha D23 culture grown to late-exponential phase (OD600=0.5-0.6 in continuous culture). Centrifuge at 10,000×g for 15 min at 20° C. Remove supernatant and resuspend the pellet in 50 ml of AOB storage buffer. Spin as above. Remove supernatant and resuspend thoroughly in a total of 50 ml storage buffer. This would be the 10× AOB stock. Store upright at 4° C. in 50 ml polypropylene tubes.
AOB Storage Buffer (for AOB storage at 4° C.): 50 mM Na 2 HPO 4 -2 mM MgCl 2 (pH 7.6) can be made as follows.
In 1 Liter ddH2O: Na 2 HPO 4 -7.098 g
MgCl 2 -0.1904 g
Adjust pH to 7.6. Filter-sterilize.
N. eutropha may be cryopreserved as follows. Transfer 1.25 ml of N. eutropha D23 mid-log culture to a 2 ml cryotube and 0.75 ml of sterile 80% glycerol. Shake tubes gently, incubate at room temperature for 15 min to enable uptake of the cryoprotective agents by the cells. Then, put tubes directly in a −80oC freezer for freezing and storage. For resuscitation of cultures, thaw frozen stocks on ice for 10-20 minutes. Centrifuge, at 8,000×g for 3 minutes at 4° C. Discard supernatant and wash the pellet by suspending it in 2 ml AOB medium followed by another centrifugation at 8,000×g for 3 minutes at 4° C. to reduce potential toxicity of the cryoprotective agents in subsequent growth experiments. Discard the supernatant and resuspend the pellet in 2 ml of AOB medium, inoculate into 50 ml of AOB medium containing 50 mM NH 4 + , and incubate in dark at 30° C. by shaking at 200 rpm.
In FIG. 2C , stability upon storage at 4° C. was studied. N. eutropha D23 previously harvested from continuous culture and stored at 4° C. was inoculated at 10 9 CFU/ml in mineral salt medium supplemented with 50 mM NH 4 + and grown shaking at 30° C. Nitrite production was determined at 24 and 48 hours post-incubation (left and right panel, respectively). Data shown are representative of a D23 suspension sampled repeatedly over a 6-month period.
Example 3
Creation of an Axenic D23 Culture
To isolate N. eutropha D23 in pure culture, four types of media (described below) were made, autoclaved and poured in plates. Sterile nylon membranes were placed on the plates.
N. europaea media+1.2% R 2 A agar
N. europaea media+1.2% agar
N. europaea media+1.2% agarose
N. europaea media+1.2% agarose+0.3 g/L pyruvate

3 day old N. eutropha D23 culture was streaked onto the nylon membranes and the plates were incubated at 30° C. The plates were monitored daily for growth of red colored N. eutropha cells. Nylon membranes were transferred to fresh plates once a week.
Reddish colored colonies appeared on plates with R 2 A agar or agar by end of 1 week. Single colonies were picked from plates with R2A agar and grown in N. europaea media. The cultures grew well in 6 days to 0.08 OD600 nm. Heterotrophic colonies appeared when the culture was plated on LB-Agar plates.
Reddish colored colonies on plates with R 2 A agar, agar, agarose, or agarose+pyruvate appeared by end of 2 weeks. Single colonies were picked from plates with agar or agarose and grown in N. europaea media. The cultures grew well in 6-8 days to 0.08 OD600 nm. Heterotrophic colonies appeared when the culture was plated on LB-Agar plates.
Bright reddish colonies on plates with R 2 A agar, agar, agarose, or agarose+pyruvate appeared by end of 4 weeks. Single colonies were picked from plates with agarose and grown in N. europaea media. The cultures grew well in 6-8 days to 0.08 OD600 nm. White colonies appeared when the culture was plated on LB-Agar plates.
Contaminating bacteria (e.g., non- N. eutropha bacteria present in the mixed culture) were identified by culturing, amplifying 16S rRNA by PCR, and sequencing of the PCR products. Contaminants were identified as Microbacterium sp. and Alcaligenaceae bacterium.
To create an axenic culture of D23 (i.e., free of contaminating bacteria) serial dilution was used. Eight single colonies (designated A-H) were picked, and each was placed into a 10 ml culture of N. europae medium. For each culture, five sequential 1:10 dilutions were created. For each culture A-H, growth was observed in the two or three most concentrated of the dilutions.
A second serial dilution was carried out. 50 ml of media was inoculated with approximately 2×10 8 N. eutropha cells, and sequential dilutions of 1:50 were made, such that after the fifth dilution, a flask was expected to have approximately one cell. Flasks that exhibited bacterial growth were plated on LB-agar to assay for contaminating bacteria, and no contaminating bacteria were observed. In addition, no contaminating gram positive cells were observed under the microscope.
Accordingly, the serial dilution process yielded an axenic or substantially axenic culture of N. eutropha.
Example 4
Sequencing of the D23 Genome
Strain D23 was obtained as described in Example 1, and was made axenic as described in Example 3.
A 10 ml aliquot the bacterial sample was inoculated into approximately 1 L of N. europaea growth medium described in Example 2. The culture grew well to optical density of 0.08 at 600 nm in a batch culture in 3 days.
Total DNA of the culture was prepared and sequenced using Illumina® technology and/or SMRT® DNA Sequencing System technology, Pacific Biosciences. The strain was identified as Nitrosomonas eutropha and was designated D23.
The genome sequence of D23 was compared to that of N. eutropha C91, which is believed to be the only other sequenced strain of N. eutropha.
The length of the D23 chromosome is 2,537,572 base pairs, which is shorter than the 2,661,057 base pair chromosome of N. eutropha strain C91 chromosome. Based on the 16S-23S operon, strain D23 has 99.46% identity to C91 and 95.38% identity to N. europaea . DNA sequencing of N. eutropha D23 indicated that this strain lacks plasmids. This contrasts with the sequence of strain C91, which has two plasmids.
Protein-encoding regions and RNA-encoding sequences were identified by sequence analysis. Supplementary Table 1 is a table of annotations that lists the positions of 2,777 genes in the D23 genome (SEQ ID NO: 1).
On the level of individual genes, several genes are present in D23 that are absent in C91. These genes are summarized in FIGS. 6-8 . FIG. 6 is a table displaying unique D23 genes with an assigned ORF number and a function based on sequence analysis, or a hypothetical gene above 200 base pairs in length. There are 162 genes in this category. FIG. 7 is a table displaying unique D23 genes below 200 base pairs that have an assigned ORF number. There are 164 of these genes. FIG. 8 is a table displaying unique D23 genes with no assigned ORF number. There are 219 of these genes (of which 180 are below 200 bp in length).
Strain D23 also lacks a number of genes that are present (or lack close homologs) in strain C91. These genes are sometimes referred to as unique C91 genes. These genes include the about 300 genes listed in FIG. 9 .
D23 contains several ammonia metabolism genes that differ from their homologs in C91. Certain of these genes are enumerated in Table 1 of the Detailed Description. Sequence alignments were performed between the D23 proteins and their homologs in strain C91. The sequence alignments are shown in FIGS. 10-16 and sequence differences between the two strains are shown in Table 2 of the Detailed Description.
The sequence comparisons revealed the percent sequence identities between the C91 and D23 homologs of each protein. More specifically, FIG. 10 is an alignment between AmoA1 and AmoA2 of strains C91 and D23. Each protein is identical at 273/276 residues, and so each is about 98.9% identical between strains. FIG. 11 is an alignment between AmoB1 and AmoB2 of strains C91 and D23. Both proteins are identical at 419/421 positions, and so are about 99.5% identical between strains. FIG. 12 is an alignment between AmoC1 and AmoC2 of strains C91 and D23. Both proteins are identical throughout. FIG. 13 is an alignment between AmoC3 of strains C91 and D23. This protein is identical at 272/274 positions, and so are about 99.3% identical between strains.
As to the Hao proteins, FIG. 14 (A and B) is an alignment between Hao1, Hao2, and Hao3 of strains C91 and D23. Hao1 is identical at 567/570 positions, and so each is about 99.5% identical between strains. Hao2 and Hao3 are each identical at 568/570 positions, and so are about 99.6% identical between strains.
Turning now to cytochrome c554 proteins, FIG. 15 is an alignment between CycA1, CycA2, and CycA3 of strains C91 and D23. CycA1 is identical at 233/235 positions, and so is about 99.1% identical between strains. CycA2 and CycA3 are each identical at 234/235 positions, and so each is about 99.6% identical between strains.
As to the cytochrome c M 552 proteins, FIG. 16 is an alignment between CycB1 and CycB2 of strains C91 and D23. CycB1 is identical at 232/239 positions, and so is about 97.1% identical between strains. CycB2 is identical at 236/239 positions, and so is about 98.7% identical between strains. Here, the length of the protein is considered 239 amino acids because that is its length in strain D23.
Alignment of the nucleic acid sequences of Table 1 shows the percent identity between homologs in C91 and D23. The amoA1 genes are about 98.8% identical (i.e., at 821/831 positions), the amoA2 genes are about 98.8% identical (i.e., at 821/831 positions), the amoB1 genes are about 99.1% identical (i.e., at 1255/1266 positions), the amoB2 genes are about 99.1% identical (i.e., at 1254/1266 positions), the amoC1 genes are about 99.8% identical (i.e., at 814/816 positions), the amoC2 genes are about 99.8% identical (i.e., at 814/816 positions), and the amoC3 genes are about 98.9% identical (i.e., at 816/825 positions). The hao1 genes are about 99.0% identical (i.e., at 1696/1713 positions), the hao2 genes are about 99.4% identical (i.e., at 1702/1713 positions), and the hao3 genes are about 99.2% identical (i.e., at 1700/1713 positions). Of the cytochrome c554 genes, the cycA1 genes are about 98.0% identical (i.e., at 694/708 positions), the cycA2 genes are about 98.7% identical (i.e., at 699/708 positions), and the cycA3 genes are about 99.3% identical (i.e., at 703/708 positions). Of the cytochrome c M 552 genes, the cycB1 genes are about 96.7% identical (i.e., at 696/720 positions) and the cycB2 genes are about 97.1% identical (i.e., at 702/723 positions).
Example 5
Competitive Growth Studies
A study was designed to determine whether N. eutropha strain D23 could inhibit the growth of undesirable bacteria such as Pseudomonas aeruginosa ( P. aeruginosa or PA), Staphylococcus aureus ( S. aureus or SA), Streptococcus pyogenes ( S. pyogenes or SP), Acinetobacter baumannii ( A. baumannii or AB), and Propionibacterium acnes , all of which are important pathogenic agents frequently isolated from either one or both of infected skin and wound sites. This protocol may also be used to test other N. eutropha strains for the ability to inhibit the growth of undesirable bacteria.
Briefly, a suitable protocol can comprise the following steps. At t=0, a culture is inoculated with N. eutropha , and then the N. eutropha is incubated for 24 hours. Culture characteristics (e.g., pH and nitrite levels) are assayed. At t=24 hours, the undesirable bacterium is added to the culture. Immediately upon addition, samples are obtained for determining CFU/ml of the undesirable bacteria and optionally CFU/ml of N. eutropha , pH, and nitrite levels. Incubation is allowed to proceed for an additional 24 hours. At subsequent timepoints, e.g., t=30 and t=48, one can take the same measurements as at t=24. To determine CFU/ml, one can plate neat/−1/−2/−3/−4/−5 (or higher) to obtain accurate counts.
A more detailed protocol is set out below.
Day 1


1. Mix the 10×AOB stock suspension stored at 4° C. by inverting several times until a homogenous suspension is obtained.
2. Aliquot 10 ml of the suspension in 8×1.5 ml polypropylene tubes.
3. Centrifuge at 17,000×g for 3 min at room temperature.
4. Remove supernatant and any residual buffer from each pellet and resuspend all pellets thoroughly into a total of 10 ml complete AOB medium in a 50 ml polypropylene tube.
5. Pipet 5 ml of 10×AOB suspension in each of two 50 ml polypropylene tubes (Tube 1-2).
6. Prepare five additional tubes (Tube 4-8) containing 10×AOB suspensions in complete AOB medium/0.5× Phosphate Buffer. Aliquot 26 ml of the 10×AOB stock suspension in 16×1.5 ml polypropylene tubes. Obtain pellets as above and resuspend in a total of 26 ml complete AOB medium/0.5× Phosphate Buffer in a 50 ml polypropylene tube.
7. Pipet 5 ml of the 10×AOB suspension in each of five 50 ml polypropylene tubes (Tube 4-8).
8. Also, prepare two tubes with 10× Heat-killed AOB suspensions in either complete AOB medium (Tube 3) or complete AOB medium/0.5× Phosphate Buffer (Tube 9). Aliquot 10 ml of the Heat-killed suspension stored at 4° C. in 8×1.5 ml polypropylene tubes. Centrifuge at 17,000×g for 3 min at room temperature and remove supernatant, as described above for live AOB. Resuspend four pellets in a total of 5 ml complete AOB medium in one 50 ml polypropylene tube (Tube 3) and the remaining four pellets in a total of 5 ml complete AOB medium/0.5× Phosphate Buffer in a second 50 ml polypropylene tube (Tube 9).
9. Add 141 μl of 1 M ammonium sulfate to obtain 25 mM final concentration (Tube 1, 3, 4, 5, 9). Add an equal volume of dH 2 O to corresponding control tubes (Tube 2, 6, 7).
10. To Tube 8, add 141 μl of fresh 1 M NaNO 2 .
11. Swirl all tubes gently, but thoroughly, to mix.
12. Immediately after mixing each suspension, remove 0.5 ml from each tube and centrifuge all samples at 17,000×g, 3 min, RT. Transfer supernatants into fresh tubes after completing step 13, and measure both pH and nitrite levels using Griess Reagent to obtain TO values.
13. Incubate all 50 ml tubes at 30° C. with mixing on an orbital shaker at 150 rpm (upright position) for 24 hr.








TABLE 5



T0














10x



T24



10x
Killed
1M

1M
SA/PA



AOB
AOB
(NH 4 ) 2 SO 4
H 2 O
NaNO 2
in saline

SAMPLE
Tube
(ml)
(ml)
(μl)
(μl)
(μl)
(ml)





Complete AOB medium










10x AOB + NH 4 +
1
5
—
141
—
—
0.5

10x AOB
2
5
—
—
141
—
0.5

10x Killed AOB +
3
—
5
141
—
—
0.5

NH 4 +










Complete AOB medium/0.5x Phosphate Buffer










10x AOB + NH 4 +
4
5
—
141
—
—
0.5

10x AOB + NH 4 +
5
5
—
141
—
—
0.5

10x AOB
6
5
—
—
141
—
0.5

10x AOB
7
5
—
—
141
—
0.5

10x AOB + NaNO 2
8
5
—
—
—
141
0.5

10x Killed AOB +
9
—
5
141
—
—
0.5

NH 4 +
















































Day 2


14. At 24 hr, prepare SA, PA, SP or AB inocula to add to the suspensions.
15. From an overnight (20-24 hr) SA or PA culture grown on Tryptic Soy Agar (TSA), or a SP or AB culture prepared on Brain Heart Infusion (BHI) Agar, prepare bacterial suspension in Tryptic Soy Broth (TSB) or BHI broth (BHIB) at ˜2×10 8 CFU/ml.
16. Pipet 50 μl of the SA/PA/SP/AB suspension in 9.95 ml saline to obtain ˜10 6 CFU/ml. Keep on ice, as needed.
17. Vortex SA/PA/SP/AB suspension and add 0.5 ml to Tube 1-9.
18. Swirl all tubes gently, but thoroughly, to mix.
19. Immediately after mixing each suspension, transfer 100 μl from each tube into 0.9 ml TSB or BHIB (10 −1 dilution) to neutralize samples for CFU determination. In addition, remove 0.5 ml from each tube and centrifuge at 17,000×g, 3 min, RT. Recover supernatants in fresh tubes after completing Step 20 and measure both pH and nitrite levels using Griess Reagent after Step 21 to obtain T24 values.
20. Incubate all 50 ml tubes at 30° C. with mixing on an orbital shaker (150 rpm) for an additional 24 hr.
21. Dilute T24 samples further in TSB or BHIB and plate −2/−3/−4 dilutions on TSA or BHI agar. Incubate plates at 37° C. for 24 hr to obtain SA, PA, SP, or AB viable counts.
22. At 6 and 24 hr post-mixing of SA/PA/SP/AB with AOB, vortex tubes and pipet 100 μl samples into 0.9 ml TSB. Dilute further in TSB or BHIB and plate neat through −5 dilutions on TSA or BHI agar. At each time point, also remove 0.5 ml from each tube and measure both pH and nitrite levels in each supernatant sample, as described above.
23. Incubate TSA or BHI agar plates at 37° C. for 24 hr to obtain T30 (6 hr) and T48 (24 hr) viable counts.
24. Count CFU to determine % killing rates for each time point


Griess Reagent Assay for Nitrite Quantification
1. Use the 0.5 ml supernatant samples obtained for pH determination at 0, 2, 6, and 24 hr.

2. Serially dilute 56 μl of the supernatant in 0.5 ml dH2O to obtain 10-100- and 1000-fold dilutions, as needed. For TO samples, use 1/10 for Tube 1-6, 8, 9, and 1/1000 for Tube 7. For T24/T30/T48 samples, use 1/10, 1/100, 1/1000 for all tubes,

3. To prepare sodium nitrite standards, dilute 10 μl of a fresh 1 M stock in 990 μl complete AOB medium-10% saline to obtain a 10 mM solution.

4. Dilute 10 μl of the 10 mM stock in 990 μl dH 2 O to obtain a 100 μM working solution.

5. Prepare standards in dH 2 O as shown below. Run standards only with TO samples.

TABLE 6 100 μM Nitrite sodium nitrite dH 2 O conc A 540nm (μl) (μl) (μM) (indicative values) 0 (blank) 500 0 0 62.5 437.5 12.5 0.307 125 375 25 0.607 250 250 50 1.164 500 0 100 2.35
6. To each 0.5 ml sample (or sodium nitrite standard), add 0.25 ml each of Reagent A (58 mM sulfanilamide in 1.5 N HCl) and Reagent B (0.77 mM n-(1-napthyl) ethylene diamine-2HCl in H 2 O (light-sensitive; store in dark).

7. Mix and let stand at room temperature for 30 min in the dark (or cover with foil). The color should change to a vivid pink/violet.

8. Read absorbance at 540 nm and determine nitrite concentrations from standard curve.

This protocol was used to test N. eutropha D23's ability to inhibit the growth of P. aeruginosa (PA), S. aureus (SA), S. pyogenes (SP), A. baumannii (AB), or P. acnes . The results of this experiment are shown in FIGS. 3A, 3B, and 3C .
The left panel of FIG. 3A plots CFU/ml of PA versus time, when PA is co-cultured with live N. eutropha and ammonium (squares), live N. eutropha without ammonium (circles), killed N. eutropha and ammonium (triangles), or live N. eutropha with NaNO 2 (inverted triangles). The right panel of FIG. 3A plots CFU/ml of SA versus time, under the same conditions. The left panel of FIG. 3B plots CFU/ml of SP versus time, under the same conditions. The right panel of FIG. 3B plots CFU/ml AB versus time, under the same conditions. FIG. 3C plots CFU/ml of P. acnes versus time, when P. acnes is co-cultured with live N. eutropha and ammonium (squares), live N. eutropha without ammonium (circles), killed N. eutropha and ammonium (triangles), or live N. eutropha with NaNO 2 (inverted triangles). In all cases, live N. eutropha with ammonium results in declining numbers of PA, SA, SP, AB, or P. acnes whereas the other culture conditions allow the undesirable bacteria to grow. Without being bound by theory, these experiments suggest that nitrite generation from ammonia concurrently with medium acidification by D23 led to strong antibacterial effects, e.g., an approximately 100-fold reduction in viable counts of methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pyogenes, Acinetobacter baumannii , or P. acnes . By contrast, control co-cultures of pathogenic bacteria either with heat-killed D23 supplemented with ammonia, or with live D23 without ammonia, did not produce comparable antibacterial effects. The control comprising live N. eutropha culture without ammonium is consistent with the model that N. eutropha 's ammonia oxidation activity contributes to its antibacterial effects. The control comprising killed N. eutropha and ammonium indicates that some biological activity of the N. eutropha (e.g., its ammonia oxidation activity) contributes to antibacterial activity. The control comprising live N. eutropha with NaNO 2 indicates that comparable nitrite levels at neutral pH (versus low pH when the bacteria use ammonia) do not have a strong antimicrobial effect, and is consistent with the model that N. eutropha 's oxidation of ammonia, rather than nitrite alone, contributes to the antibacterial activity.
The top panel of FIG. 4A plots the NO 2 − concentration over time in the co-cultures described in the paragraph above. NO 2 − concentration is an indication of the rate of NH 3 metabolism in the cultures. As above, PA is co-cultured with N. eutropha and ammonium (squares), N. eutropha without ammonium (circles), or killed N. eutropha and ammonium (triangles). Live N. eutropha with ammonium produces dramatically higher NO 2 − levels than the two control cultures, indicating that the live N. eutropha converts ammonium into NO 2 − under the culture conditions.
The bottom panel of FIG. 4A plots pH over time in the same co-culturing conditions. pH indicates the metabolic activity of the N. eutropha because the conversion of ammonia to nitrite produces hydrogen ions. PA is co-cultured with N. eutropha and ammonium (squares), N. eutropha without ammonium (circles), killed N. eutropha and ammonium (triangles), or live N. eutropha with NaNO 2 (inverted triangles). Live N. eutropha with ammonium acidifies the medium, in contrast to the three control cultures, indicating that the live N. eutropha metabolizes ammonium under the culture conditions.
The top panels of FIG. 4B plot the NO 2 − concentration over time in the co-cultures described above. NO 2 − concentration is an indication of the rate of NH 3 metabolism in the cultures. As above, S. pyogenes (SP) and A. baumannii (AB) are co-cultured with N. eutropha and ammonium (squares), N. eutropha without ammonium (circles), or killed N. eutropha and ammonium (triangles). Live N. eutropha with ammonium produces dramatically higher NO 2 levels than the two control cultures, indicating that the live N. eutropha converts ammonium into NO 2 − under the culture conditions.
The bottom panels of FIG. 4B plot pH over time in the same co-culturing conditions. pH indicates the metabolic activity of the N. eutropha because the conversion of ammonia to nitrite produces hydrogen ions. SP and AB are co-cultured with N. eutropha and ammonium (squares), N. eutropha without ammonium (circles), killed N. eutropha and ammonium (triangles), or live N. eutropha with NaNO 2 (inverted triangles). Live N. eutropha with ammonium acidifies the medium, in contrast to the three control cultures, indicating that the live N. eutropha metabolizes ammonium under the culture conditions.
FIG. 4E shows an alternative visualization the data of FIGS. 4A and 4B .
The capacity of Nitrosomonas eutropha D23 to inhibit proliferation of pathogenic bacteria due to nitrite production concurrent with acidification (acidified nitrite) was assessed by testing the survival of 5 strains of pathogenic bacteria in co-culture studies with D23 in vitro. The five strains of pathogenic bacteria included Propionibacterium acnes, Streptococcus pyogenes , methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa , and multidrug-resistant Acinetobacter baumannii . Incubation of N. eutropha D23 (10 10 cells/ml) in the presence of ammonium led to nitrite concentrations of 10 mM or higher and acidification to pH 6 or lower ( FIG. 4B ). The combination of increased nitrite concentration and lowering of pH led to bactericidal or bacteriostatic effects and a marked reduction (up to 965-fold) in viable counts of the pathogenic bacterial species tested. The results of these studies are summarized in FIG. 4D and Table 7, below. In contrast to the D23 co-cultures incubated in the presence of ammonium, control co-cultures of the five pathogenic agents with D23 without ammonium, or with heat-killed D23 (B244) supplemented with ammonium, did not lead to any inhibitory or antimicrobial effects.





TABLE 7



Effect of N . eutropha D23 (D23) on relative survival of pathogenic

bacteria in vitro





Relative Survival (Fold Change)









Heat-Killed

Pathogen Tested
AOB + NH 3
AOB − NH 3
AOB + NH 3









Priopionibacterium
acnes

−114
−19,067
−1.05

ATCC 6919




Staphylococcus aureus (MRSA)
−117.6
8.2
2.03

ATCC BAA-1717





Pseudomonas
aeruginosa

−84.3
2.65
379

ATCC 15442





Streptococcus
pyogenes

−965
−2.88
−3.81

ATCC 19615




Acinetobacter baumannii (MDR)
−5.43
92.4
89.8

ATCC BAA-1605










































Example 6
Wound Healing
The effect of Nitrosomonas eutropha D23 (sometimes also called B244) on wound closure in diabetic mice was evaluated in two separate studies. In Study 1, db/db mice (8 mice/group) were pre-treated by body immersion daily for one week with 3 concentrations of D23 (10 7 , 10 8 or 10 9 cells/ml) supplemented with ammonium chloride, or with vehicle control suspension only. Subsequently, full-thickness wounds generated on the back of each animal were treated topically once daily for 14 days with vehicle alone or equal volumes of 3 concentrations of D23 (10 7 , 10 8 or 10 9 cells/ml) in PBS supplemented ammonium chloride. Of the three D23-treated groups, the group receiving the highest dose showed significant improvement in wound closure from day 5 to day 15, with the most pronounced improvement of 83% observed on day 9 post-wounding. The median time to 50% wound closure was significantly reduced (P<0.05) for the animals treated with 10 9 cells/ml of D23, as compared to the animal group receiving vehicle treatment alone.
Initial histopathology analyses of wound tissue samples collected on Day 15 upon study completion did not reveal any gross differences between vehicle- and D23-treated animals. Subsequently, a more in-depth examination of the tissue sections was performed according to the scoring system and parameters adapted and modified form Altavilla, et al (2001). This analysis suggested a trend of increased levels of angiogenesis and maturity of granulation tissue with decreased levels of dermal inflammation in animals treated with 10 9 cells/ml of D23 versus the vehicle control group, which was consistent with the observed improvement in wound healing rates of the D23-treated animals
N. eutropha strain D23 was tested for its ability to accelerate wound healing in a diabetic mouse model, using C57BLKS/J Iar−+Lepr db /+Lepr db male mice (non-GLP). A detailed protocol is set out below.
Day −6 to Day 1: Whole-Body Immersion Pre-Treatment of Mice with Test Organism
1. Mix the 10×D23 stock suspension stored at 4° C. by inverting several times until a homogenous suspension is obtained. 2. Pipet 2×29 ml of the 10× stock suspension into two 50 ml polypropylene centrifuge tubes. 3. Centrifuge at 8,000×g for 15 min at 20° C. 4. Remove supernatant and any residual buffer from the pellets and resuspend the two pellets gently but thoroughly into a total of 58 ml room-temperature Phosphate Buffered Saline, pH 7.4 (PBS). This is the 10×D23 (Test Organism) suspension to use for the following steps. 5. Prepare 500 ml baths containing the Test Organism at 1×, 0.1× and 0.01× strength in pre-warmed PBS at 30° C. supplemented with 2 mM NH 4 Cl, or a Vehicle control bath, as shown below. Prepare and use one bath at a time from the 10×D23 suspension kept at room temperature before continuing with the next bath. This will prevent keeping the Test Substance at 30° C. for long time periods without ammonium. To prevent contamination of the Vehicle control group with the Test Substance, begin with the Vehicle control group before proceeding with the D23 baths. 6. Immerse each group of mice in corresponding baths for 60 sec daily for seven days. 7. Use a fresh 500 ml baths for each daily immersion into the Test Organism or Vehicle control.












TABLE 8






10× D23

1M




(room
PBS
NH 4 /



BATH/
temp.)
pH 7.4
Cl
CFU/


GROUP
(ml)
(ml)
(ml)
ml














Vehicle
—
500
1.0
0


(control)






1× D23
50
450
1.0
109


0.1× D23
5
495
1.0
108


0.01× D23
0.5
499
1.0
107





























Day 1: Wounding of Mice by Skin Puncture




1. Generate skin wounds on the back of each mouse by skin puncture after shaving of the back and shoulders.
2. House each mouse separately for the remainder of the study.

Day 1 to Day 15: Topical Treatment of Skin Wounds with Test Organism

1. Mix the 10×D23 stock suspension stored at 4° C. by inverting several times until a homogenous suspension is obtained.
2. Pipet 1 ml of the 10× stock suspension into a 1.5 ml polypropylene tube.
3. Centrifuge at 17,000×g for 3 min at room temperature.
4. Remove supernatant and any residual buffer from the pellet and resuspend pellet gently but thoroughly into a total of 10 ml pre-warmed Phosphate Buffered Saline, pH 7.4 (PBS) at 30° C. This is the 1×D23 (Test Organism) suspension to use for the following steps.
5. Prepare 1×, 0.1× and 0.01× suspensions of the Test Organism in pre-warmed PBS supplemented with 2 mM NH 4 Cl, or a Vehicle control solution, in 50 ml polypropylene tubes as shown below.
6. Draw 2.0 ml of each suspension using a repetitive pipet.
7. Drip slowly 0.2 ml of the Test Organism (1×, 0.1×, 0.01× groups), or an equal volume of Vehicle control, onto each wound and surrounding shaved skin area. Gently spread applied suspension onto the wound and the entire shaved skin area using a pipet tip.
8. Repeat application of Test Organism or Vehicle control daily for a total of 14 days.
9. Measure wound size by wound planimetry and obtain photo images of each wound on Day 1, 3, 5, 7, 9, 11, 13 and 15 using Image Analyzer (Image-pro plus version 4.5, Media Cybernetics Inc).
10. Calculate % wound closure and wound half-closure time (CT 50 ) for each group.














TABLE 9





PBS
1M




1× D23
pH 7.4
NH 4 Cl
CFU/
CFU/

GROUP
(ml)
(ml)
(μl)
ml
wound












Vehicle

5.0
10
0
0

(control)






1× D23
5.0
0
10
10 9
2 × 10 8

0.1× D23
0.5
4.5
10
10 8
2 × 10 7

0.01× D23
0.05
4.95
10
10 7
2 × 10 6



























Day 15 (Upon Study Completion): Collection of Wound Tissues Samples and Histopathology Analyses




1. Obtain half-wound tissue samples from four mice per group using aseptic technique to avoid cross-contamination of tissues.
2. Proceed with histopathology analyses.
3. Store temporarily at −70° C. the remainder half-wound samples and the additional four full-size wound tissues from each group for further evaluation.




As shown in FIG. 5A , topical application of 10 9 CFU/ml of strain D23 significantly (*p<0.05) accelerated wound healing. The sample size was N=8 animals/gp. The group receiving the highest doses showed significant improvement in would closure from day 5 to day 15, with the most pronounced improvement of 83% observed on day 9, post-wounding. This study demonstrates the potential therapeutic benefit of ammonia oxidizing bacteria, e.g., D23, to diabetic foot ulcers, chronic wounds, and other related indications.
FIG. 5B is a plot showing CT 50 versus control (vehicle) and 10 9 CFU/ml D23. CT50 is the time required to achieve a 50% wound closure. As shown in the plot, those wounds having application of D23 provided for lower CT 50 values.
FIG. 5C is a plot of another experiment in which the protocol above was carried out to obtain wound closure measurements versus time. Control (vehicle) wounds were tested and compared to D23 at 10 9 CFU/ml wounds. This plot shows the effects of D23 when immersion pre-treatment and topical application was carried out.
FIG. 5D is a plot of another experiment in which the protocol above was carried out, without immersion pre-treatment, to obtain wound closure measurements versus time. Control (vehicle) wounds were tested and compared to applications of D23 at 10 9 CFU/ml and 10 10 CFU/ml to wounds. This plot shows the effects of D23 when topical application was carried out.
FIG. 5E is a plot showing CT 50 versus control (vehicle) and 10 9 CFU/ml D23, with and without immersion pre-treatment, and 10 9 CFU/ml D23 without pre-treatment. As shown in the plot, those wounds having application of D23 provided for lower CT50 values.
FIG. 5F are images of the wound healing experiments, at Day 1, Day 11, and Day 15. AOB represents D23.
Possible modulation of inflammatory responses coupled with ant-infective action of D23 could prove an effective topical treatment against diabetic and other chronic wounds.
FIG. 5G are plots of blood glucose levels in the mice tested for the control (vehicle) and various concentrations of D23. “IM” shown in the x-axis of the right-hand panel plot represents those tests down with an immersion pre-treatment of D23. FIG. 5H is a plot of body weight of the animals used in testing for the study including immersion pre-treatment, over the time of the study. FIG. 5I are plots of body weight of the animals used in testing for the study, including the immersion pre-treatment study, and the study done without immersion pre-treatment, over the time of the studies.
In Study 2, the effect of pretreatment of db/db mice with 10 9 cells/ml of B244 on wound closure was examined. Groups of seven mice were treated topically with 10 9 cells/ml of B244 with and without prior body immersion. One additional group of seven mice was treated topically with 10 10 cells/ml of D23 (B244). Corresponding vehicle groups (seven mice) were run in parallel with and without body immersion as negative controls. Wound surface area and photo images of each wound were obtained as before. These studies reproduced the findings of Study 1 suggesting improvement of wound closure with a B244 dose of approximately 10 9 cells/ml. Moreover, topical treatment alone with 10 9 cells/ml improved wound closure rates similar to the animals receiving topical treatments with immersion. Additional histopathology analyses by of H & E—stained wound tissue sections recovered on Day 5 did not reveal any differences between vehicle and D23 (B244)-treated wounds.
Cytokine and growth factor expression in D23-treated diabetic animals was investigated using Luminex technology. Specifically, expression of growth-regulated oncogene/keratinocyte chemoattractant (Gro/KC), interleukin-1 (IL-1), interleukin-6 (IL-6), macrophage inflammatory protein-2 (MIP-2), tumor necrosis factor (TNF), and vascular endothelial growth factor (VEGF) was compared between D23-treated and control diabetic animals in serum samples obtained on Day 5 and Day 15 from four mice per group treated with or without prior body immersion. In similar Luminex analyses, lysates of tissues from D23-treated or Vehicle control animals obtained upon completion of the study (Day 15) were also analyzed. Abnormally high and sustained expression of inflammation markers, including MIP-2, TNFα and IL-1β, has been previously associated with a dysregulated inflammatory response and impaired wound healing processes in db/db mice (Wetzler, 2000). Analyses of Day 5 and Day 15 serum samples yielded very low signal for all six cytokines in both D23-treated and vehicle control animals, a result indicating the lack of systemic effects following wound treatment with high D23 doses. In wound tissue lysates obtained on Day 15, MIP-2 levels (1155-1516 pg/100 g total protein) were significantly higher than the remaining five cytokines, with IL-6 and Gro/KC measured at much lower levels (44-48 pg/100 g total protein) and both IL-1 and VEGF being close to undetectable (≦3.8 pg/100 g total protein). Overall, no difference was observed between D23-treated animals and vehicle control animals with or without full-body immersion in D23 suspensions. The levels of all six cytokines or growth factors measured in tissue lysates of all four groups of mice examined are summarized in Table 10 below.





TABLE 10



Cytokine levels measured in wound tissue lysates of D23-treated and vehicle

control-treated db/db mice















MIP-2





Gro/KC
IL-1β
IL-6
(pg/
TNFα
VEGF



(pg/100 g
(pg/100 g
(pg/100 g
100 g
(pg/100 g
(pg/100 g

Treatment
Animal
protein)
protein)
protein)
protein)
protein)
protein)












Vehicle
1-1
49
2.4
78
1089
28.7
5.8

(with prior
1-3
66
2.4
134
1335
31.2
4.5

immersion)
1-5
59
2.7
128
1112
25.7
4.2


1-7
76
1.2
148
1013
9.4
4.1


MEAN
62
2.2
122
1137
23.7
4.7

D23
3-1
49
2.1
66
1830
24.7
4.1

10 9 cells/ml
3-3
75
1.8
162
1615
32.3
3.6

(with prior
3-5
50
2.4
132
1896
23.9
4.3

immersion)
3-7
17
1.5
28
720
9.0
3.4


MEAN
48
1.9
97
1516
22.5
3.8

Vehicle
5-1
43
1.5
90
833
13.2
3.6

(topical
5-3
55
2.2
104
1312
18.6
3.6

only)
5-5
44
1.4
59
644
17.6
3.2


5-7
100
3.8
168
1308
48.6
4.0


MEAN
60
2.2
105
1024
24.5
3.6

D23
6-1
82
2.2
105
1573
28.5
2.9

10 9 cells/ml
6-3
18
0.8
36
943
8.0
2.5

(topical
6-5
25
1.2
45
1027
9.5
2.2

only)
6-7
49
1.5
92
1077
18.5
2.9


MEAN
44
1.4
69
1155
16.1
2.6















































Pharmacokinetic evaluation of D23 (B244) in rodents was conducted during a 28-day repeat dose toxicology study as described in the section below. No separate single dose pharmacokinetic studies were run for D23 (B244).
Example 7
Toxicology
28-Day Safety Study of Nitrosomonas eutropha D23 (B244) Application on Full-Thickness Wounds of Streptozotocin-Induced Diabetic Sprague-Dawley Rats
The objectives of this study were to determine the potential toxicity of Nitrosomonas eutropha D23 (B244) in rats when given dermally on wounded skin for a minimum of 28 days, and to evaluate the potential reversibility of any findings. In addition, the toxicokinetic characteristics of D23 (B244) were determined.
Study Design and Methods
The design was based on the study objectives, the overall product development strategy for the test article, and the following study design guidelines: OECD Guidelines 407 and 417, Committee for Human Medicinal Products (CHMP), and ICH Harmonised Tripartite Guidelines M3 (R2), S3a, and S6 (R1). The study design is outlined herein and results are shown in Table 11.





TABLE 11



28-Day Safety Study design







Dose




Volume
Dose
No. of Animals









Group
Test
Dose Level
(mL/kg)
Conc.
Main Study
Recovery











No.
Material
(CFU/kg/day)
Split
(CFU/mL)
M
F
M
F



1
Control
0
0.8
0
10
10
5
5


Article








2
AOB-D23-
6 × 10 7
0.8
8 × 10 7
10
10
0
0


100








3
AOB-D23-
6 × 10 8
0.8
8 × 10 8
10
10
0
0


100








4
AOB-D23-
6 × 10 9
0.8
8 × 10 9
10
10
5
5


100



M = Male,

F = Female,

Conc. = Concentration,

CFU = Colony Forming Unit.

Control Article = 99.998% Phosphate Buffered Saline, pH 7.4 (PBS), 0.002% 1M NH4Cl








































For induction of diabetes, Streptozotocin was administered to Sprague Dawley rats via intraperitoneal injection on Day −4. Animals with blood glucose levels of >200 mg/dL were considered as responders to the Streptozotocin treatment and were used for the dosing phase of the study. Two full-thickness skin wounds were created per animal (1 on each side of the back of each anesthetized animal) using an 8-mm skin biopsy punch. The wounds were left uncovered during administration of the control and test article and also for the duration of the study. The test and control articles were administered to the appropriate animals dermally once daily (for 24 hours±1 hour) from Days 1 to 28. The end points evaluated in this study were the following: clinical signs, dermal findings, body weights, body weight changes, food consumption, ophthalmology, glucose analysis, clinical pathology parameters (hematology, coagulation, clinical chemistry, urinalysis, hemoglobin A1c, and methemoglobulin), C-reactive protein and serum ferritin analysis, toxicokinetic parameters, gross necropsy findings, organ weights, and wound histopathology.
Results
The results for the endpoints evaluated in the 28-day GLP toxicology study are outlined below in Table 12.





TABLE 12



28-Day Safety Study-Results





End points
Observations
Comments



Mortality
No unscheduled deaths during the course of



the study were attributed to D23 (B244).



One control male was found dead on Day



41; the cause of death due to necrosis in the



kidney, liver, pancreas, and spleen


Clinical
No test article D23 (B244)-related clinical
Similar clinical signs

Observations
signs were observed during the study.
have been previously


Clinical signs including abdominal
associated with an


distension, prominent backbone, fur
uncontrolled diabetic


staining, soft stools and ungroomed
state in rats and other


appearance were related to the diabetic state
animal models


of the animals



Skin discoloration (red/black) was present



in both control and treated animals


Dermal Scores
No dermal irritation occurred during the



study



No erythema or edema was observed



following dermal administration of the test



article


Body Weights and
No D23 (B244)-related effects on body


Body Weight
weight or body weight change were noted


Changes
during the study.



Mean weight gain was observed throughout



the study interval, with isolated instances of



slight loss in individual animals across the



dose groups which did not follow specific



dose-related trends


Food Consumption
There were no test article-related effects on



food consumption.


Ophthalmic
There were no D23 (B244)-related
The appearance of

Examinations
ophthalmologic changes during the study. The
cataracts is a known


majority of the animals on study developed
complication of


cataracts and there were no differences among
diabetes


dose groups.


Hematology,
No test article-related changes were noted in


Coagulation,
hematology, coagulation, hemoglobin A1c,


Hemoglobin A1c,
and methemoglobin parameters on


and Methemoglobin
Day 29 or 43.



Isolated statistically significant differences



were noted during the study; however, the



values were within the historical control



ranges and were not considered meaningful


Clinical Chemistry
No test article-related changes were noted on



Days 29 or 43.



Isolated statistically significant differences



were noted during the study; however, the



values were within the historical control



ranges and not considered meaningful


Urinalysis
No test article-related effects


C-reactive Protein
No test article-related effects


and Serum Ferritin



Analysis



Gross Pathology
No test article-related gross findings were
Any gross findings


noted on Day 29 or Day 43
observed were



considered to be related



to the diabetic



condition of the rats



and incidental in nature

Organ Weights
There was an increase in adrenal weight in



females at ≧6 × 10 8 CFU/kg/day on Day 29,



whereas adrenal weight was decreased in



males and there were no associated gross



pathology findings making the association



of this finding to D23 (B244) administration



equivocal



Potential D23 (B244)-related organ weight



changes noted at the terminal euthanasia



(Day 29) were not observed at the end of the



recovery period (Day 43)


Histopathology
No D23 (B244)-related microscopic findings


Terminal
on Day 29.


Euthanasia (Day 29)
Changes observed in the kidneys, large and



small intestine, and urinary bladder were



related to the diabetic state of the animals.



The incidence and severity of these



findings were similar in all study groups



including controls.



Changes at the administration/wound sites



included epidermal regeneration, fibrosis,



and granulomatous inflammation. The



incidence and severity of these findings



were similar in all groups including



controls


Histopathology
Changes observed on Day 43 were similar


Recovery
to those reported on Day 29


Euthanasia (Day 43)










































































































Conclusions




Once daily application of D23 (B244) on rat wounds was well tolerated at levels of 6×10 7 , 6×10 8 , and 6×10 9 CFU/kg/day.
No D23 (B244)-related mortality observed during the study
Healing of full tissue thickness excisions was similar in all groups
No D23 (B244)-related clinical signs or dermal irritation were observed
No effects observed during the study on body weight, food consumption, clinical pathology parameters, c-reactive protein, or serum ferritin
No test article-related gross necropsy findings or histopathologic findings
The no-observed-adverse-effect level (NOAEL) was determined to be 6×10 9 CFU/kg/day (8×10 9 cells/ml)
No specific target organs were identified




No D23 related mortality occurred during the study. There were no D23-related clinical signs or dermal irritation, and there were no effects on body weight, body weight changes, food consumption, clinical pathology parameters, C-reactive protein, or serum ferritin during the study. There were no test article-related gross necropsy findings or histopathologic findings. Increases in adrenal weights were noted in the >6×10 8 CFU/kg/day females on Day 29; however, association with D23 was considered equivocal based on the lack of a similar effect in the males, the lack of corresponding gross findings, and the lack of microscopic evaluation of this tissue.
All wound sites were completely covered by epidermis and appeared to be in the remodeling/resolution phase, which was characterized by stratification of the epidermis with keratinization and refinement of the dermal collagen (synthesis, bundling, and degradation) and capillaries to restore the normal architecture of the epidermis and dermis. The incidence and severity were similar in all groups, including controls.
Example 8
Antibiotic Susceptibility
The activities of five antibiotics, each representing a different antibiotic class, were tested against Nitrosomonas eutropha D23. The antibiotics tested included clindamycin, erythromycin, gentamicin, piperacillin with or without the β-lactamase inhibitor Tazobactam, and tetracycline. These were chosen based on the Clinical and Laboratory Standards Institute (CLSI) recommendations for routine testing and reporting of phylogenetically-related proteobacteria ( Pseudomonas aeruginosa ) listed under Non-fastidious organisms and Non-Enterobacteriaceae in the CLSI 24th Informational Supplement (M100-524), and also included topical or systemic antimicrobial agents commonly used against acne, such as clindamycin or tetracycline. Studies with clindamycin were included even though this antibiotic was not expected to be very effective at inhibiting Nitrosomonas , as is the case for other aerobic Gram-negative bacteria.
Minimal Inhibitory Concentrations (MICs) were determined by culturing N. eutropha D23 in decreasing concentrations of each of the five antibiotics. Bacterial growth at 30° C. was monitored for 48-72 hr by determining optical density (OD 600 ) values in samples collected at 24 hr intervals. MIC values were identified as the lowest antibiotic concentration from a two-fold dilution series leading to no increase in OD 600 measurements for the 2 or 3-day incubation period. The N. eutropha D23 phenotype in each antibiotic test was determined as Susceptible, Intermediate, or Resistant according to the MIC Interpretive Criteria provided by the CLSI. As summarized in Table 13, these studies demonstrated susceptibility of N. eutropha D23 to erythromycin and gentamicin and intermediate resistance to tetracycline and piperacillin suggesting the lack of strong antibiotic-resistance potential by the Drug Substance. Clindamycin resistance observed for N. eutropha D23 is in agreement with previous reports for natural resistance of aerobic Gram-negative bacteria to this antibiotic. In addition to testing the β-lactam antibiotic piperacillin alone, the broad range β-lactamase inhibitor Tazobactam was also tested in combination with piperacillin to assess the possible expression of β-lactamase(s) by N. eutropha D 23. The results from this comparison showed no increase in N. eutropha D23 susceptibility, indicating the absence of β-lactamase expression by N. eutropha D23, at least under the conditions tested.





TABLE 13



MIC values for five antibiotics tested against N . eutropha

D23 cultures in vitro








MIC
MIC Interpretive

Antibiotic
Antibiotic Class
(μg/ml)
Criteria*








Clindamycin
Lincosamide
>16
Resistant (≧4 μg/ml)

Erythromycin
Macrolide
0.16
Susceptible (≦0.5 μg/ml)

Gentamicin
Aminoglycoside
0.25
Susceptible (≦4 μg/ml)

Piperacillin
β-lactam
64
Intermediate




(32-64 μg/ml)

Piperacillin/
β-lactam/
64/4
Intermediate

Tazobactam
β-lactamase

(32/4-64/4 μg/ml)


inhibitor



Tetracycline
Tetracycline
8
Intermediate (8 μg/ml)



*as recommended by the Clinical and Laboratory Standards Institute (values in parentheses represent MIC levels for corresponding Susceptible, Intermediate or Resistant outcomes)

































Conclusions
These studies demonstrate susceptibility of D23 (B244) to macrolide and aminoglycoside antibiotics and resistance to lincosamides, results that indicate the lack of strong antibiotic-resistance potential by the Drug Substance.
Example 9
Elucidation of Structure of N. eutropha
N. eutropha was defined at the species and the strain level using PCR and gene sequencing methodologies. The species level was defined as N. eutropha by sequencing of the V1-V5 variable regions of the 16S rRNA gene. N. eutropha was defined as a novel N. eutropha strain D23 by identification of a unique gene from whole genome sequence analysis. N. eutropha was defined at the species level as N. eutropha by 16S rRNA gene sequencing using the MicroSeq 500 rDNA Bacterial Identification PCL and sequencing kit.
Strain identity may be determined using custom primers, which correspond to the underlined portions of the following sequence and the D23 1c1355 sequence & primers Table 14 below. While not wishing to be bound by theory, it is believed that gene D23 1c1355 is unique to N. eutropha D23, and thus performing a PCR amplification reaction within gene D23 1c1355 will indicate whether N. eutropha D23 is present in a given sample.





TABLE 14



D23_1c1355 sequence & primers











Product



Tm
Posi-
size

Primer
Sequence (5′-3′)
(° C.)
tion
(bp)



D23_
AATCTGTCTCCACAGGCAGC
54
287-305
595

1c1355-F
(SEQ ID NO: 64)






D23_
TATACCCACCACCCACGCTA
54
881-862


1c1355-R
(SEQ ID NO: 65)
































D23_1c1355 outer membrane autotransporter

barrel domain-containing protein

(SEQ ID NO: 66)

TTGGTTGGTTTGAAACAGGTAAGGGAGAAGGAGGAAAATCGCCAGAATAT

10 20 30 40 50



CGTCGCCAAAGGTTATCGGATCACCATAGCTTATCCACTCAAAGGGGAGA

60 70 80 90 100



TTATCATGAGCAAGGTTCGTCGATTAAAAAAGAGTTTATATACGGTTACT

110 120 130 140 150



GCACTAACTCTCGGTTTCGGACCATTTGTGACAGCGAGTGGACAATCATT

160 170 180 190 200



CGAAGAAACACCCGTACAAACACCCGGACGAGCTTTTGCAGTGGACAATT

210 220 230 240 250



TAAAGGGTATCTGTGTACAAAACACAAGTGAAGACCCCTCATTAGCAATA

260 270 280 290 300



GCTTGCACCTTCGCACTGGGCGGGATAAATGATATTACCGCGCAG AATCT

310 320 330 340 350



GTCTCCACAGGCAGC GATTCAGGCCGAGTCGATCGCGATTACTTCTCCCT

360 370 380 390 400



ATCAGTTTATTCGCAGCACGAATGAAAGCATACAGCGGCTAACAGGTCGC

410 420 430 440 450



TCTGCTGAGAAACGTCAGCAACAATCCTCTTTTTTACTACAAAGCTCAGC

460 470 480 490 500



GTCGGTAGCAGGCACGCCATCATTTGGCACTTCTGGTTTTATAGGGCCTG

510 520 530 540 550



TAGGGGTTTCGCTGAGCGGTGGCGGGAGCTTTGGTGAACGCAATACCGCT

560 570 580 590 600



GAAGGGCAGACCGGTTTTCAATTGAATACCCGGCAAACCAGCCTGATGAT

610 620 630 640 650



CGATTATTCATTTAATCAAAAATTGATTGGCGGCTTTTCCTTTAATTATC

660 670 680 690 700



TGGGGACAGATCGTAATTTGAGATTGGCGAGTGGGGACTTGAATTCCGAT

710 720 730 740 750



AGCTATCGGTTTGCACCCTTTGTGCTTTTCAGACCAACTACCAATAGCTA

760 770 780 790 800



CTTAACTCTGATGGGAGGGTATGCTTTGGTTAATTATCGTTCCACGCGCA

810 820 830 840 850



GCGTTTCGAGTCAAAATGACATCACGTTTGATAACGCCACAGCCAACTAT

860 870 880 890 900



GATGCTAATCAGTTTTTTGC TAGCGTGGGTGGTGGGTATA CCTTTACTTT

910 920 930 940 950



AATGGATGGATGGAATCTGCGAGGATATGGTCGCGGGGACTTTAGTGATA

960 970 980 990 1000



TTAGTATCCAGAGCTTTCAGGAAAAAGGTGGCGTTGCTCATAGTGGGAAC

1010 1020 1030 1040 1050



GATAGTTTATCTCTTGCTATGTCTGTGAATAAACAAACCATACGCTCGGT

1060 1070 1080 1090 1100



TACCAGTACATTAGGCGTTGAACTTAGTCATGCAATTAGCACCAGAACTT

1110 1120 1130 1140 1150



TTATTCCCGTCATTATCCCGAGACTGCGTGCAGAATGGGTGCATGAATTT

1160 1170 1180 1190 1200



GAAAACAATGCCAGAACTATCACGGCCGGTTTCACTGGCCAGAACTATAG

1210 1220 1230 1240 1250



TCCCACTTCTGCATCAATGGCAGTTGCAAGCTCAGTGCGTAATTGGGCAA

1260 1270 1280 1290 1300



ACCTGGGGGTTGGAGTGCAAATGCTGTTTGCCCGCTCGATTATCGGGTAC

1310 1320 1330 1340 1350



ATTAATTACGACAGATTAATTATCAAGCACGCGGAGAACAATATCATTTC

1360 1370 1380



TGGTGGGATTCGTATGAATTTCTAA































































































Example 10
Administering Ammonia Oxidizing Bacteria to the Back of the Head to Change the Skin Microbiome
Ammonia oxidizing bacteria ( N. eutropha D23) was applied topically to the back of the head of a subject for over 2 weeks. The dose was 3×10 10 CFU applied per day. The product concentration was 1×10 9 CFU/ml (15 ml, two times a day) in a phosphate buffer with magnesium chloride. On each day a skin swab was taken to isolate and sequence all the bacterial DNA that was present, using isolation and sequencing protocols known in the art.
Ammonia oxidizing bacteria of the genus Nitrosomonas was not present in the Day 0 sample, and was detected and present in the Day 7, 14, and 16 skin swabs.
As shown in FIGS. 17 and 18 , which plots the proportion versus bacterial genus for Day 0, 1, 8, 14, and 16, the application of ammonia oxidizing bacteria led to proportional increases in commensal non-pathogenic Staphylococcus (which was at least 98% Staphylococcus epidermidis ) from close to 0% on day 0 to approximately 50% on day 16. Additionally, application of ammonia oxidizing bacteria led to a proportional reduction in potentially pathogenic or disease associated Propionibacteria over the time period tested (from over 75% on day 0 to less than 50% on day 16). Application of ammonia oxidizing bacteria also led to reductions in potentially pathogenic or disease associated Stenotrophomonas over the time period tested (from 0.1% on day 0 to less than 0.01% on day 16.)
Some of the data shown in FIGS. 1 and 2 is also presented below in Table 15.





TABLE 15



Genera by Day









Proportion
Proportion
Proportion



by genus:
by genus:
by genus:


Day

Propionibacteria


Staphylococci


Stenotrophomonas












0
0.78
0.01
0.13


1
0.79
0.1
0


8
0.8
0.15
0


14
0.55
0.45
0.001


16
0.48
0.49
0































As shown in Table 15, the proportion of Propionibacteria was reduced after about 14 days (compare data for Day 0, 1, and 8 with Day 14 and 16 in Table 15). The proportion of Staphylococci increased after about two weeks (compare data for Day 0, 1, and 8 with Day 14 and 16 in Table 15). The proportion of Stenotrophomonas decreased after about 1 day (compare data for Day 0 with Day 1, 8, 14, and 16 in Table 15).
These changes in the skin microbiome composition to a less pathogenic state indicate that application of ammonia oxidizing bacteria would be useful in treatment of dermatologic diseases including but not limited to acne, eczema, skin infections, and rosacea.
Example 11
Studies with Ammonia-Oxidizing Bacteria for the Human Skin: Cosmetic Effects, Safety, Detection and Skin Metagenomics
A blinded, placebo-controlled 24 human volunteer study randomized 4:1 AOB to placebo control was performed. Subjects applied a Nitrosomonas suspension (10 9 CFU/ml, 2 times per day, for a total of 3×10 10 CFU per day) to their face and scalp twice daily for one week and were followed for two additional weeks post-application. Volunteers were instructed to refrain from using hair products during the one-week AOB application as well as the week following application, then returned to regular shampoo use for the third week. Scalp swabs were obtained on Day 0 as baseline controls and on Day 1, 3, 8, 14 and 21 to assess presence/absence of AOB by PCR and 16S rRNA sequencing analyses.
No serious adverse events were associated with AOB application for one week and the product was deemed safe. AOB users reported a clear improvement in skin condition and quality, as indicated by self-assessment reports completed after the seven-day application period. Using AOB-specific PCR analyses of the skin samples, we could demonstrate presence of the bacteria in 83-100% of AOB users during the application period, whereas no AOB were detected in the placebo control samples. All subjects lacked AOB from baseline swabs obtained prior to study initiation, consistent with the predicted sensitivity of these bacteria to soaps and other commercial products. Amplification of the 16S rRNA gene and sequencing of a subset of samples confirmed presence of AOB in corresponding samples and suggested potential trends in modulating the skin microbiome by topical AOB application. In summary, live AOB-based products are safe and could hold great promise as novel self-regulating topical delivery agents of nitrite and nitric oxide to the human skin.
As shown in Table 16, below, the proportion of Nitrosomonas (AOB) went up when comparing Day 0 versus Day 8. The proportion of other bacteria, Propionibacterium, Enterobacter , and Citrobacter went down, when comparing Day 0 versus Day 8. The p-values indicated in Table 16 demonstrate that the most significant change between Day 0 and Day 8 was observed with Nitrosomonas (AOB) followed by Propionibacterium. Enterobacter and Citrobacter also showed changes between Day 0 and Day 8 to a lesser degree.





TABLE 16



Trends in microbiome composition following AOB application

(Day 0 versus Day 8)







Genus
P-value (unadjusted)
Trend





Nitrosomonas (AOB)
0.0039
Up



Propionibacterium

0.0078
Down



Enterobacter

0.0346
Down



Citrobacter

0.036
Down


























Because nitrite and nitric oxide have been implicated in critical physiological functions, such as vasodilation, skin inflammation and wound healing, we have hypothesized that AOB may have beneficial effects on both healthy and immunopathological skin conditions by metabolizing ammonia from sweat while concurrently driving skin acidification. We reasoned that Nitrosomonas would be safe for human use because they are slow-growing and incapable of utilizing organic carbon sources, they are sensitive to antibiotics, and they have never been linked to animal or human disease. Here we describe a blinded, placebo-controlled 24 human volunteer study where subjects applied a live Nitrosomonas suspension to their face and scalp twice daily for one week and were subsequently followed for two additional weeks. Volunteers did not use hair products during the first and second week, then they returned to their regular routine for the third week. Scalp swabs were obtained on Day 0 as baseline controls and on Day 1, 3, 8, 14 and 21 to assess presence/absence of Nitrosomonas and to examine microbial diversity. Importantly, no adverse events were associated with topical application. PCR analyses demonstrated presence of the bacteria in 83%-100% of skin swabs obtained from AOB users during or immediately after completion of the one-week application period (Day 1, 3 or 8) and in 60% of the users on Day 14, but not in any of the placebo control samples. All subjects lacked AOB from baseline swabs obtained prior to study initiation. Increased levels of AOB during the one-week application period correlated with a qualitative improvement in skin condition, in contrast to no improvement reported by placebo control subjects. Sequencing of the 16S rRNA gene amplification product obtained from a subset of subjects verified the presence of AOB in corresponding samples and suggested potential modulation of the skin microbiome composition. In summary, live Nitrosomonas are well tolerated and may hold promise as novel self-regulating topical delivery agents of nitrite and nitric oxide to the human skin.
Here, we present the results from preliminary studies in humans where we have begun evaluating topical application of a Nitrosomonas suspension to the human skin and the potential of using AOB as natural delivery systems of NO/NO 2 − in vivo. We have explored methodologies for AOB detection in skin specimens and the possible effects of AOB in skin microbial communities, as well as collected important user feedback from the early adopters of our topical cosmetic.
Methods
Culture Conditions.
N. eutropha D23 was propagated in batch culture at 28-30° C. in mineral salt medium supplemented with 20-50 mM NH 4 + and sodium carbonate as the carbon source [Ensign et al, 1993]. For continuous culture, D23 was grown at ˜10 9 cells/ml in a 1 liter mini-Bioreactor (Applikon Biotechnology) at 28° C. using sodium carbonate for both pH neutralization and the carbon source.
Nitrite Quantification.
Nitrite concentrations in culture supernatants were determined using the Griess colorimetric assay [Hageman and Kucklesby, 1971] and sodium nitrite as standards.
DNA Extraction from Skin Swabs.
Samples were maintained in 1 ml of 10% AssayAssure Bioservative (Thermo Scientific) diluted in PBS. Biomass was centrifuged and cells were lysed using a method developed for skin specimens [Grice, 2009] with modifications to the buffer designed to maintain long DNA integrity. DNA was then purified using the PowerLyzer UltraClean microbial DNA isolation kit (Mo Bio Laboratories). N. eutropha D23 was identified using a 3-gene PCR signature amplifying the ammonia monooxygenase encoding locus amoCAB.
PCR and Library Preparation.
Full-length 16S rRNA genes were amplified in duplicate reactions using a cocktail of primers and AccuPrime DNA polymerase SuperMix kit (Life Technologies). All PCR products were directly treated with the SMRTbell Template Prep Kit followed by the DNA/Polymerase Binding Kit P4 (Pacific Biosciences).
16S rDNA Sequencing and Analysis.
PCR products were sequenced using the Pacific Biosciences RS instrument [Eid, 2009]. Raw base calls were transformed to consensus DNA sequences using the Pacific Biosciences Consensus Tools package and then processed with the Whole Biome Microbiome Profiling Platform to obtain phylum-genus and strain-level frequency measures for each sample.
Human Volunteer Study.
A total of 24 male volunteers were included in a blinded, placebo-controlled, study each for a total of three weeks according to a protocol for topical AOB-001 use approved by the Allendale Institutional Review Board (Old Lyme, Conn.). Written informed consent was obtained from each study participant. Subjects applied 15 ml of an aqueous suspension of N. eutropha (AOB-001), or placebo (vehicle), twice daily containing ˜10 9 cells/ml.
The human volunteer study design for the preliminary evaluation of a Nitrosomonas -containing topical suspension (AOB-001) is shown in FIG. 5K . Detection of AOB was performed by PCR in scalp swab samples. FIG. 5L shows PCR analyses of scalp swabs collected during the study. The left panel indicates the percent-positive samples for AOB-specific three-gene signature (amoA, amoB, amoC). The right panel indicates the Composite PCR scores for a total of six samples collected from each of 23 volunteers. The scoring scheme used for the positive samples collected at each of six sampling points is indicated.
Skin microbiome composition prior and during AOB-001 application were obtained by 16S rDNA sequencing. FIG. 5M indicates that genus-level bacterial diversity as determined by 16S rDNA sequencing in skin swab samples collected before and after topical application of AOB-001.
The percentage of the total sequence reads representing each of twelve bacterial genera in samples collected at baseline prior to application (Day 0) and immediately after the one week application (Day 8), or one week after stopping topical application (Day 14), are shown.
FIG. 5N indicates changes in abundance of Nitrosomonas and other species in skin samples collected before and after AOB-001 application. Panel A shows percentages of the total 16S rDNA sequence reads representing Nitrosomonas prior to application (Day 0), immediately after the one-week application (Day 8), or one week after terminating application (Day 14) are shown. Panel B shows a change in patterns in abundance of species detected by 16S rDNA sequencing in Day 0 versus Day 8 samples collected from AOB users.
AOB-001 users report an improvement in skin condition. FIG. 5O shows a user evaluation of AOB-001. Assessment of AOB-001 cosmetic effects was provided by 23 volunteers upon completion of the one week application to their scalp and face. Subjects were plotted in order of increasing composite PCR scores. (The responses were categorized as 2=agree strongly; 0=no change; −2=disagree strongly). In summary, AOB-001 is well-tolerated. The user responses in a blind study indicate improved skin/scalp condition. AOB ( Nitrosomonas ) are readily detectable in skin microbiome samples by PCR and 16S rRNA gene sequencing. Preliminary microbiome analyses indicate modulation of skin microbiota by AOB.





SUPPLEMENTARY TABLE 1



Annotation of genes in SEQ ID NO: 1.













Feature





Length


D23
C91

ID
Type
Start
Stop
Frame
Strand
(bp)
Function
Subsystem
Gbkld
Alias















fig|6666666.60966.peg.1
CDS
35
1414
2
+
1380
Chromosomal
Cell Division Subsystem
D23_1c0001
Neut_0001








replication initiator
including YidCD;










protein DnaA
<br>DNA replication











cluster 1



fig|6666666.60966.peg.2
CDS
1619
2740
2
+
1122
DNA polymerase III beta
Cell Division Subsystem
D23_1c0002
Neut_0002








subunit (EC 2.7.7.7)
including YidCD;











<br>DNA replication











cluster 1



fig|6666666.60966.peg.3
CDS
2798
5227
2
+
2430
DNA gyrase subunit B
Cell Division Subsystem
D23_1c0003
Neut_0003








(EC 5.99.1.3)
including YidCD;











<br>DNA gyrase











subunits; <br>DNA











replication cluster 1;











<br>DNA











topoisomerases, Type II,











ATP-dependent;











<br>Resistance to











fluoroquinolones



fig|6666666.60966.peg.4
CDS
5248
5691
1
+
444
FIG039061:
-none-
D23_1c0004
Neut_0004








hypothetical protein











related to heme











utilization




fig|6666666.60966.peg.5
CDS
5748
6479
3
+
732
tRNA pseudouridine
Colicin V and Bacteriocin
D23_1c0005
Neut_0005








synthase A (EC 4.2.1.70)
Production Cluster;











<br>RNA pseudouridine











syntheses; <br>tRNA











modification Bacteria;











<br>tRNA processing



fig|6666666.60966.peg.6
CDS
7261
7518
1
+
258
4Fe—4S ferredoxin, iron-
Inorganic Sulfur
D23_1c0009
Neut_0127








sulfur binding
Assimilation



fig|6666666.60966.peg.7
CDS
7584
7946
3
+
363
FIG00858425:
-none-
D23_1c0010
Neut_0128








hypothetical protein




fig|6666666.60966.peg.8
CDS
11430
7966
−3
−
3465
Transcription-repair
Transcription factors
D23_1c0011
Neut_0129








coupling factor
bacterial;











<br>Transcription repair











cluster



fig|6666666.60966.peg.9
CDS
12737
11457
−2
−
1281
InterPro IPR003416
-none-
D23_1c0012
Neut_0130








COGs COG3174




fig|6666666.60966.peg.10
CDS
14499
12730
−3
−
1770
Single-stranded-DNA-
DNA Repair Base
D23_1c0013
Neut_0131








specific exonuclease
Excision










RecJ (EC 3.1.—.—)




fig|6666666.60966.peg.11
CDS
15277
14681
−1
−
597
InterPro IPR000345
-none-
D23_1c0014
Neut_0132

fig|6666666.60966.peg.12
CDS
16285
15365
−1
−
921
Indole-3-glycerol
Chorismate:
D23_1c0015
Neut_0133








phosphate synthase (EC
Intermediate for










4.1.1.48)
synthesis of Tryptophan,











PAPA antibiotics, PABA,











3-hydroxyanthranilate











and more.;











<br>Tryptophan











synthesis



fig|6666666.60966.peg.13
CDS
17321
16296
−2
−
1026
Anthranilate
Auxin biosynthesis;
D23_1c0016
Neut_0134








phosphoribosyltransferase
<br>Chorismate:










(EC 2.4.2.18)
Intermediate for











synthesis of Tryptophan,











PAPA antibiotics, PABA,











3-hydroxyanthranilate











and more.;











<br>Tryptophan











synthesis



fig|6666666.60966.peg.14
CDS
17920
17318
−1
−
603
Anthranilate synthase,
Chorismate:
D23_1c0017
Neut_0135








amidotransferase
Intermediate for










component (EC
synthesis of Tryptophan,










4.1.3.27)
PAPA antibiotics, PABA,











3-hydroxyanthranilate











and more.;











<br>Tryptophan











synthesis



fig|6666666.60966.peg.15
CDS
18046
19545
1
+
1500
Putative sensor-like
-none-
D23_1c0018
Neut_0136








histidine kinase YfhK




fig|6666666.60966.peg.16
CDS
19644
20081
3
+
438
FIG00858754:
-none-
D23_1c0019
Neut_0137








hypothetical protein




fig|6666666.60966.peg.17
CDS
20101
21465
1
+
1365
Putative sensory
-none-
D23_1c0020
Neut_0138








histidine kinase YfhA




fig|6666666.60966.peg.18
CDS
22742
21474
−2
−
1269
PDZ/DHR/GLGF domain
-none-
D23_1c0021
Neut_0139








protein




fig|6666666.60966.peg.19
CDS
26700
22798
−3
−
3903
Phosphoribosylformylglycinamidine
De Novo Purine
D23_1c0022
Neut_0140








synthase,
Biosynthesis; <br>De










synthetase subunit (EC
Novo Purine










6.3.5.3)/
Biosynthesis










Phosphoribosylformylglycinamidine











synthase,











glutamine











amidotransferase











subunit (EC 6.3.5.3)




fig|6666666.60966.peg.20
CDS
26942
28510
2
+
1569
hypothetical protein
-none-
D23_1c0023
Neut_0141

fig|6666666.60966.peg.22
CDS
28682
28867
2
+
186
hypothetical protein
-none-
D23_1c0024
NA

fig|6666666.60966.peg.23
CDS
29060
28851
−2
−
210
Death on curing
Phd-Doc, YdcE-YdcD
D23_1c0025
NA








protein, Doc toxin
toxin-antitoxin











(programmed cell death)











systems



fig|6666666.60966.peg.24
CDS
29367
29227
−3
−
141
Prevent host death
Phd-Doc, YdcE-YdcD
D23_1c0026
Neut_0143








protein, Phd antitoxin
toxin-antitoxin











(programmed cell death)











systems



fig|6666666.60966.peg.25
CDS
29726
30082
2
+
357
blr1219; hypothetical
-none-
D23_1c0028
Neut_0144








protein




fig|6666666.60966.peg.26
CDS
30113
31672
2
+
1560
NAD(P)HX epimerase/
YjeE; <br>YjeE
D23_1c0029
Neut_0145








NAD(P)HX dehydratase




fig|6666666.60966.peg.29
CDS
31959
32078
3
+
120
hypothetical protein
-none-
D23_1c0030
NA

fig|6666666.60966.peg.30
CDS
32096
32914
2
+
819
O-antigen export
-none-
D23_1c0031
Neut_0146








system permease











protein RfbD




fig|6666666.60966.peg.31
CDS
33063
33266
3
+
204
hypothetical protein
-none-
D23_1c0032
Neut_0147

fig|6666666.60966.peg.32
CDS
33441
33995
3
+
555
hypothetical protein
-none-
D23_1c0033
Neut_0148

fig|6666666.60966.peg.33
CDS
34044
34424
3
+
381
hypothetical protein
-none-
D23_1c0034
NA

fig|6666666.60966.peg.34
CDS
34530
35588
3
+
1059
putative transposase
-none-
D23_1c0035
Neut_0149

fig|6666666.60966.peg.36
CDS
36348
36064
−3
−
285
HigA protein (antitoxin
Toxin-antitoxin replicon
D23_1c0037
Neut_0150








to HigB)
stabilization systems



fig|6666666.60966.peg.37
CDS
36621
36379
−3
−
243
HigB toxin protein
Toxin-antitoxin replicon
D23_1c0038
Neut_0151









stabilization systems



fig|6666666.60966.peg.38
CDS
36580
36750
1
+
171
hypothetical protein
-none-
D23_1c0039
NA

fig|6666666.60966.peg.39
CDS
36747
38108
3
+
1362
Teichoic acid export
Rhamnose containing
D23_1c0040
Neut_0152








ATP-binding protein
glycans










TagH (EC 3.6.3.40)




fig|6666666.60966.peg.40
CDS
38105
42433
2
+
4329
Glycosyl transferase,
-none-
D23_1c0041
Neut_0153








group 2 family protein




fig|6666666.60966.peg.41
CDS
42537
43733
3
+
1197
glycosyl transferase,
-none-
D23_1c0042
NA








group 1/2 family











protein




fig|6666666.60966.peg.42
CDS
43945
44838
1
+
894
Alpha-L-Rha alpha-1,3-
Rhamnose containing
D23_1c0043
Neut_0166








L-rhamnosyltransferase
glycans










(EC 2.4.1.—)




fig|6666666.60966.peg.43
CDS
45457
45140
−1
−
318
HigA protein (antitoxin
Toxin-antitoxin replicon
D23_1c0044
Neut_0167








to HigB)
stabilization systems



fig|6666666.60966.peg.44
CDS
45610
45470
−1
−
141
HigB toxin protein
Toxin-antitoxin replicon
D23_1c0045
Neut_0168









stabilization systems



fig|6666666.60966.peg.45
CDS
45950
46279
2
+
330
Glycosyl transferase,
-none-
D23_1c0046
Neut_0169








group 2 family protein




fig|6666666.60966.peg.47
CDS
47082
46804
−3
−
279
hypothetical protein
-none-
D23_1c0047
NA

fig|6666666.60966.peg.49
CDS
48719
47757
−2
−
963
Mobile element protein
-none-
D23_1c0049
Neut_0978

fig|6666666.60966.peg.50
CDS
48899
48777
−2
−
123
Mobile element protein
-none-
D23_1c0050
Neut_0357

fig|6666666.60966.peg.51
CDS
49218
48970
−3
−
249
Mobile element protein
-none-
D23_1c0051
Neut_2405

fig|6666666.60966.peg.52
CDS
49615
49502
−1
−
114
hypothetical protein
-none-
D23_1c0052
NA

fig|6666666.60966.peg.53
CDS
49842
50255
3
+
414
Nucleotidyltransferase
-none-
D23_1c0053
Neut_0172








(EC 2.7.7.—)




fig|6666666.60966.peg.54
CDS
50257
50622
1
+
366
Nucleotidyltransferase
-none-
D23_1c0054
Neut_0173








(EC 2.7.7.—)




fig|6666666.60966.peg.55
CDS
51293
50880
−2
−
414
Mobile element protein
-none-
D23_1c0056
NA

fig|6666666.60966.peg.56
CDS
51432
51253
−3
−
180
hypothetical protein
-none-
D23_1c0057
Neut_0176

fig|6666666.60966.peg.57
CDS
51530
52492
2
+
963
Mobile element protein
-none-
D23_1c0058
Neut_1746

fig|6666666.60966.peg.58
CDS
52657
52908
1
+
252
Mobile element protein
-none-
D23_1c0059
Neut_0884

fig|6666666.60966.peg.59
CDS
52964
53326
2
+
363
Mobile element protein
-none-
D23_1c0060
Neut_2499

fig|6666666.60966.peg.60
CDS
54452
53361
−2
−
1092
putative transposase
-none-
D23_1c0061
Neut_0177

fig|6666666.60966.peg.61
CDS
54765
54430
−3
−
336
FIG00859125:
-none-
D23_1c0062
Neut_0178








hypothetical protein




fig|6666666.60966.peg.62
CDS
55016
55774
2
+
759
dTDP-Rha:A-D-GlcNAc-
dTDP-rhamnose
D23_1c0063
Neut_0179








diphosphoryl
synthesis










polyprenol, A-3-L-











rhamnosyl transferase











WbbL




fig|6666666.60966.peg.63
CDS
56735
55788
−2
−
948
UDP-glucose 4-
CBSS-
D23_1c0064
Neut_0180








epimerase (EC 5.1.3.2)
296591.1.peg.2330;











<br>N-linked











Glycosylation in











Bacteria; <br>Rhamnose











containing glycans



fig|6666666.60966.peg.64
CDS
56874
56746
−3
−
129
hypothetical protein
-none-
D23_1c0065
NA

fig|6666666.60966.peg.65
CDS
60470
57075
−2
−
3396
Adenylate cyclase (EC
cAMP signaling in
D23_1c0066
Neut_0181








4.6.1.1)/Guanylate
bacteria










cyclase (EC 4.6.1.2)




fig|6666666.60966.peg.66
CDS
60633
60755
3
+
123
hypothetical protein
-none-
D23_1c0067
NA

fig|6666666.60966.peg.67
CDS
62853
60769
−3
−
2085
Ubiquinone
Ubiquinone
D23_1c0068
Neut_0182








biosynthesis
Biosynthesis;










monooxygenase UbiB
<br>Ubiquinone











Biosynthesis-gjo



fig|6666666.60966.peg.68
CDS
63084
63821
3
+
738
hypothetical protein
-none-
D23_1c0069
Neut_0183

fig|6666666.60966.peg.69
CDS
64515
66023
3
+
1509
CBSS-
-none-
D23_1c0070
NA








498211.3.peg.1514:











hypothetical protein




fig|6666666.60966.peg.70
CDS
66074
66751
2
+
678
FIG039767:
-none-
D23_1c0071
NA








hypothetical protein




fig|6666666.60966.peg.71
CDS
66741
70157
3
+
3417
FIG007317:
-none-
D23_1c0072
NA








hypothetical protein




fig|6666666.60966.peg.72
CDS
70190
71326
2
+
1137
FIG005429:
-none-
D23_1c0073
Neut_0184








hypothetical protein




fig|6666666.60966.peg.73
CDS
71379
71939
3
+
561
Lipid carrier: UDP-N-
CBSS-
D23_1c0074
Neut_0185








acetylgalactosaminyltransferase
296591.1.peg.2330;










(EC 2.4.1.—)
<br>N-linked











Glycosylation in Bacteria



fig|6666666.60966.peg.74
CDS
71949
73931
3
+
1983
Nucleoside-diphosphate
CBSS-296591.1.peg.2330
D23_1c0075
Neut_0186








sugar











epimerase/dehydratase




fig|6666666.60966.peg.75
CDS
74467
73949
−1
−
519
cytidine and
-none-
D23_1c0076
Neut_0187








deoxycytidylate











deaminase family











protein




fig|6666666.60966.peg.76
CDS
74956
74594
−1
−
363
Mobile element protein
-none-
D23_1c0077
Neut_2499

fig|6666666.60966.peg.77
CDS
75263
75012
−2
−
252
Mobile element protein
-none-
D23_1c0078
Neut_0884

fig|6666666.60966.peg.78
CDS
75586
76446
1
+
861
Flagellar motor rotation
Flagellar motility;
D23_1c0079
Neut_0188








protein MotA
<br>Flagellum



fig|6666666.60966.peg.79
CDS
76489
77433
1
+
945
Flagellar motor rotation
Flagellar motility;
D23_1c0080
Neut_0189








protein MotB
<br>Flagellum



fig|6666666.60966.peg.80
CDS
77408
78205
2
+
798
FIG00858624:
-none-
D23_1c0081
Neut_0190








hypothetical protein




fig|6666666.60966.peg.81
CDS
79621
78218
−1
−
1404
Cysteinyl-tRNA
Zinc regulated enzymes;
D23_1c0082
Neut_0191








synthetase (EC 6.1.1.16)
<br>tRNA











aminoacylation, Cys



fig|6666666.60966.peg.83
CDS
79830
80384
3
+
555
Peptidyl-prolyl cis-trans
Peptidyl-prolyl cis-trans
D23_1c0083
Neut_0192








isomerase PpiB (EC
isomerase;










5.2.1.8)
<br>Queuosine-











Archaeosine











Biosynthesis



fig|6666666.60966.peg.84
CDS
80403
80894
3
+
492
Peptidyl-prolyl cis-trans
Peptidyl-prolyl cis-trans
D23_1c0084
Neut_0193








isomerase PpiB (EC
isomerase;










5.2.1.8)
<br>Queuosine-











Archaeosine











Biosynthesis



fig|6666666.60966.peg.85
CDS
80972
81424
2
+
453
Rhodanese-related
-none-
D23_1c0085
Neut_0194








sulfurtransferase




fig|6666666.60966.peg.86
CDS
82260
81439
−3
−
822
Undecaprenyl-
-none-
D23_1c0086
Neut_0195








diphosphatase (EC











3.6.1.27)




fig|6666666.60966.peg.87
CDS
84206
82308
−2
−
1899
Thiamin biosynthesis
Thiamin biosynthesis
D23_1c0087
Neut_0196








protein ThiC




fig|6666666.60966.peg.88
CDS
84412
85068
1
+
657
Protein-L-isoaspartate
Protein-L-isoaspartate O-
D23_1c0088
Neut_0197








O-methyltransferase
methyltransferase;










(EC 2.1.1.77)
<br>Stationary phase











repair cluster; <br>Ton











and Tol transport











systems



fig|6666666.60966.peg.90
CDS
85216
86493
1
+
1278
Type I secretion outer
Multidrug Resistance
D23_1c0089
Neut_0198








membrane protein,
Efflux Pumps; <br>Ton










TolC precursor
and Tol transport











systems



fig|6666666.60966.peg.91
CDS
89009
86556
−2
−
2454
ATP-dependent
Proteasome bacterial;
D23_1c0090
Neut_0199








protease La (EC
<br>Proteolysis in










3.4.21.53) Type II
bacteria, ATP-dependent



fig|6666666.60966.peg.92
CDS
89253
89375
3
+
123
hypothetical protein
-none-
D23_1c0091
NA

fig|6666666.60966.peg.93
CDS
89433
89579
3
+
147
hypothetical protein
-none-
D23_1c0092
NA

fig|6666666.60966.peg.94
CDS
90769
89555
−1
−
1215
Serine--pyruvate
Photorespiration
D23_1c0093
Neut_0200








aminotransferase (EC
(oxidative C2 cycle);










2.6.1.51)/L-
<br>Pyruvate Alanine










alanine:glyoxylate
Serine Interconversions










aminotransferase (EC











2.6.1.44)




fig|6666666.60966.peg.95
CDS
93514
91088
−1
−
2427
ATP-dependent
Proteasome bacterial;
D23_1c0095
Neut_0201








protease La (EC
<br>Proteolysis in










3.4.21.53) Type I
bacteria, ATP-dependent



fig|6666666.60966.peg.96
CDS
94903
93620
−1
−
1284
ATP-dependent Clp
Proteasome bacterial;
D23_1c0096
Neut_0202








protease ATP-binding
<br>Proteolysis in










subunit ClpX
bacteria, ATP-dependent



fig|6666666.60966.peg.97
CDS
95607
94963
−3
−
645
ATP-dependent Clp
Proteasome bacterial;
D23_1c0097
Neut_0203








protease proteolytic
<br>Proteolysis in










subunit (EC 3.4.21.92)
bacteria, ATP-











dependent; <br>cAMP











signaling in bacteria



fig|6666666.60966.peg.98
CDS
96907
95591
−1
−
1317
Cell division trigger
Bacterial Cell Division
D23_1c0098
Neut_0204








factor (EC 5.2.1.8)




fig|6666666.60966.peg.99
CDS
97996
97241
−1
−
756
Short-chain
Transcription repair
D23_1c0100
Neut_0205








dehydrogenase/reductase
cluster










SDR




fig|6666666.60966.peg.100
CDS
99750
98107
−3
−
1644
Heat shock protein 60
GroEL GroES
D23_1c0101
Neut_0206








family chaperone GroEL




fig|6666666.60966.peg.101
CDS
100080
99790
−3
−
291
Heat shock protein 60
GroEL GroES
D23_1c0102
Neut_0207








family co-chaperone











GroES




fig|6666666.60966.peg.102
CDS
100244
101554
2
+
1311
Adenosylmethionine-8-
Biotin biosynthesis;
D23_1c0103
Neut_0208








amino-7-oxononanoate
<br>Biotin biosynthesis










aminotransferase (EC
Experimental; <br>Biotin










2.6.1.62)
synthesis cluster



fig|6666666.60966.peg.103
CDS
101561
102967
2
+
1407
Metallo-beta-lactamase
Bacterial RNA-
D23_1c0104
Neut_0209








family protein, RNA-
metabolizing Zn-










specific
dependent hydrolases;











<br>Ribonucleases in











Bacillus



fig|6666666.60966.peg.104
CDS
103374
103066
−3
−
309
Cytochrome c, class I
-none-
D23_1c0105
Neut_0210

fig|6666666.60966.peg.105
CDS
103536
104300
3
+
765
Exodeoxyribonuclease
DNA repair, bacterial
D23_1c0106
Neut_0211








III (EC 3.1.11.2)




fig|6666666.60966.peg.106
CDS
104347
105459
1
+
1113
Alanine dehydrogenase
Pyruvate Alanine Serine
D23_1c0107
Neut_0212








(EC 1.4.1.1)
Interconversions



fig|6666666.60966.peg.107
CDS
106118
105597
−2
−
522
Conserved
Tolerance to colicin E2
D23_1c0108
Neut_0213








uncharacterized protein











CreA




fig|6666666.60966.peg.109
CDS
107425
106253
−1
−
1173
Permeases of the major
-none-
D23_1c0109
Neut_0214








facilitator superfamily




fig|6666666.60966.peg.110
CDS
108032
107454
−2
−
579
Uncharacterized protein
-none-
D23_1c0110
Neut_0215








family UPF0016




fig|6666666.60966.peg.112
CDS
108821
109603
2
+
783
Ribulose-5-phosphate
-none-
D23_1c0113
Neut_0218








4-epimerase and











related epimerases and











aldolases




fig|6666666.60966.peg.113
CDS
109609
113274
1
+
3666
InterPro
-none-
D23_1c0114
Neut_0219








IPR000014:IPR001789:IPR002106:











IPR002570:IPR003594:











IPR003660:











IPR003661:IPR004358:IPR005467











COGs











COG0642




fig|6666666.60966.peg.114
CDS
113292
114485
3
+
1194
Succinyl-CoA ligase
TCA Cycle
D23_1c0115
Neut_0220








[ADP-forming] beta











chain (EC 6.2.1.5)




fig|6666666.60966.peg.115
CDS
114489
115364
3
+
876
Succinyl-CoA ligase
TCA Cycle
D23_1c0116
Neut_0221








[ADP-forming] alpha











chain (EC 6.2.1.5)




fig|6666666.60966.peg.116
CDS
115402
115722
1
+
321
FIG00858523:
-none-
D23_1c0117
Neut_0222








hypothetical protein




fig|6666666.60966.peg.117
CDS
115750
117177
1
+
1428
D-alanyl-D-alanine
CBSS-84588.1.peg.1247;
D23_1c0118
Neut_0223








carboxypeptidase (EC
<br>Metallocarboxypeptidases










3.4.16.4)
(EC 3.4.17.—);











<br>Murein Hydrolases;











<br>Peptidoglycan











Biosynthesis



fig|6666666.60966.peg.118
CDS
117265
118227
1
+
963
Mobile element protein
-none-
D23_1c0119
Neut_1278

fig|6666666.60966.peg.119
CDS
120193
120056
−1
−
138
hypothetical protein
-none-
D23_1c0120
NA

fig|6666666.60966.rna.5
RNA
118725
120255
3
+
1531
Small Subunit











Ribosomal RNA;
-none-
D23_1c0120









ssuRNA; SSU rRNA




fig|6666666.60966.peg.121
CDS
122376
122495
3
+
120
hypothetical protein
-none-
D23_1c0124
NA

fig|6666666.60966.peg.120
CDS
121863
121994
3
+
132
hypothetical protein
-none-
D23_1c0124
NA

fig|6666666.60966.rna.8
RNA
120652
123535
1
+
2884
Large Subunit
-none-
D23_1c0124









Ribosomal RNA;











IsuRNA; LSU rRNA




fig|6666666.60966.rna.9
RNA
123600
123716
3
+
117
5S RNA
-none-
D23_1c0126


fig|6666666.60966.peg.123
CDS
124878
124708
−3
−
171
hypothetical protein
-none-
D23_1c0127
NA

fig|6666666.60966.peg.124
CDS
125317
125496
1
+
180
hypothetical protein
-none-
D23_1c0129
Neut_0547

fig|6666666.60966.peg.125
CDS
125792
126799
2
+
1008
NAD-dependent
CBSS-296591.1.peg.2330
D23_1c0130
Neut_0225








epimerase/dehydratase




fig|6666666.60966.peg.126
CDS
126808
128082
1
+
1275
UDP-glucose
-none-
D23_1c0131
Neut_0226








dehydrogenase (EC











1.1.1.22)




fig|6666666.60966.peg.127
CDS
128985
128089
−3
−
897
Permeases of the
-none-
D23_1c0132
Neut_0227








drug/metabolite











transporter (DMT)











superfamily




fig|6666666.60966.peg.128
CDS
129078
130283
3
+
1206
N-succinyl-L,L-
Lysine Biosynthesis DAP
D23_1c0133
Neut_0228








diaminopimelate
Pathway, GJO scratch










aminotransferase











alternative (EC 2.6.1.17)




fig|6666666.60966.peg.129
CDS
130311
131132
3
+
822
2,3,4,5-
Lysine Biosynthesis DAP
D23_1c0134
Neut_0229








tetrahydropyridine-2,6-
Pathway, GJO scratch










dicarboxylate N-











succinyltransferase (EC











2.3.1.117)




fig|6666666.60966.peg.130
CDS
131322
131693
3
+
372
FIG00858507:
-none-
D23_1c0135
Neut_0230








hypothetical protein




fig|6666666.60966.peg.131
CDS
131801
132127
2
+
327
FIG00858507:
-none-
D23_1c0136
Neut_0231








hypothetical protein




fig|6666666.60966.peg.132
CDS
132190
132312
1
+
123
hypothetical protein
-none-
D23_1c0137
NA

fig|6666666.60966.peg.133
CDS
132314
133303
2
+
990
Biotin operon repressor/
Biotin biosynthesis;
D23_1c0138
Neut_0232








Biotin-protein ligase
<br>Biotin biosynthesis;










(EC 6.3.4.15)
<br>Biotin synthesis











cluster; <br>Biotin











synthesis cluster



fig|6666666.60966.peg.134
CDS
133331
134104
2
+
774
Pantothenate kinase
Coenzyme A
D23_1c0139
Neut_0233








type III, CoaX-like (EC
Biosynthesis;










2.7.1.33)
<br>Coenzyme A











Biosynthesis cluster



fig|6666666.60966.peg.135
CDS
134123
134794
2
+
672
GTP-binding protein
Universal GTPases
D23_1c0140
Neut_0234








EngB




fig|6666666.60966.peg.136
CDS
134938
135945
1
+
1008
Porphobilinogen
Heme and Siroheme
D23_1c0141
Neut_0235








synthase (EC 4.2.1.24)
Biosynthesis; <br>Zinc











regulated enzymes



fig|6666666.60966.peg.137
CDS
136861
136064
−1
−
798
Phosphate transport
High affinity phosphate
D23_1c0142
Neut_0236








ATP-binding protein
transporter and control










PstB (TC 3.A.1.7.1)
of PHO regulon;











<br>Phosphate











metabolism



fig|6666666.60966.peg.138
CDS
137797
136871
−1
−
927
Phosphate transport
High affinity phosphate
D23_1c0143
Neut_0237








system permease
transporter and control










protein PstA (TC
of PHO regulon;










3.A.1.7.1)
<br>Phosphate











metabolism



fig|6666666.60966.peg.139
CDS
138817
137876
−1
−
942
Phosphate transport
High affinity phosphate
D23_1c0144
Neut_0238








system permease
transporter and control










protein PstC (TC
of PHO regulon;










3.A.1.7.1)
<br>Phosphate











metabolism



fig|6666666.60966.peg.140
CDS
139048
139299
1
+
252
FIG00858998:
-none-
D23_1c0146
Neut_0239








hypothetical protein




fig|6666666.60966.peg.141
CDS
140580
139432
−3
−
1149
Cell division protein
Bacterial Cell Division;
D23_1c0147
Neut_0240








FtsZ (EC 3.4.24.—)
<br>Bacterial











Cytoskeleton; <br>cell











division cluster











containing FtsQ; <br>cell











division core of larger











cluster



fig|6666666.60966.peg.142
CDS
141909
140650
−3
−
1260
Cell division protein
Bacterial Cell Division;
D23_1c0149
Neut_0241








FtsA
<br>Bacterial











Cytoskeleton; <br>cell











division cluster











containing FtsQ; <br>cell











division core of larger











cluster



fig|6666666.60966.peg.143
CDS
142678
141950
−1
−
729
Cell division protein
Bacterial Cell Division;
D23_1c0150
Neut_0242








FtsQ
<br>Bacterial











Cytoskeleton; <br>cell











division cluster











containing FtsQ; <br>cell











division core of larger











cluster



fig|6666666.60966.peg.144
CDS
143654
142734
−2
−
921
D-alanine--D-alanine
Peptidoglycan
D23_1c0152
Neut_0243








ligase (EC 6.3.2.4)
Biosynthesis;











<br>Peptidoglycan











biosynthesis--gjo;











<br>cell division cluster











containing FtsQ



fig|6666666.60966.peg.145
CDS
144649
143651
−1
−
999
UDP-N-
Peptidoglycan
D23_1c0153
Neut_0244








acetylenolpyruvoylglucosamine
Biosynthesis; <br>UDP-










reductase (EC
N-acetylmuramate from










1.1.1.158)
Fructose-6-phosphate











Biosynthesis



fig|6666666.60966.peg.146
CDS
146080
144659
−1
−
1422
UDP-N-
Peptidoglycan
D23_1c0154
Neut_0245








acetylmuramate--
Biosynthesis;










alanine ligase (EC
<br>Peptidoglycan










6.3.2.8)
biosynthesis--gjo;











<br>cell division cluster











containing FtsQ



fig|6666666.60966.peg.147
CDS
147159
146077
−3
−
1083
UDP-N-
Peptidoglycan
D23_1c0155
Neut_0246








acetylglucosamine--N-
Biosynthesis; <br>cell










acetylmuramyl-
division core of larger










(pentapeptide)
cluster










pyrophosphoryl-











undecaprenol N-











acetylglucosamine











transferase (EC











2.4.1.227)




fig|6666666.60966.peg.148
CDS
148372
147212
−1
−
1161
Cell division protein
Bacterial Cell Division;
D23_1c0156
Neut_0247








FtsW
<br>Bacterial











Cytoskeleton; <br>cell











division cluster











containing FtsQ



fig|6666666.60966.peg.149
CDS
149789
148377
−2
−
1413
UDP-N-
Peptidoglycan
D23_1c0157
Neut_0248








acetylmuramoylalanine--
Biosynthesis;










D-glutamate ligase (EC
<br>Peptidoglycan










6.3.2.9)
biosynthesis--gjo



fig|6666666.60966.peg.150
CDS
150871
149786
−1
−
1086
Phospho-N-
Peptidoglycan
D23_1c0158
Neut_0249








acetylmuramoyl-
Biosynthesis










pentapeptide-











transferase (EC











2.7.8.13)




fig|6666666.60966.peg.151
CDS
152316
150943
−3
−
1374
UDP-N-
Peptidoglycan
D23_1c0159
Neut_0250








acetylmuramoylalanyl-
Biosynthesis;










D-glutamyl-2,6-
<br>Peptidoglycan










diaminopimelate--D-
biosynthesis--gjo










alanyl-D-alanine ligase











(EC 6.3.2.10)




fig|6666666.60966.peg.152
CDS
153875
152313
−2
−
1563
UDP-N-
Peptidoglycan
D23_1c0160
Neut_0251








acetylmuramoylalanyl-
Biosynthesis;










D-glutamate--2,6-
<br>Peptidoglycan










diaminopimelate ligase
biosynthesis--gjo










(EC 6.3.2.13)




fig|6666666.60966.peg.153
CDS
155545
153872
−1
−
1674
Cell division protein Ftsl
16S rRNA modification
D23_1c0161
Neut_0252








[Peptidoglycan
within P site of










synthetase] (EC
ribosome; <br>Bacterial










2.4.1.129)
Cell Division;











<br>Bacterial











Cytoskeleton; <br>CBSS-











83331.1.peg.3039;











<br>Flagellum in











Campylobacter ;











<br>Peptidoglycan











Biosynthesis



fig|6666666.60966.peg.155
CDS
155895
155608
−3
−
288
Cell division protein FtsL
16S rRNA modification
D23_1c0162
Neut_0253









within P site of











ribosome; <br>Bacterial











Cell Division;











<br>Bacterial











Cytoskeleton;











<br>Stationary phase











repair cluster



fig|6666666.60966.peg.156
CDS
156845
155892
−2
−
954
rRNA small subunit
16S rRNA modification
D23_1c0163
Neut_0254








methyltransferase H
within P site of











ribosome; <br>Bacterial











Cell Division



fig|6666666.60966.peg.157
CDS
157094
156861
−2
−
234
Cell division protein
16S rRNA modification
D23_1c0164
Neut_0255








MraZ
within P site of











ribosome; <br>Bacterial











Cell Division;











<br>Bacterial











Cytoskeleton



fig|6666666.60966.peg.158
CDS
157584
157859
3
+
276
DNA-3-methyladenine
DNA Repair Base
D23_1c0165
NA








glycosylase II (EC
Excision










3.2.2.21)




fig|6666666.60966.peg.159
CDS
158202
158420
3
+
219
Rho-specific inhibitor of
Transcription factors
D23_1c0166
Neut_0257








transcription
bacterial










termination (YaeO)




fig|6666666.60966.peg.160
CDS
159328
158561
−1
−
768
InterPro IPR001173
-none-
D23_1c0167
Neut_0258








COGs COG0463




fig|6666666.60966.peg.161
CDS
159475
159924
1
+
450
InterPro IPR000086
-none-
D23_1c0168
Neut_0259








COGs COG0494




fig|6666666.60966.peg.162
CDS
160257
160814
3
+
558
possible (U92432) ORF4
-none-
D23_1c0169
Neut_0260








[ Nitrosospira sp. NpAV]




fig|6666666.60966.peg.164
CDS
160969
161451
1
+
483
FIG00859298:
-none-
D23_1c0170
Neut_0261








hypothetical protein




fig|6666666.60966.peg.165
CDS
161593
162063
1
+
471
Adenine
Purine conversions;
D23_1c0171
Neut_0262








phosphoribosyltransferase
<br>cAMP signaling in










(EC 2.4.2.7)
bacteria



fig|6666666.60966.peg.166
CDS
162260
163573
2
+
1314
Seryl-tRNA synthetase
CBSS-
D23_1c0172
Neut_0263








(EC 6.1.1.11)
326442.4.peg.1852;











<br>Glycine and Serine











Utilization; <br>tRNA











aminoacylation, Ser



fig|6666666.60966.peg.167
CDS
163620
164306
3
+
687
FIG00858527:
-none-
D23_1c0173
Neut_0264








hypothetical protein




fig|6666666.60966.peg.168
CDS
165061
164351
−1
−
711
Phosphoglycerate
Glycolysis and
D23_1c0174
Neut_0265








mutase (EC 5.4.2.1)
Gluconeogenesis;











<br>Phosphoglycerate











mutase protein family



fig|6666666.60966.peg.169
CDS
166178
165111
−2
−
1068
InterPro IPR001225
-none-
D23_1c0175
Neut_0266

fig|6666666.60966.peg.170
CDS
166643
166200
−2
−
444
FIG00858776:
-none-
D23_1c0176
Neut_0267








hypothetical protein




fig|6666666.60966.peg.171
CDS
167465
166659
−2
−
807
CTP:Inositol-1-
-none-
D23_1c0177
Neut_0268








phosphate











cytidylyltransferase











(2.7.7.—)




fig|6666666.60966.peg.172
CDS
168669
167509
−3
−
1161
Cysteine desulfurase
Alanine biosynthesis;
D23_1c0178
Neut_0269








(EC 2.8.1.7)
<br>CBSS-











84588.1.peg.1247;











<br>mnm5U34











biosynthesis bacteria;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.174
CDS
169251
169631
3
+
381
FIG048548: ATP
-none-
D23_1c0180
Neut_0270








synthase protein I2




fig|6666666.60966.peg.175
CDS
169720
170472
1
+
753
ATP synthase A chain
-none-
D23_1c0181
Neut_0271








(EC 3.6.3.14)




fig|6666666.60966.peg.176
CDS
170516
170788
2
+
273
ATP synthase C chain
-none-
D23_1c0182
Neut_0272








(EC 3.6.3.14)




fig|6666666.60966.peg.177
CDS
170900
171301
2
+
402
ATP synthase B chain
-none-
D23_1c0183
Neut_0273








(EC 3.6.3.14)




fig|6666666.60966.peg.178
CDS
171302
171838
2
+
537
ATP synthase delta
-none-
D23_1c0184
Neut_0274








chain (EC 3.6.3.14)




fig|6666666.60966.peg.179
CDS
171851
173392
2
+
1542
ATP synthase alpha
-none-
D23_1c0185
Neut_0275








chain (EC 3.6.3.14)




fig|6666666.60966.peg.180
CDS
173396
174280
2
+
885
ATP synthase gamma
-none-
D23_1c0186
Neut_0276








chain (EC 3.6.3.14)




fig|6666666.60966.peg.181
CDS
174311
175693
2
+
1383
ATP synthase beta chain
-none-
D23_1c0187
Neut_0277








(EC 3.6.3.14)




fig|6666666.60966.peg.182
CDS
175842
176141
3
+
300
ATP synthase epsilon
-none-
D23_1c0188
Neut_0278








chain (EC 3.6.3.14)




fig|6666666.60966.peg.183
CDS
176389
177765
1
+
1377
N-acetylglucosamine-1-
Peptidoglycan
D23_1c0189
Neut_0279








phosphate
Biosynthesis;










uridyltransferase (EC
<br>Peptidoglycan










2.7.7.23)/
Biosynthesis; <br>Sialic










Glucosamine-1-
Acid Metabolism;










phosphate N-
<br>Sialic Acid










acetyltransferase (EC
Metabolism;










2.3.1.157)
<br>Transcription repair











cluster;











<br>Transcription repair











cluster; <br>UDP-N-











acetylmuramate from











Fructose-6-phosphate











Biosynthesis; <br>UDP-











N-acetylmuramate from











Fructose-6-phosphate











Biosynthesis



fig|6666666.60966.peg.184
CDS
177805
179652
1
+
1848
Glucosamine-fructose-
Sialic Acid Metabolism;
D23_1c0190
Neut_0280








6-phosphate
<br>UDP-N-










aminotransferase
acetylmuramate from










[isomerizing] (EC
Fructose-6-phosphate










2.6.1.16)
Biosynthesis



fig|6666666.60966.peg.185
CDS
179795
180520
2
+
726
FIG000859:
Riboflavin, FMN and FAD
D23_1c0191
Neut_0281








hypothetical protein
metabolism in plants;










YebC
<br>RuvABC plus a











hypothetical



fig|6666666.60966.peg.186
CDS
180523
181059
1
+
537
Crossover junction
RuvABC plus a
D23_1c0192
Neut_0282








endodeoxyribonuclease
hypothetical










RuvC (EC 3.1.22.4)




fig|6666666.60966.peg.187
CDS
181056
181640
3
+
585
Holliday junction DNA
RuvABC plus a
D23_1c0193
Neut_0283








helicase RuvA
hypothetical



fig|6666666.60966.peg.188
CDS
181659
182699
3
+
1041
Holliday junction DNA
RuvABC plus a
D23_1c0194
Neut_0284








helicase RuvB
hypothetical



fig|6666666.60966.peg.189
CDS
182760
183173
3
+
414
4-hydroxybenzoyl-CoA
Ton and Tol transport
D23_1c0195
Neut_0285








thioesterase family
systems










active site




fig|6666666.60966.peg.190
CDS
183166
183870
1
+
705
MotA/TolQ/ExbB
Ton and Tol transport
D23_1c0196
Neut_0286








proton channel family
systems










protein




fig|6666666.60966.peg.191
CDS
183867
184283
3
+
417
Tol biopolymer
Ton and Tol transport
D23_1c0197
Neut_0287








transport system, TolR
systems










protein




fig|6666666.60966.peg.192
CDS
184304
185200
2
+
897
TolA protein
Ton and Tol transport
D23_1c0198
Neut_0288









systems



fig|6666666.60966.peg.193
CDS
185239
186510
1
+
1272
tolB protein precursor,
Ton and Tol transport
D23_1c0199
Neut_0289








periplasmic protein
systems










involved in the tonb-











independent uptake of











group A colicins




fig|6666666.60966.peg.194
CDS
186565
187086
1
+
522
18K peptidoglycan-
Ton and Tol transport
D23_1c0200
Neut_0290








associated outer
systems










membrane lipoprotein;











Peptidoglycan-











associated lipoprotein











precursor; Outer











membrane protein P6;











OmpA/MotB precursor




fig|6666666.60966.peg.195
CDS
187086
187907
3
+
822
TPR repeat containing
Ton and Tol transport
D23_1c0201
Neut_0291








exported protein;
systems










Putative periplasmic











protein contains a











protein











prenylyltransferase











domain




fig|6666666.60966.peg.196
CDS
188060
188644
2
+
585
Queuosine Biosynthesis
Queuosine-Archaeosine
D23_1c0202
Neut_0292








QueE Radical SAM
Biosynthesis; <br>tRNA











modification Bacteria



fig|6666666.60966.peg.197
CDS
188666
189346
2
+
681
Queuosine Biosynthesis
Queuosine-Archaeosine
D23_1c0203
Neut_0293








QueC ATPase
Biosynthesis; <br>tRNA











modification Bacteria



fig|6666666.60966.peg.198
CDS
189700
189347
−1
−
354
Dihydroneopterin
Folate Biosynthesis
D23_1c0204
Neut_0294








aldolase (EC 4.1.2.25)




fig|6666666.60966.peg.199
CDS
189786
190388
3
+
603
Acyl-
Glycerolipid and
D23_1c0205
Neut_0295








phosphate:glycerol-3-
Glycerophospholipid










phosphate O-
Metabolism in Bacteria










acyltransferase PlsY




fig|6666666.60966.peg.200
CDS
191422
190406
−1
−
1017
TsaD/Kae1/Qri7
Bacterial RNA-
D23_1c0206
Neut_0296








protein, required for
metabolizing Zn-










threonylcarbamoyladenosine
dependent hydrolases;










t(6)A37 formation
<br>Macromolecular










in tRNA
synthesis operon;











<br>YgjD and YeaZ



fig|6666666.60966.peg.201
CDS
191698
191910
1
+
213
SSU ribosomal protein
Macromolecular
D23_1c0207
Neut_0297








S21p
synthesis operon



fig|6666666.60966.peg.202
CDS
191984
192391
2
+
408
Transamidase GatB
Macromolecular
D23_1c0208
Neut_0298








domain protein
synthesis operon



fig|6666666.60966.peg.203
CDS
192486
194279
3
+
1794
DNA primase (EC 2.7.7.—)
CBSS-
D23_1c0209
Neut_0299









349161.4.peg.2417;











<br>Macromolecular











synthesis operon



fig|6666666.60966.peg.204
CDS
194461
196710
1
+
2250
RNA polymerase sigma
CBSS-
D23_1c0210
Neut_0300








factor RpoD
349161.4.peg.2417;











<br>Flagellum;











<br>Macromolecular











synthesis operon;











<br>Transcription











initiation, bacterial











sigma factors



fig|6666666.60966.peg.206
CDS
197605
197180
−1
−
426
Mobile element protein
-none-
D23_1c0212
Neut_0357

fig|6666666.60966.peg.207
CDS
198088
198819
1
+
732
Mobile element protein
-none-
D23_1c0213
NA

fig|6666666.60966.peg.209
CDS
200235
199564
−3
−
672
transposase and
-none-
D23_1c0214
Neut_2192








inactivated derivatives




fig|6666666.60966.peg.210
CDS
200398
200210
−1
−
189
hypothetical protein
-none-
D23_1c0215
NA

fig|6666666.60966.peg.211
CDS
200852
200995
2
+
144
Mobile element protein
-none-
D23_1c0216
Neut_0978

fig|6666666.60966.peg.212
CDS
201848
200970
−2
−
879
Mobile element protein
-none-
D23_1c0217
Neut_1720

fig|6666666.60966.peg.213
CDS
202240
201947
−1
−
294
Mobile element protein
-none-
D23_1c0218
Neut_1719

fig|6666666.60966.peg.214
CDS
202367
203209
2
+
843
Mobile element protein
-none-
D23_1c0219
Neut_1524

fig|6666666.60966.peg.215
CDS
203592
203461
−3
−
132
Phage Rha protein
-none-
D23_1c0220
NA

fig|6666666.60966.peg.216
CDS
203906
203571
−2
−
336
Mobile element protein
-none-
D23_1c0221
Neut_2450

fig|6666666.60966.peg.218
CDS
204442
204113
−1
−
330
hypothetical protein
-none-
D23_1c0222
Neut_2449

fig|6666666.60966.peg.219
CDS
205381
204746
−1
−
636
Cytochrome c4
Soluble cytochromes
D23_1c0223
Neut_0305









and functionally related











electron carriers



fig|6666666.60966.peg.220
CDS
205494
206096
3
+
603
FIG00859469:
-none-
D23_1c0224
Neut_0306








hypothetical protein




fig|6666666.60966.peg.221
CDS
206204
207016
2
+
813
Methionine
CBSS-
D23_1c0225
Neut_0307








aminopeptidase (EC
312309.3.peg.1965;










3.4.11.18)
<br>Translation











termination factors











bacterial



fig|6666666.60966.peg.222
CDS
207076
207840
1
+
765
Ribonuclease PH (EC
Heat shock dnaK gene
D23_1c0226
Neut_0308








2.7.7.56)
cluster extended;











<br>tRNA processing



fig|6666666.60966.peg.223
CDS
207825
208439
3
+
615
Xanthosine/inosine
CBSS-630.2.peg.3360;
D23_1c0227
Neut_0309








triphosphate
<br>Heat shock dnaK










pyrophosphatase;
gene cluster extended










HAM1-like protein




fig|6666666.60966.peg.224
CDS
208474
209709
1
+
1236
Radical SAM family
CBSS-630.2.peg.3360;
D23_1c0228
Neut_0310








enzyme, similar to
<br>Heat shock dnaK










coproporphyrinogen III
gene cluster extended;










oxidase, oxygen-
<br>Heme and Siroheme










independent, clustered
Biosynthesis;










with nucleoside-
<br>Queuosine-










triphosphatase RdgB
Archaeosine











Biosynthesis



fig|6666666.60966.peg.225
CDS
209741
211540
2
+
1800
Multicopper oxidase
Copper homeostasis
D23_1c0229
Neut_0311

fig|6666666.60966.peg.226
CDS
211537
212352
1
+
816
Copper resistance
Copper homeostasis
D23_1c0230
Neut_0312








protein B




fig|6666666.60966.peg.227
CDS
213327
212398
−3
−
930
hypothetical protein
-none-
D23_1c0231
Neut_0313

fig|6666666.60966.peg.228
CDS
213918
213340
−3
−
579
LemA PROTEIN
-none-
D23_1c0232
Neut_1392

fig|6666666.60966.peg.229
CDS
214368
214553
3
+
186
Mobile element protein
-none-
D23_1c0233
Neut_2500

fig|6666666.60966.peg.230
CDS
214610
215206
2
+
597
Mobile element protein
-none-
D23_1c0234
Neut_1375

fig|6666666.60966.peg.231
CDS
215510
215623
2
+
114
hypothetical protein
-none-
D23_1c0235
NA

fig|6666666.60966.peg.232
CDS
215668
215847
1
+
180
hypothetical protein
-none-
D23_1c0236
Neut_0314

fig|6666666.60966.peg.233
CDS
217943
216069
−2
−
1875
Glutathione-regulated
Glutathione-regulated
D23_1c0237
Neut_0315








potassium-efflux system
potassium-efflux system










ATP-binding protein
and associated











functions;











<br>Potassium











homeostasis



fig|6666666.60966.peg.234
CDS
218233
219195
1
+
963
Mobile element protein
-none-
D23_1c0238
Neut_1862

fig|6666666.60966.peg.235
CDS
219960
219271
−3
−
690
InterPro IPR001687
-none-
D23_1c0239
NA

fig|6666666.60966.peg.236
CDS
220560
222266
3
+
1707
Glutathione-regulated
Glutathione-regulated
D23_1c0241
Neut_0318








potassium-efflux system
potassium-efflux system










protein KefB
and associated functions



fig|6666666.60966.peg.237
CDS
222848
223903
2
+
1056
SAM-dependent
-none-
D23_1c0242
Neut_0320








methyltransferase











SCO3452 (UbiE paralog)




fig|6666666.60966.peg.238
CDS
223971
224243
3
+
273
Phosphate transport
High affinity phosphate
D23_1c0244
Neut_0321








system permease
transporter and control










protein PstA (TC
of PHO regulon;










3.A.1.7.1)
<br>Phosphate











metabolism



fig|6666666.60966.peg.239
CDS
225095
224421
−2
−
675
tRNA (guanine46-N7-)-
RNA methylation;
D23_1c0245
Neut_0322








methyltransferase (EC
<br>tRNA modification










2.1.1.33)
Bacteria



fig|6666666.60966.peg.240
CDS
225934
225128
−1
−
807
Thiazole biosynthesis
Thiamin biosynthesis
D23_1c0246
Neut_0323








protein ThiG




fig|6666666.60966.peg.241
CDS
226194
225994
−3
−
201
Sulfur carrier protein
Thiamin biosynthesis
D23_1c0247
Neut_0324








ThiS




fig|6666666.60966.peg.242
CDS
226421
227008
2
+
588
FIG008443:
CBSS-208964.1.peg.1768
D23_1c0249
Neut_0325








hypothetical protein




fig|6666666.60966.peg.243
CDS
227005
228537
1
+
1533
FIG139976:
CBSS-208964.1.peg.1768
D23_1c0250
Neut_0326








hypothetical protein




fig|6666666.60966.peg.244
CDS
228587
229492
2
+
906
FIG002781: Alpha-L-
CBSS-208964.1.peg.1768
D23_1c0251
Neut_0327








glutamate ligase family











protein




fig|6666666.60966.peg.245
CDS
231155
229677
−2
−
1479
Cardiolipin synthetase
Cardiolipin synthesis;
D23_1c0252
Neut_0328








(EC 2.7.8.—)
<br>Glycerolipid and











Glycerophospholipid











Metabolism in Bacteria



fig|6666666.60966.peg.246
CDS
231229
231411
1
+
183
hypothetical protein
-none-
D23_1c0253
NA

fig|6666666.60966.peg.248
CDS
232352
231813
−2
−
540
Urea channel Urel
Urea decomposition
D23_1c0255
Neut_0329

fig|6666666.60966.peg.249
CDS
232767
232585
−3
−
183
hypothetical protein
-none-
D23_1c0256
NA

fig|6666666.60966.peg.251
CDS
233588
234748
2
+
1161
FIG00855934:
-none-
D23_1c0259
Neut_0331








hypothetical protein




fig|6666666.60966.peg.252
CDS
235271
234831
−2
−
441
Mobile element protein
-none-
D23_1c0260
Neut_0332

fig|6666666.60966.peg.253
CDS
235792
235397
−1
−
396
NAD-dependent
Calvin-Benson cycle;
D23_1c0261
Neut_0333








glyceraldehyde-3-
<br>Glycolysis and










phosphate
Gluconeogenesis;










dehydrogenase (EC
<br>Pyridoxin (Vitamin










1.2.1.12)
B6) Biosynthesis



fig|6666666.60966.peg.254
CDS
235832
236260
2
+
429
hypothetical protein
-none-
D23_1c0261
Neut_0333

fig|6666666.60966.peg.255
CDS
237167
236592
−2
−
576
Flagellar basal-body P-
Flagellum
D23_1c0262
Neut_0334








ring formation protein











FlgA




fig|6666666.60966.peg.256
CDS
237299
237415
2
+
117
hypothetical protein
-none-
D23_1c0264
NA

fig|6666666.60966.peg.257
CDS
237436
237924
1
+
489
Flagellar basal-body rod
Flagellum; <br>Flagellum
D23_1c0265
Neut_0335








protein FlgB
in Campylobacter



fig|6666666.60966.peg.258
CDS
237930
238334
3
+
405
Flagellar basal-body rod
Flagellum; <br>Flagellum
D23_1c0266
Neut_0336








protein FlgC
in Campylobacter



fig|6666666.60966.peg.259
CDS
238347
239021
3
+
675
Flagellar basal-body rod
Flagellar motility;
D23_1c0267
Neut_0337








modification protein
<br>Flagellum










FlgD




fig|6666666.60966.peg.260
CDS
239037
240296
3
+
1260
Flagellar hook protein
Flagellum
D23_1c0268
Neut_0338








FlgE




fig|6666666.60966.peg.261
CDS
240337
241080
1
+
744
Flagellar basal-body rod
Flagellum
D23_1c0269
Neut_0339








protein FlgF




fig|6666666.60966.peg.262
CDS
241119
241901
3
+
783
Flagellar basal-body rod
Flagellum
D23_1c0270
Neut_0340








protein FlgG




fig|6666666.60966.peg.263
CDS
242034
242828
3
+
795
Flagellar L-ring protein
Flagellar motility;
D23_1c0271
Neut_0341








FlgH
<br>Flagellum



fig|6666666.60966.peg.264
CDS
242850
243977
3
+
1128
Flagellar P-ring protein
Flagellum
D23_1c0272
Neut_0342








FlgI




fig|6666666.60966.peg.265
CDS
243991
244998
1
+
1008
Flagellar protein FlgJ
Flagellum
D23_1c0273
Neut_0343








[peptidoglycan











hydrolase] (EC 3.2.1.—)




fig|6666666.60966.peg.266
CDS
245257
246660
1
+
1404
Flagellar hook-
Flagellum
D23_1c0274
Neut_0344








associated protein FlgK




fig|6666666.60966.peg.267
CDS
246638
247588
2
+
951
Flagellar hook-
Flagellum
D23_1c0275
Neut_0345








associated protein FlgL




fig|6666666.60966.peg.268
CDS
247665
248210
3
+
546
FIG00859049:
-none-
D23_1c0276
Neut_0346








hypothetical protein




fig|6666666.60966.peg.269
CDS
249330
248200
−3
−
1131
FIG00859091:
-none-
D23_1c0277
Neut_0347








hypothetical protein




fig|6666666.60966.peg.270
CDS
249439
249960
1
+
522
FIG00859511:
-none-
D23_1c0278
Neut_0348








hypothetical protein




fig|6666666.60966.peg.271
CDS
249932
250513
2
+
582
GCN5-related N-
-none-
D23_1c0279
Neut_0349








acetyltransferase




fig|6666666.60966.peg.272
CDS
250589
250861
2
+
273
FIG001341: Probable
Heat shock dnaK gene
D23_1c0280
Neut_0350








Fe(2+)-trafficking
cluster extended










protein YggX




fig|6666666.60966.peg.273
CDS
250912
253038
1
+
2127
Polyphosphate kinase
High affinity phosphate
D23_1c0281
Neut_0351








(EC 2.7.4.1)
transporter and control











of PHO regulon;











<br>Phosphate











metabolism;











<br>Polyphosphate;











<br>Purine conversions



fig|6666666.60966.peg.274
CDS
254786
253059
−2
−
1728
Sulfate permease
Cysteine Biosynthesis
D23_1c0282
Neut_0352

fig|6666666.60966.peg.275
CDS
255133
254783
−1
−
351
Transcriptional
-none-
D23_1c0283
Neut_0353








regulator, ArsR family




fig|6666666.60966.peg.277
CDS
256153
255827
−1
−
327
hypothetical protein
-none-
D23_1c0285
Neut_0355

fig|6666666.60966.peg.278
CDS
256608
257603
3
+
996
hypothetical protein
-none-
D23_1c0286
Neut_0356

fig|6666666.60966.peg.279
CDS
258986
257739
−2
−
1248
Mobile element protein
-none-
D23_1c0287
Neut_0357

fig|6666666.60966.peg.280
CDS
259004
259126
2
+
123
patatin family protein
-none-
D23_1c0288
Neut_1317

fig|6666666.60966.peg.281
CDS
259254
259123
−3
−
132
cAMP-binding proteins-
cAMP signaling in
D23_1c0289
NA








catabolite gene
bacteria










activator and regulatory











subunit of cAMP-











dependent protein











kinases




fig|6666666.60966.peg.282
CDS
259543
260031
1
+
489
Cytochrome c&#39;
-none-
D23_1c0291
NA

fig|6666666.60966.peg.283
CDS
260060
260947
2
+
888
Putative diheme
Soluble cytochromes
D23_1c0292
Neut_1381








cytochrome c-553
and functionally related











electron carriers



fig|6666666.60966.peg.285
CDS
261917
261708
−2
−
210
hypothetical protein
-none-
D23_1c0294
Neut_0363

fig|6666666.60966.peg.288
CDS
262640
262440
−2
−
201
Mobile element protein
-none-
D23_1c0296
Neut_1696

fig|6666666.60966.peg.289
CDS
263106
264041
3
+
936
hypothetical protein
-none-
D23_1c0297
NA

fig|6666666.60966.peg.290
CDS
264137
265633
2
+
1497
SII1503 protein
-none-
D23_1c0298
NA

fig|6666666.60966.peg.294
CDS
266897
266760
−2
−
138
hypothetical protein
-none-
D23_1c0300
NA

fig|6666666.60966.peg.295
CDS
267026
267370
2
+
345
COGs COG3339
-none-
D23_1c0301
Neut_0371

fig|6666666.60966.peg.297
CDS
268862
267765
−2
−
1098
L-lactate
Lactate utilization;
D23_1c0302
Neut_0372








dehydrogenase (EC
<br>Respiratory










1.1.2.3)
dehydrogenases 1



fig|6666666.60966.peg.298
CDS
269655
268972
−3
−
684
Iron-uptake factor PiuC
-none-
D23_1c0303
Neut_0373

fig|6666666.60966.peg.299
CDS
271893
269683
−3
−
2211
TonB-dependent
Ton and Tol transport
D23_1c0304
Neut_0374








siderophore receptor
systems



fig|6666666.60966.peg.301
CDS
272682
273740
3
+
1059
protein of unknown
-none-
D23_1c0306
Neut_0377








function DUF81




fig|6666666.60966.peg.302
CDS
273758
274108
2
+
351
hypothetical protein
-none-
D23_1c0307
NA

fig|6666666.60966.peg.303
CDS
274775
274182
−2
−
594
InterPro IPR001226
-none-
D23_1c0308
Neut_0379








COGs COG0790




fig|6666666.60966.peg.304
CDS
274944
274792
−3
−
153
hypothetical protein
-none-
D23_1c0309
NA

fig|6666666.60966.peg.305
CDS
276110
274986
−2
−
1125
dNTP
Purine conversions;
D23_1c0310
Neut_0380








triphosphohydrolase,
<br>dNTP










broad substrate
triphosphohydrolase










specificity, subgroup 2
protein family



fig|6666666.60966.peg.306
CDS
277212
276103
−3
−
1110
3-dehydroquinate
Chorismate Synthesis;
D23_1c0311
Neut_0381








synthase (EC 4.2.3.4)
<br>Common Pathway











For Synthesis of











Aromatic Compounds











(DAHP synthase to











chorismate)



fig|6666666.60966.peg.308
CDS
277726
277896
1
+
171
hypothetical protein
-none-
D23_1c0312
Neut_0382

fig|6666666.60966.peg.307
CDS
277692
277261
−3
−
432
Shikimate kinase I (EC
Chorismate Synthesis;
D23_1c0312
Neut_0382








2.7.1.71)
<br>Common Pathway











For Synthesis of











Aromatic Compounds











(DAHP synthase to











chorismate)



fig|6666666.60966.peg.309
CDS
279343
277982
−1
−
1362
Putative protease
-none-
D23_1c0313
Neut_0383

fig|6666666.60966.peg.310
CDS
279362
282934
2
+
3573
DNA polymerase III
Phage replication
D23_1c0314
Neut_0384








alpha subunit (EC











2.7.7.7)




fig|6666666.60966.peg.311
CDS
283139
282948
−2
−
192
putative
-none-
D23_1c0315
Neut_0385








transmembrane protein




fig|6666666.60966.peg.312
CDS
283290
284243
3
+
954
tRNA
tRNA modification
D23_1c0316
Neut_0386








dimethylallyltransferase
Bacteria; <br>tRNA










(EC 2.5.1.75)
processing



fig|6666666.60966.peg.313
CDS
284258
284401
2
+
144
hypothetical protein
-none-
D23_1c0317
NA

fig|6666666.60966.peg.314
CDS
286041
284776
−3
−
1266
Two component,
-none-
D23_1c0320
Neut_0387








sigma54 specific,











transcriptional











regulator, Fis family




fig|6666666.60966.peg.315
CDS
286328
286191
−2
−
138
hypothetical protein
-none-
D23_1c0321
NA

fig|6666666.60966.peg.316
CDS
288462
286330
−3
−
2133
Nitrogen regulation
Possible RNA
D23_1c0322
Neut_0388








protein NtrY (EC 2.7.3.—)
degradation cluster



fig|6666666.60966.peg.317
CDS
289077
288514
−3
−
564
Probable proline rich
-none-
D23_1c0323
Neut_0389








signal peptide protein




fig|6666666.60966.peg.318
CDS
290401
289121
−1
−
1281
16S rRNA
RNA methylation
D23_1c0324
Neut_0390








(cytosine(967)-C(5))-











methyltransferase (EC











2.1.1.176) ## SSU rRNA











m5C967




fig|6666666.60966.peg.319
CDS
291388
290414
−1
−
975
Methionyl-tRNA
Translation initiation
D23_1c0325
Neut_0391








formyltransferase (EC
factors bacterial










2.1.2.9)




fig|6666666.60966.peg.320
CDS
291933
291427
−3
−
507
Peptide deformylase
Bacterial RNA-
D23_1c0326
Neut_0392








(EC 3.5.1.88)
metabolizing Zn-











dependent hydrolases;











<br>Translation











termination factors











bacterial



fig|6666666.60966.peg.321
CDS
292108
293136
1
+
1029
Uncharacterized protein
-none-
D23_1c0327
Neut_0393








with LysM domain,











COG1652




fig|6666666.60966.peg.322
CDS
293235
294356
3
+
1122
Rossmann fold
-none-
D23_1c0328
Neut_0394








nucleotide-binding











protein Smf possibly











involved in DNA uptake




fig|6666666.60966.peg.323
CDS
294438
294896
3
+
459
Protein of unknown
-none-
D23_1c0329
Neut_0395








function Smg




fig|6666666.60966.peg.324
CDS
295024
297522
1
+
2499
DNA topoisomerase III,
DNA topoisomerases,
D23_1c0330
Neut_0396








Burkholderia type (EC
Type I, ATP-independent










5.99.1.2)




fig|6666666.60966.peg.325
CDS
297826
297575
−1
−
252
FIG00858730:
-none-
D23_1c0331
Neut_0397








hypothetical protein




fig|6666666.60966.peg.326
CDS
298176
299477
3
+
1302
5-Enolpyruvylshikimate-
Chorismate Synthesis;
D23_1c0333
Neut_0398








3-phosphate synthase
<br>Common Pathway










(EC 2.5.1.19)
For Synthesis of











Aromatic Compounds











(DAHP synthase to











chorismate)



fig|6666666.60966.peg.327
CDS
299557
300228
1
+
672
Cytidylate kinase (EC
-none-
D23_1c0335
Neut_0399








2.7.4.14)




fig|6666666.60966.peg.328
CDS
300339
302051
3
+
1713
SSU ribosomal protein
-none-
D23_1c0336
Neut_0400








S1p




fig|6666666.60966.peg.329
CDS
302061
302378
3
+
318
Integration host factor
DNA structural proteins,
D23_1c0337
Neut_0401








beta subunit
bacterial



fig|6666666.60966.peg.330
CDS
302493
302368
−3
−
126
hypothetical protein
-none-
D23_1c0338
NA

fig|6666666.60966.peg.33 1
CDS
302902
303597
1
+
696
Orotidine 5&#39;-
De Novo Pyrimidine
D23_1c0339
Neut_0402








phosphate
Synthesis; <br>Riboflavin










decarboxylase (EC
synthesis cluster










4.1.1.23)




fig|6666666.60966.peg.332
CDS
304632
303592
−3
−
1041
Squalene synthase (EC
Hopanes
D23_1c0340
Neut_0403








2.5.1.21)




fig|6666666.60966.peg.333
CDS
305907
304654
−3
−
1254
Diaminopimelate
Lysine Biosynthesis DAP
D23_1c0341
Neut_0404








decarboxylase (EC
Pathway, GJO scratch










4.1.1.20)




fig|6666666.60966.peg.334
CDS
306026
305904
−2
−
123
hypothetical protein
-none-
D23_1c0342
NA

fig|6666666.60966.peg.335
CDS
306654
306052
−3
−
603
Probable lipoprotein
-none-
D23_1c0343
Neut_0405

fig|6666666.60966.peg.336
CDS
307556
306651
−2
−
906
ABC-type transport
-none-
D23_1c0344
Neut_0406








system involved in











resistance to organic











solvents, periplasmic











component




fig|6666666.60966.peg.337
CDS
308341
307583
−1
−
759
Inositol-1-
-none-
D23_1c0345
Neut_0407








monophosphatase (EC











3.1.3.25)




fig|6666666.60966.peg.339
CDS
308500
309207
1
+
708
tRNA:Cm32/Um32
RNA methylation;
D23_1c0346
Neut_0408








methyltransferase
<br>tRNA modification











Bacteria



fig|6666666.60966.peg.340
CDS
309905
309291
−2
−
615
Glutathione S-
Glutathione: Non-redox
D23_1c0347
Neut_0409








transferase family
reactions; <br>Scaffold










protein
proteins for [4Fe-4S]











cluster assembly (MRP











family)



fig|6666666.60966.peg.341
CDS
310042
311418
1
+
1377
Adenylosuccinate lyase
De Novo Purine
D23_1c0348
Neut_0410








(EC 4.3.2.2)
Biosynthesis; <br>Purine











conversions



fig|6666666.60966.peg.342
CDS
311556
312146
3
+
591
Heat shock protein
GroEL GroES; <br>Heat
D23_1c0349
Neut_0411








GrpE
shock dnaK gene cluster











extended; <br>Protein











chaperones



fig|6666666.60966.peg.343
CDS
312210
314153
3
+
1944
Chaperone protein
GroEL GroES; <br>Heat
D23_1c0350
Neut_0412








DnaK
shock dnaK gene cluster











extended; <br>Protein











chaperones



fig|6666666.60966.peg.344
CDS
314344
315453
1
+
1110
Chaperone protein DnaJ
GroEL GroES; <br>Heat
D23_1c0351
Neut_0413









shock dnaK gene cluster











extended; <br>Protein











chaperones



fig|6666666.60966.peg.345
CDS
318894
315550
−3
−
3345
Potassium efflux system
Potassium homeostasis
D23_1c0352
Neut_0414








KefA protein/Small-











conductance











mechanosensitive











channel




fig|6666666.60966.peg.346
CDS
319923
319357
−3
−
567
Transcriptional
-none-
D23_1c0353
Neut_0415








regulator, TetR family




fig|6666666.60966.peg.347
CDS
321174
319990
−3
−
1185
InterPro IPR001327
-none-
D23_1c0354
Neut_0416








COGs COG2072




fig|6666666.60966.peg.348
CDS
321778
321236
−1
−
543
hypothetical protein
-none-
D23_1c0355
Neut_0417

fig|6666666.60966.peg.349
CDS
322196
322363
2
+
168
hypothetical protein
-none-
D23_1c0356
NA

fig|6666666.60966.peg.350
CDS
325140
322522
−3
−
2619
Membrane alanine
Aminopeptidases (EC
D23_1c0357
Neut_0418








aminopeptidase N (EC
3.4.11.—)










3.4.11.2)




fig|6666666.60966.peg.351
CDS
325139
325255
2
+
117
hypothetical protein
-none-
D23_1c0358
NA

fig|6666666.60966.peg.352
CDS
326547
325213
−3
−
1335
Peptide methionine
Peptide methionine
D23_1c0359
Neut_0419








sulfoxide reductase
sulfoxide reductase;










MsrA (EC 1.8.4.11)/
<br>Peptide methionine










Thiol:disulfide
sulfoxide reductase;










oxidoreductase
<br>Peptide methionine










associated with MetSO
sulfoxide reductase










reductase/Peptide











Methionine sulfoxide











reductase MsrB (EC











1.8.4.12)




fig|6666666.60966.peg.354
CDS
326909
329791
2
+
2883
Diguanylate
-none-
D23_1c0360
Neut_0422








cyclase/phosphodiesterase











domain 2 (EAL)




fig|6666666.60966.peg.355
CDS
331130
329874
−2
−
1257
FIG00858721:
-none-
D23_1c0361
Neut_0423








hypothetical protein




fig|6666666.60966.peg.356
CDS
331369
332730
1
+
1362
O-acetylhomoserine
Methionine
D23_1c0363
Neut_0424








sulfhydrylase (EC
Biosynthesis;










2.5.1.49)/O-
<br>Methionine










succinylhomoserine
Biosynthesis










sulfhydrylase (EC











2.5.1.48)




fig|6666666.60966.peg.357
CDS
334115
332718
−2
−
1398
NnrS protein involved in
Denitrification;
D23_1c0364
Neut_0425








response to NO
<br>Nitrosative stress;











<br>Oxidative stress



fig|6666666.60966.peg.358
CDS
334992
334066
−3
−
927
Serine acetyltransferase
Cysteine Biosynthesis;
D23_1c0365
Neut_0426








(EC 2.3.1.30)
<br>Methionine











Biosynthesis



fig|6666666.60966.peg.360
CDS
335392
336399
1
+
1008
Glucokinase (EC 2.7.1.2)
Glycolysis and
D23_1c0367
Neut_0427









Gluconeogenesis



fig|6666666.60966.peg.361
CDS
336414
337073
3
+
660
Probable
-none-
D23_1c0368
Neut_0428








transmembrane protein




fig|6666666.60966.peg.362
CDS
337412
337101
−2
−
312
FIG00858769:
-none-
D23_1c0369
Neut_0429








hypothetical protein




fig|6666666.60966.peg.363
CDS
338169
337483
−3
−
687
6-
Pentose phosphate
D23_1c0370
Neut_0430








phosphogluconolactonase
pathway










(EC 3.1.1.31),











eukaryotic type




fig|6666666.60966.peg.364
CDS
338807
338151
−2
−
657
hydrolase, haloacid
-none-
D23_1c0371
Neut_0431








dehalogenase-like











family




fig|6666666.60966.peg.365
CDS
339746
338814
−2
−
933
NAD-dependent
CBSS-296591.1.peg.2330
D23_1c0372
Neut_0432








epimerase/dehydratase




fig|6666666.60966.peg.366
CDS
340674
339739
−3
−
936
D-3-phosphoglycerate
Glycine and Serine
D23_1c0373
Neut_0433








dehydrogenase (EC
Utilization;










1.1.1.95)
<br>Pyridoxin (Vitamin











B6) Biosynthesis;











<br>Serine Biosynthesis



fig|6666666.60966.peg.367
CDS
341432
340671
−2
−
762
2,4-dihydroxyhept-2-
-none-
D23_1c0374
Neut_0434








ene-1,7-dioic acid











aldolase (EC 4.1.2.—)




fig|6666666.60966.peg.368
CDS
342202
341444
−1
−
759
3-deoxy-manno-
KDO2-Lipid A
D23_1c0375
Neut_0435








octulosonate
biosynthesis cluster 2










cytidylyltransferase (EC











2.7.7.38)




fig|6666666.60966.peg.370
CDS
342384
342509
3
+
126
hypothetical protein
-none-
D23_1c0376
NA

fig|6666666.60966.peg.371
CDS
342506
343585
2
+
1080
Glycosyl transferase,
-none-
D23_1c0377
Neut_0436








group 2 family protein




fig|6666666.60966.peg.372
CDS
343660
344931
1
+
1272
O-antigen ligase
-none-
D23_1c0378
Neut_0437

fig|6666666.60966.peg.373
CDS
344931
345620
3
+
690
O-methyltransferase
-none-
D23_1c0379
Neut_0438








family protein [C1]




fig|6666666.60966.peg.374
CDS
345673
345930
1
+
258
FIG00859064:
-none-
D23_1c0380
Neut_0439








hypothetical protein




fig|6666666.60966.peg.375
CDS
345980
346498
2
+
519
Mlr4354 like protein
-none-
D23_1c0381
Neut_0440

fig|6666666.60966.peg.376
CDS
346511
346858
2
+
348
Arsenate reductase (EC
Anaerobic respiratory
D23_1c0382
Neut_0441








1.20.4.1)
reductases;











<br>Transcription repair











cluster



fig|6666666.60966.peg.377
CDS
347305
346916
−1
−
390
LSU ribosomal protein
-none-
D23_1c0383
Neut_0442








L19p




fig|6666666.60966.peg.378
CDS
348122
347277
−2
−
846
tRNA (Guanine37-N1)-
RNA methylation;
D23_1c0384
Neut_0443








methyltransferase (EC
<br>Ribosome










2.1.1.31)
biogenesis bacterial;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.379
CDS
348636
348130
−3
−
507
16S rRNA processing
Ribosome biogenesis
D23_1c0385
Neut_0444








protein RimM
bacterial



fig|6666666.60966.peg.381
CDS
349157
350437
2
+
1281
Glycolate
Glycolate, glyoxylate
D23_1c0386
Neut_0446








dehydrogenase (EC
interconversions;










1.1.99.14), iron-sulfur
<br>Photorespiration










subunit GlcF
(oxidative C2 cycle)



fig|6666666.60966.peg.382
CDS
350492
351118
2
+
627
Uncharacterized
Ubiquinone Biosynthesis-
D23_1c0387
Neut_0447








hydroxylase PA0655
gjo



fig|6666666.60966.peg.383
CDS
351152
351712
2
+
561
UPF0301 protein YqgE
-none-
D23_1c0388
Neut_0448

fig|6666666.60966.peg.384
CDS
351705
352178
3
+
474
Putative Holliday
-none-
D23_1c0389
Neut_0449








junction resolvase (EC











3.1.—.—)




fig|6666666.60966.peg.385
CDS
352165
352668
1
+
504
Uracil
De Novo Pyrimidine
D23_1c0390
Neut_0450








phosphoribosyltransferase
Synthesis; <br>De Novo










(EC 2.4.2.9)/
Pyrimidine Synthesis;










Pyrimidine operon
<br>pyrimidine










regulatory protein PyrR
conversions



fig|6666666.60966.peg.386
CDS
352856
353806
2
+
951
Aspartate
De Novo Pyrimidine
D23_1c0391
Neut_0451








carbamoyltransferase
Synthesis










(EC 2.1.3.2)




fig|6666666.60966.peg.387
CDS
353822
355093
2
+
1272
Dihydroorotase (EC
De Novo Pyrimidine
D23_1c0392
Neut_0452








3.5.2.3)
Synthesis; <br>Zinc











regulated enzymes



fig|6666666.60966.peg.388
CDS
355217
357322
2
+
2106
Oligopeptidase A (EC
Protein degradation
D23_1c0393
Neut_0453








3.4.24.70)




fig|6666666.60966.peg.389
CDS
357558
358709
3
+
1152
Carbamoyl-phosphate
De Novo Pyrimidine
D23_1c0394
Neut_0454








synthase small chain
Synthesis;










(EC 6.3.5.5)
<br>Macromolecular











synthesis operon



fig|6666666.60966.peg.390
CDS
358735
361932
1
+
3198
Carbamoyl-phosphate
De Novo Pyrimidine
D23_1c0395
Neut_0455








synthase large chain (EC
Synthesis;










6.3.5.5)
<br>Macromolecular











synthesis operon



fig|6666666.60966.peg.391
CDS
362117
362593
2
+
477
Transcription
Transcription factors
D23_1c0396
Neut_0456








elongation factor GreA
bacterial



fig|6666666.60966.peg.392
CDS
363579
362608
−3
−
972
ErfK/YbiS/YcfS/YnhG
-none-
D23_1c0397
Neut_0457








family protein




fig|6666666.60966.peg.393
CDS
364226
366052
2
+
1827
Long-chain-fatty-acid--
Biotin biosynthesis;
D23_1c0398
Neut_0458








CoA ligase (EC 6.2.1.3)
<br>Biotin synthesis











cluster; <br>Fatty acid











metabolism cluster



fig|6666666.60966.peg.394
CDS
366141
367064
3
+
924
FIG010773: NAD-
-none-
D23_1c0399
Neut_0459








dependent











epimerase/dehydratase




fig|6666666.60966.peg.395
CDS
367176
367430
3
+
255
phosphopantetheine-
-none-
D23_1c0400
Neut_0460








binding




fig|6666666.60966.peg.396
CDS
367430
368617
2
+
1188
Aminotransferase class
-none-
D23_1c0401
Neut_0461








II, serine











palmitoyltransferase











like (EC 2.3.1.50)




fig|6666666.60966.peg.397
CDS
368669
369427
2
+
759
COG1496:
-none-
D23_1c0402
Neut_0462








Uncharacterized











conserved protein




fig|6666666.60966.peg.398
CDS
369615
370427
3
+
813
Zinc transporter, ZIP
-none-
D23_1c0403
Neut_0463








family




fig|6666666.60966.peg.399
CDS
373049
370434
−2
−
2616
Dolichyl-phosphate
-none-
D23_1c0404
Neut_0464








beta-D-











mannosyltransferase











(EC: 2.4.1.83)




fig|6666666.60966.peg.400
CDS
374173
373157
−1
−
1017
FIG004453: protein
CBSS-
D23_1c0405
Neut_0465








YceG like
323097.3.peg.2594;











<br>Cluster containing











Alanyl-tRNA synthetase;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.401
CDS
374277
374140
−3
−
138
hypothetical protein
-none-
D23_1c0406
NA

fig|6666666.60966.peg.402
CDS
375542
374301
−2
−
1242
3-oxoacyl-[acyl-carrier-
Fatty Acid Biosynthesis
D23_1c0407
Neut_0466








protein] synthase, KASII
FASII










(EC 2.3.1.41)




fig|6666666.60966.peg.403
CDS
375822
375577
−3
−
246
Acyl carrier protein
Fatty Acid Biosynthesis
D23_1c0408
Neut_0467









FASII; <br>Glycerolipid











and Glycerophospholipid











Metabolism in Bacteria



fig|6666666.60966.peg.405
CDS
376731
375988
−3
−
744
3-oxoacyl-[acyl-carrier
Fatty Acid Biosynthesis
D23_1c0409
Neut_0468








protein] reductase (EC
FASII










1.1.1.100)




fig|6666666.60966.peg.406
CDS
377726
376788
−2
−
939
Malonyl CoA-acyl
Fatty Acid Biosynthesis
D23_1c0410
Neut_0469








carrier protein
FASII










transacylase (EC











2.3.1.39)




fig|6666666.60966.peg.407
CDS
378692
377730
−2
−
963
3-oxoacyl-[acyl-carrier-
Fatty Acid Biosynthesis
D23_1c0411
Neut_0470








protein] synthase,
FASII










KASIII (EC 2.3.1.41)




fig|6666666.60966.peg.408
CDS
379722
378703
−3
−
1020
Phosphate:acyl-ACP
Glycerolipid and
D23_1c0412
Neut_0471








acyltransferase PlsX
Glycerophospholipid











Metabolism in Bacteria



fig|6666666.60966.peg.409
CDS
379982
379800
−2
−
183
LSU ribosomal protein
-none-
D23_1c0414
Neut_0472








L32p




fig|6666666.60966.peg.410
CDS
380510
380007
−2
−
504
COG1399 protein,
-none-
D23_1c0415
Neut_0473








clustered with











ribosomal protein L32p




fig|6666666.60966.peg.411
CDS
380534
381175
2
+
642
FIG146278:
-none-
D23_1c0416
Neut_0474








Maf/YceF/YhdE family











protein




fig|6666666.60966.peg.412
CDS
381292
381684
1
+
393
FIG00858587:
-none-
D23_1c0417
Neut_0475








hypothetical protein




fig|6666666.60966.peg.413
CDS
381793
383217
1
+
1425
Heavy metal RND efflux
Cobalt-zinc-cadmium
D23_1c0418
Neut_0476








outer membrane
resistance










protein, CzcC family




fig|6666666.60966.peg.414
CDS
383214
384710
3
+
1497
Cobalt/zinc/cadmium
Cobalt-zinc-cadmium
D23_1c0419
Neut_0477








efflux RND transporter,
resistance










membrane fusion











protein, CzcB family




fig|6666666.60966.peg.415
CDS
384811
388020
1
+
3210
Cobalt-zinc-cadmium
Cobalt-zinc-cadmium
D23_1c0421
Neut_0478








resistance protein CzcA;
resistance; <br>Cobalt-










Cation efflux system
zinc-cadmium resistance










protein CusA




fig|6666666.60966.peg.416
CDS
388294
388731
1
+
438
FIG00858457:
-none-
D23_1c0423
Neut_0479








hypothetical protein




fig|6666666.60966.peg.417
CDS
388756
389043
1
+
288
FIG00858508:
-none-
D23_1c0424
Neut_0480








hypothetical protein




fig|6666666.60966.peg.418
CDS
389040
389948
3
+
909
FIG00858931:
-none-
D23_1c0425
Neut_0481








hypothetical protein




fig|6666666.60966.peg.419
CDS
389941
391068
1
+
1128
hypothetical protein
-none-
D23_1c0426
Neut_0482

fig|6666666.60966.peg.420
CDS
392521
391079
−1
−
1443
Mg/Co/Ni transporter
Magnesium transport
D23_1c0427
Neut_0483








MgtE/CBS domain




fig|6666666.60966.peg.424
CDS
394723
393761
−1
−
963
Mobile element protein
-none-
D23_1c0430
Neut_1746

fig|6666666.60966.peg.425
CDS
394947
394834
−3
−
114
hypothetical protein
-none-
D23_1c0431
NA

fig|6666666.60966.peg.426
CDS
394946
395251
2
+
306
hypothetical protein
-none-
D23_1c0432
Neut_0486

fig|6666666.60966.peg.427
CDS
395968
395309
−1
−
660
COG1272: Predicted
-none-
D23_1c0433
Neut_0487








membrane protein











hemolysin III homolog




fig|6666666.60966.peg.428
CDS
396481
396179
−1
−
303
hypothetical protein
-none-
D23_1c0434
Neut_0488

fig|6666666.60966.peg.430
CDS
397189
396863
−1
−
327
hypothetical protein
-none-
D23_1c0435
Neut_0490

fig|6666666.60966.peg.433
CDS
397653
398393
3
+
741
cAMP-binding proteins-
cAMP signaling in
D23_1c0436
Neut_0491








catabolite gene
bacteria










activator and regulatory











subunit of cAMP-











dependent protein











kinases




fig|6666666.60966.peg.434
CDS
398690
398424
−2
−
267
Putative lipoprotein
-none-
D23_1c0437
Neut_0492

fig|6666666.60966.peg.435
CDS
399146
398973
−2
−
174
hypothetical protein
-none-
D23_1c0438
NA

fig|6666666.60966.peg.436
CDS
399498
399373
−3
−
126
hypothetical protein
-none-
D23_1c0439
NA

fig|6666666.60966.peg.437
CDS
400841
399609
−2
−
1233
hypothetical protein
-none-
D23_1c0440
Neut_0494

fig|6666666.60966.peg.438
CDS
401592
400858
−3
−
735
Monofunctional
Peptidoglycan
D23_1c0441
Neut_0495








biosynthetic
Biosynthesis










peptidoglycan











transglycosylase (EC











2.4.2.—)




fig|6666666.60966.peg.439
CDS
402422
401589
−2
−
834
Shikimate 5-
Chorismate Synthesis;
D23_1c0442
Neut_0496








dehydrogenase I alpha
<br>Cluster containing










(EC 1.1.1.25)
Alanyl-tRNA synthetase;











<br>Common Pathway











For Synthesis of











Aromatic Compounds











(DAHP synthase to











chorismate)



fig|6666666.60966.peg.440
CDS
403340
402456
−2
−
885
TonB protein
-none-
D23_1c0443
Neut_0497

fig|6666666.60966.peg.441
CDS
405237
403378
−3
−
1860
Exoribonuclease II (EC
RNA processing and
D23_1c0444
Neut_0498








3.1.13.1)
degradation, bacterial



fig|6666666.60966.peg.443
CDS
405594
406985
3
+
1392
Glutamyl-tRNA
Heme and Siroheme
D23_1c0445
Neut_0499








synthetase (EC 6.1.1.17)
Biosynthesis; <br>tRNA











aminoacylation, Glu and











Gln



fig|6666666.60966.peg.444
CDS
407045
410752
2
+
3708
5-
Methionine Biosynthesis
D23_1c0446
Neut_0500








methyltetrahydrofolate--











homocysteine











methyltransferase (EC











2.1.1.13)




fig|6666666.60966.peg.445
CDS
410924
412267
2
+
1344
NADP-specific
Arginine and Ornithine
D23_1c0447
Neut_0501








glutamate
Degradation;










dehydrogenase (EC
<br>Glutamate










1.4.1.4)
dehydrogenases;











<br>Glutamine,











Glutamate, Aspartate











and Asparagine











Biosynthesis;











<br>Proline Synthesis



fig|6666666.60966.peg.446
CDS
412461
414368
3
+
1908
Soluble lytic murein
Murein Hydrolases
D23_1c0449
Neut_0502








transglycosylase











precursor (EC 3.2.1.—)




fig|6666666.60966.peg.447
CDS
414379
415617
1
+
1239
tRNA
A cluster relating to
D23_1c0450
Neut_0503








nucleotidyltransferase
Tryptophanyl-tRNA










(EC 2.7.7.21) (EC
synthetase;










2.7.7.25)
<br>Polyadenylation











bacterial; <br>tRNA











nucleotidyltransferase



fig|6666666.60966.peg.448
CDS
417316
415592
−1
−
1725
Phospholipid-
N-linked Glycosylation in
D23_1c0451
Neut_0504








lipopolysaccharide ABC
Bacteria










transporter




fig|6666666.60966.peg.449
CDS
418171
417335
−1
−
837
Diaminopimelate
CBSS-84588.1.peg.1247;
D23_1c0452
Neut_0505








epimerase (EC 5.1.1.7)
<br>Lysine Biosynthesis











DAP Pathway, GJO











scratch



fig|6666666.60966.peg.450
CDS
418345
418193
−1
−
153
hypothetical protein
-none-
D23_1c0453
NA

fig|6666666.60966.peg.451
CDS
418574
419011
2
+
438
Predicted secretion
Predicted secretion
D23_1c0454
Neut_0506








system X protein GspG-
system X










like 3




fig|6666666.60966.peg.452
CDS
419030
420214
2
+
1185
Predicted secretion
Predicted secretion
D23_1c0455
Neut_0507








system X protein GspF-
system X










like




fig|6666666.60966.peg.453
CDS
420211
421905
1
+
1695
Predicted secretion
Predicted secretion
D23_1c0456
Neut_0508








system X protein GspE-
system X










like




fig|6666666.60966.peg.454
CDS
421910
422731
2
+
822
Predicted secretion
Predicted secretion
D23_1c0457
Neut_0509








system X FIG084745:
system X










hypothetical protein




fig|6666666.60966.peg.455
CDS
422772
423260
3
+
489
Predicted secretion
Predicted secretion
D23_1c0458
Neut_0510








system X
system X










transmembrane protein 1




fig|6666666.60966.peg.472
CDS
440367
440753
3
+
387
Mobile element protein
-none-
D23_1c0476
Neut_0884

fig|6666666.60966.peg.473
CDS
440716
441171
1
+
456
Mobile element protein
-none-
D23_1c0477
Neut_2502

fig|6666666.60966.peg.474
CDS
441829
441158
−1
−
672
Gluconate 2-
D-gluconate and
D23_1c0478
NA








dehydrogenase (EC
ketogluconates










1.1.99.3), membrane-
metabolism










bound, gamma subunit




fig|6666666.60966.peg.475
CDS
444093
441973
−3
−
2121
diguanylate
-none-
D23_1c0479
Neut_0525








cyclase/phosphodiesterase











(GGDEF & EAL











domains) with PAS/PAC











sensor(s)




fig|6666666.60966.peg.476
CDS
444457
444311
−1
−
147
hypothetical protein
-none-
D23_1c0480
NA

fig|6666666.60966.peg.478
CDS
444629
445810
2
+
1182
NAD(FAD)-utilizing
-none-
D23_1c0481
Neut_0526








dehydrogenases




fig|6666666.60966.peg.479
CDS
446569
445952
−1
—
618
Methionine
-none-
D23_1c0482
Neut_0527








biosynthesis protein











MetW




fig|6666666.60966.peg.480
CDS
447733
446600
−1
−
1134
Homoserine O-
Methionine Biosynthesis
D23_1c0483
Neut_0528








acetyltransferase (EC











2.3.1.31)




fig|6666666.60966.peg.481
CDS
449559
447832
−3
−
1728
Phosphoenolpyruvate-
-none-
D23_1c0484
Neut_0529








protein











phosphotransferase of











PTS system (EC 2.7.3.9)




fig|6666666.60966.peg.482
CDS
449825
449556
−2
−
270
Phosphocarrier protein,
-none-
D23_1c0485
Neut_0530








nitrogen regulation











associated




fig|6666666.60966.peg.483
CDS
450219
449815
−3
−
405
Sugar transport PTS
-none-
D23_1c0486
Neut_0531








system IIa component




fig|6666666.60966.peg.484
CDS
450568
451605
1
+
1038
Phosphatidylglycerophosphatase
Glycerolipid and
D23_1c0488
Neut_0532








B (EC 3.1.3.27)
Glycerophospholipid











Metabolism in Bacteria



fig|6666666.60966.peg.485
CDS
451971
451705
−3
−
267
HrgA protein
-none-
D23_1c0489
Neut_2454

fig|6666666.60966.peg.486
CDS
452384
453631
2
+
1248
Mobile element protein
-none-
D23_1c0490
Neut_0357

fig|6666666.60966.peg.487
CDS
455203
454049
−1
−
1155
hypothetical protein
-none-
D23_1c0491
NA

fig|6666666.60966.peg.488
CDS
455538
455371
−3
−
168
hypothetical protein
-none-
D23_1c0492
NA

fig|6666666.60966.peg.489
CDS
455581
456603
1
+
1023
Lipolytic enzyme, G-D-S-L
-none-
D23_1c0493
Neut_0534

fig|6666666.60966.peg.490
CDS
457214
456669
−2
−
546
N-acetylmuramoyl-L-
Recycling of
D23_1c0494
Neut_0535








alanine amidase (EC
Peptidoglycan Amino










3.5.1.28) AmpD
Acids



fig|6666666.60966.peg.491
CDS
457304
457951
2
+
648
Thymidylate kinase (EC
pyrimidine conversions
D23_1c0495
Neut_0536








2.7.4.9)




fig|6666666.60966.peg.492
CDS
461332
458087
−1
−
3246
Type I restriction-
Restriction-Modification
D23_1c0496
Neut_0537








modification system,
System; <br>Type I










restriction subunit R (EC
Restriction-Modification










3.1.21.3)




fig|6666666.60966.peg.493
CDS
462292
461345
−1
−
948
Putative DNA-binding
Restriction-Modification
D23_1c0497
NA








protein in cluster with
System










Type I restriction-











modification system




fig|6666666.60966.peg.494
CDS
462416
462285
−2
−
132
hypothetical protein
-none-
D23_1c0498
NA

fig|6666666.60966.peg.495
CDS
463405
462413
−1
−
993
hypothetical protein
-none-
D23_1c0499
NA

fig|6666666.60966.peg.496
CDS
464694
463405
−3
−
1290
Type I restriction-
Restriction-Modification
D23_1c0500
Neut_0540








modification system,
System; <br>Type I










specificity subunit S (EC
Restriction-Modification










3.1.21.3)




fig|6666666.60966.peg.497
CDS
466246
464684
−1
−
1563
Type I restriction-
Restriction-Modification
D23_1c0501
Neut_0541








modification system,
System; <br>Type I










DNA-methyltransferase
Restriction-Modification










subunit M (EC 2.1.1.72)




fig|6666666.60966.peg.498
CDS
467880
466453
−3
−
1428
Na+/H+ antiporter
-none-
D23_1c0502
Neut_0542








NhaC




fig|6666666.60966.peg.499
CDS
468057
467896
−3
−
162
hypothetical protein
-none-
D23_1c0503
NA

fig|6666666.60966.peg.500
CDS
468126
469190
3
+
1065
DNA polymerase III
-none-
D23_1c0504
Neut_0543








delta prime subunit (EC











2.7.7.7)




fig|6666666.60966.peg.501
CDS
469691
469194
−2
−
498
hypothetical protein
-none-
D23_1c0505
Neut_0544

fig|6666666.60966.peg.502
CDS
469703
469870
2
+
168
hypothetical protein
-none-
D23_1c0506
NA

fig|6666666.60966.peg.503
CDS
470025
471155
3
+
1131
Magnesium and cobalt
Magnesium transport
D23_1c0508
Neut_0545








transport protein CorA




fig|6666666.60966.peg.504
CDS
471202
471447
1
+
246
Mobile element protein
-none-
D23_1c0509
Neut_0884

fig|6666666.60966.peg.505
CDS
471504
471617
3
+
114
hypothetical protein
-none-
D23_1c0510
Neut_0547

fig|6666666.60966.peg.506
CDS
471862
473013
1
+
1152
conserved hypothetical
-none-
D23_1c0511
Neut_0548








protein




fig|6666666.60966.peg.507
CDS
473412
473957
3
+
546
Uncharacterized protein
-none-
D23_1c0512
Neut_0550








conserved in bacteria




fig|6666666.60966.peg.508
CDS
474111
474269
3
+
159
Mobile element protein
-none-
D23_1c0513
NA

fig|6666666.60966.peg.510
CDS
474450
474653
3
+
204
hypothetical protein
-none-
D23_1c0514
NA

fig|6666666.60966.peg.512
CDS
475553
476005
2
+
453
SSU ribosomal protein

Mycobacterium

D23_1c0515
Neut_0554








S7p (S5e)
virulence operon











involved in protein











synthesis (SSU ribosomal











proteins)



fig|6666666.60966.peg.513
CDS
476121
478166
3
+
2046
Translation elongation

Mycobacterium

D23_1c0516
Neut_0555








factor G
virulence operon











involved in protein











synthesis (SSU ribosomal











proteins);











<br>Translation











elongation factor G











family; <br>Translation











elongation factors











bacterial; <br>Universal











GTPases



fig|6666666.60966.peg.514
CDS
478196
479386
2
+
1191
Translation elongation

Mycobacterium

D23_1c0517
Neut_0556








factor Tu
virulence operon











involved in protein











synthesis (SSU ribosomal











proteins);











<br>Translation











elongation factors











bacterial; <br>Universal











GTPases



fig|6666666.60966.peg.515
CDS
479569
479775
1
+
207
SSU ribosomal protein
-none-
D23_1c0518
Neut_0557








S10p (S20e)




fig|6666666.60966.peg.516
CDS
479823
480476
3
+
654
LSU ribosomal protein
-none-
D23_1c0519
Neut_0558








L3p (L3e)




fig|6666666.60966.peg.517
CDS
480494
481114
2
+
621
LSU ribosomal protein
-none-
D23_1c0520
Neut_0559








L4p (L1e)




fig|6666666.60966.peg.518
CDS
481111
481446
1
+
336
LSU ribosomal protein
-none-
D23_1c0521
Neut_0560








L23p (L23Ae)




fig|6666666.60966.peg.519
CDS
481446
482279
3
+
834
LSU ribosomal protein
-none-
D23_1c0522
Neut_0561








L2p (L8e)




fig|6666666.60966.peg.520
CDS
482948
483595
2
+
648
SSU ribosomal protein
-none-
D23_1c0523
Neut_0564








S3p (S3e)




fig|6666666.60966.peg.521
CDS
483680
484096
2
+
417
LSU ribosomal protein
-none-
D23_1c0524
Neut_0565








L16p (L10e)




fig|6666666.60966.peg.524
CDS
485008
485331
1
+
324
LSU ribosomal protein
-none-
D23_1c0525
Neut_0569








L24p (L26e)




fig|6666666.60966.peg.525
CDS
485458
485886
1
+
429
LSU ribosomal protein
-none-
D23_1c0526
Neut_0570








L5p (L11e)




fig|6666666.60966.peg.526
CDS
486881
487222
2
+
342
LSU ribosomal protein
-none-
D23_1c0527
Neut_0573








L6p (L9e)




fig|6666666.60966.peg.527
CDS
487678
488151
1
+
474
SSU ribosomal protein
-none-
D23_1c0528
Neut_0575








S5p (S2e)




fig|6666666.60966.peg.528
CDS
488796
490118
3
+
1323
Preprotein translocase
-none-
D23_1c0530
Neut_0578








secY subunit (TC











3.A.5.1.1)




fig|6666666.60966.peg.530
CDS
491337
491963
3
+
627
SSU ribosomal protein
-none-
D23_1c0531
Neut_0582








S4p (S9e)




fig|6666666.60966.peg.531
CDS
492065
492997
2
+
933
DNA-directed RNA
RNA polymerase
D23_1c0532
Neut_0583








polymerase alpha
bacterial










subunit (EC 2.7.7.6)




fig|6666666.60966.peg.532
CDS
494213
493998
−2
−
216
Putative oligoketide
Possible RNA
D23_1c0534
Neut_0586








cyclase/dehydratase or
degradation cluster










lipid transport protein











YfjG




fig|6666666.60966.peg.533
CDS
494546
494995
2
+
450
tmRNA-binding protein
Heat shock dnaK gene
D23_1c0535
Neut_0587








SmpB
cluster extended;











<br>Translation











termination factors











bacterial



fig|6666666.60966.peg.534
CDS
495005
496075
2
+
1071
Heme A synthase,
Biogenesis of
D23_1c0536
Neut_0588








cytochrome oxidase
cytochrome c oxidases










biogenesis protein











Cox15-CtaA




fig|6666666.60966.peg.535
CDS
496163
496582
2
+
420
Probable
-none-
D23_1c0537
Neut_0589








transmembrane protein




fig|6666666.60966.peg.537
CDS
496945
498528
1
+
1584
DNA polymerase III
DNA processing cluster
D23_1c0538
Neut_0590








subunits gamma and











tau (EC 2.7.7.7)




fig|6666666.60966.peg.538
CDS
498545
498868
2
+
324
FIG000557:
DNA processing cluster
D23_1c0539
Neut_0591








hypothetical protein co-











occurring with RecR




fig|6666666.60966.peg.539
CDS
498922
499740
1
+
819
Pseudouridine synthase
-none-
D23_1c0540
Neut_0592








family protein




fig|6666666.60966.peg.540
CDS
500690
499770
−2
−
921
Protein-N(5)-glutamine
-none-
D23_1c0541
Neut_0593








methyltransferase











PrmB, methylates LSU











ribosomal protein L3p




fig|6666666.60966.peg.541
CDS
500738
501241
2
+
504
tRNA-specific
tRNA modification
D23_1c0542
Neut_0594








adenosine-34
Bacteria; <br>tRNA










deaminase (EC 3.5.4.—)
processing



fig|6666666.60966.peg.542
CDS
501238
501717
1
+
480
Conserved domain
-none-
D23_1c0543
Neut_0595








protein




fig|6666666.60966.peg.543
CDS
501779
503389
2
+
1611
NAD-dependent malic
Pyruvate metabolism I:
D23_1c0544
Neut_0596








enzyme (EC 1.1.1.38)
anaplerotic reactions,











PEP



fig|6666666.60966.peg.544
CDS
504268
503438
−1
−
831
Phosphoserine
Glycine and Serine
D23_1c0545
Neut_0597








phosphatase (EC
Utilization; <br>Serine










3.1.3.3)
Biosynthesis; <br>Serine











Biosynthesis



fig|6666666.60966.peg.545
CDS
505831
504356
−1
−
1476
FIG00858790:
-none-
D23_1c0546
Neut_0598








hypothetical protein




fig|6666666.60966.peg.547
CDS
506088
507581
3
+
1494
Cytosol aminopeptidase
Aminopeptidases (EC
D23_1c0547
Neut_0599








PepA (EC 3.4.11.1)
3.4.11.—);











<br>Dehydrogenase











complexes



fig|6666666.60966.peg.548
CDS
507615
508043
3
+
429
DNA polymerase III chi
-none-
D23_1c0548
Neut_0600








subunit (EC 2.7.7.7)




fig|6666666.60966.peg.549
CDS
508116
508517
3
+
402
FIG00859089:
-none-
D23_1c0549
Neut_0601








hypothetical protein




fig|6666666.60966.peg.550
CDS
508581
511334
3
+
2754
Valyl-tRNA synthetase
tRNA aminoacylation,
D23_1c0550
Neut_0602








(EC 6.1.1.9)
Val



fig|6666666.60966.peg.551
CDS
511430
512500
2
+
1071
Uroporphyrinogen III
Heme and Siroheme
D23_1c0551
Neut_0603








decarboxylase (EC
Biosynthesis










4.1.1.37)




fig|6666666.60966.peg.552
CDS
513466
512660
−1
−
807
Maebl
-none-
D23_1c0552
Neut_0604

fig|6666666.60966.peg.553
CDS
514503
513616
−3
−
888
Succinyl-CoA ligase
TCA Cycle
D23_1c0553
Neut_0605








[ADP-forming] alpha











chain (EC 6.2.1.5)




fig|6666666.60966.peg.554
CDS
515705
514533
−2
−
1173
Succinyl-CoA ligase
TCA Cycle
D23_1c0554
Neut_0606








[ADP-forming] beta











chain (EC 6.2.1.5)




fig|6666666.60966.peg.555
CDS
516828
515878
−3
−
951
Malyl-CoA lyase (EC
Photorespiration
D23_1c0555
Neut_0607








4.1.3.24)
(oxidative C2 cycle)



fig|6666666.60966.peg.557
CDS
518554
517079
−1
−
1476
Glycogen synthase,
Glycogen metabolism
D23_1c0557
Neut_0608








ADP-glucose











transglucosylase (EC











2.4.1.21)




fig|6666666.60966.peg.558
CDS
520242
518608
−3
−
1635
Glucose-6-phosphate
Glycolysis and
D23_1c0558
Neut_0609








isomerase (EC 5.3.1.9)
Gluconeogenesis



fig|6666666.60966.peg.559
CDS
521449
520271
−1
−
1179
3-ketoacyl-CoA thiolase
Acetyl-CoA fermentation
D23_1c0559
Neut_0610








(EC 2.3.1.16) @ Acetyl-
to Butyrate; <br>Biotin










CoA acetyltransferase
biosynthesis; <br>Biotin










(EC 2.3.1.9)
synthesis cluster;











<br>Butanol











Biosynthesis;











<br>Butyrate











metabolism cluster;











<br>Fatty acid











metabolism cluster;











<br>Isoprenoid











Biosynthesis;











<br>Polyhydroxybutyrate











metabolism;











<br>Polyhydroxybutyrate











metabolism



fig|6666666.60966.peg.560
CDS
522790
521459
−1
−
1332
ATP-dependent hsl
Proteasome bacterial;
D23_1c0560
Neut_0611








protease ATP-binding
<br>Proteolysis in










subunit HslU
bacteria, ATP-dependent



fig|6666666.60966.peg.561
CDS
523346
522825
−2
−
522
ATP-dependent
Proteasome bacterial;
D23_1c0561
Neut_0612








protease HslV (EC
<br>Proteolysis in










3.4.25.—)
bacteria, ATP-dependent



fig|6666666.60966.peg.563
CDS
523758
523555
−3
−
204
DNA-directed RNA
RNA polymerase
D23_1c0562
Neut_0613








polymerase omega
bacterial










subunit (EC 2.7.7.6)




fig|6666666.60966.peg.564
CDS
524414
523809
−2
−
606
Guanylate kinase (EC
CBSS-
D23_1c0563
Neut_0614








2.7.4.8)
323097.3.peg.2594;











<br>Purine conversions



fig|6666666.60966.peg.565
CDS
525166
524684
−1
−
483
Dihydroneopterin
Folate Biosynthesis
D23_1c0565
Neut_0615








triphosphate











pyrophosphohydrolase











type 2 (nudB)




fig|6666666.60966.peg.566
CDS
526961
525180
−2
−
1782
Aspartyl-tRNA
tRNA aminoacylation,
D23_1c0566
Neut_0616








synthetase (EC 6.1.1.12)
Asp and Asn; <br>tRNA










@ Aspartyl-tRNA(Asn)
aminoacylation, Asp and










synthetase (EC 6.1.1.23)
Asn



fig|6666666.60966.peg.567
CDS
527054
527206
2
+
153
hypothetical protein
-none-
D23_1c0567
NA

fig|6666666.60966.peg.568
CDS
528907
527456
−1
−
1452
Mannose-1-phosphate
Mannose Metabolism;
D23_1c0569
Neut_0618








guanylyltransferase
<br>Mannose










(GDP) (EC 2.7.7.22)/
Metabolism










Mannose-6-phosphate











isomerase (EC 5.3.1.8)




fig|6666666.60966.peg.569
CDS
530083
528971
−1
−
1113
UDP-N-
CMP-N-
D23_1c0570
Neut_0619








acetylglucosamine 2-
acetylneuraminate










epimerase (EC 5.1.3.14)
Biosynthesis; <br>Sialic











Acid Metabolism



fig|6666666.60966.peg.570
CDS
530171
530284
2
+
114
hypothetical protein
-none-
D23_1c0571
NA

fig|6666666.60966.peg.571
CDS
530407
530535
1
+
129
hypothetical protein
-none-
D23_1c0572
NA

fig|6666666.60966.peg.572
CDS
530637
531041
3
+
405
Truncated hemoglobins
-none-
D23_1c0573
Neut_0620

fig|6666666.60966.peg.573
CDS
531034
532257
1
+
1224
NnrS protein involved in
Denitrification;
D23_1c0574
Neut_0621








response to NO
<br>Nitrosative stress;











<br>Oxidative stress



fig|6666666.60966.peg.574
CDS
532298
532738
2
+
441
putative membrane
-none-
D23_1c0575
Neut_0622








protein




fig|6666666.60966.peg.575
CDS
532841
533326
2
+
486
FIG001943:
Broadly distributed
D23_1c0576
Neut_0623








hypothetical protein
proteins not in










YajQ
subsystems



fig|6666666.60966.peg.576
CDS
534972
533485
−3
−
1488
FIG00859034:
-none-
D23_1c0577
Neut_0624








hypothetical protein




fig|6666666.60966.peg.577
CDS
535028
535240
2
+
213
hypothetical protein
-none-
D23_1c0578
NA

fig|6666666.60966.peg.578
CDS
536092
535289
−1
−
804
FIG00858513:
-none-
D23_1c0579
Neut_0626








hypothetical protein




fig|6666666.60966.peg.579
CDS
537497
536616
−2
−
882
hypothetical protein
-none-
D23_1c0581
NA

fig|6666666.60966.peg.580
CDS
538547
537726
−2
−
822
hypothetical protein
-none-
D23_1c0582
NA

fig|6666666.60966.peg.581
CDS
539856
538789
−3
−
1068
Conserved domain
-none-
D23_1c0583
NA








protein




fig|6666666.60966.peg.582
CDS
540712
539849
−1
−
864
Conserved domain
-none-
D23_1c0584
NA








protein




fig|6666666.60966.peg.583
CDS
541704
540841
−3
−
864
possible long-chain N-
-none-
D23_1c0585
Neut_0638








acyl amino acid











synthase




fig|6666666.60966.peg.584
CDS
541934
541812
−2
−
123
hypothetical protein
-none-
D23_1c0586
NA

fig|6666666.60966.peg.586
CDS
542270
542467
2
+
198
conserved hypothetical
-none-
D23_1c0587
Neut_0639








protein




fig|6666666.60966.peg.587
CDS
542451
542618
3
+
168
hypothetical protein
-none-
D23_1c0588
Neut_0640

fig|6666666.60966.peg.588
CDS
542602
542724
1
+
123
hypothetical protein
-none-
D23_1c0589
Neut_0641

fig|6666666.60966.peg.590
CDS
543111
544673
3
+
1563
Putative inner
-none-
D23_1c0590
Neut_0642








membrane protein




fig|6666666.60966.peg.591
CDS
544721
544834
2
+
114
hypothetical protein
-none-
D23_1c0591
NA

fig|6666666.60966.peg.592
CDS
545193
546098
3
+
906
Membrane-bound lytic
CBSS-228410.1.peg.134;
D23_1c0592
Neut_0643








murein transglycosylase
<br>CBSS-










D precursor (EC 3.2.1.—)
342610.3.peg.1536;











<br>Murein Hydrolases



fig|6666666.60966.peg.593
CDS
546933
546274
−3
−
660
Endonuclease III (EC
DNA Repair Base
D23_1c0593
Neut_0644








4.2.99.18)
Excision



fig|6666666.60966.peg.594
CDS
547586
546930
−2
−
657
Electron transport
-none-
D23_1c0594
Neut_0645








complex protein RnfB




fig|6666666.60966.peg.595
CDS
548604
547576
−3
−
1029
Dihydroorotate
De Novo Pyrimidine
D23_1c0595
Neut_0646








dehydrogenase (EC
Synthesis










1.3.3.1)




fig|6666666.60966.peg.596
CDS
549246
548605
−3
−
642
Arginine-tRNA-protein
Protein degradation
D23_1c0596
Neut_0647








transferase (EC 2.3.2.8)




fig|6666666.60966.peg.597
CDS
550041
549343
−3
−
699
Leucyl/phenylalanyl-
Protein degradation
D23_1c0597
Neut_0648








tRNA-protein











transferase (EC 2.3.2.6)




fig|6666666.60966.peg.598
CDS
550783
550328
−1
−
456
Mobile element protein
-none-
D23_1c0598
Neut_2502

fig|6666666.60966.peg.599
CDS
551132
550746
−2
−
387
Mobile element protein
-none-
D23_1c0599
Neut_0884

fig|6666666.60966.peg.600
CDS
551404
551517
1
+
114
hypothetical protein
-none-
D23_1c0600
NA

fig|6666666.60966.peg.601
CDS
551625
552500
3
+
876
FIG00859053:
-none-
D23_1c0601
Neut_0650








hypothetical protein




fig|6666666.60966.peg.602
CDS
554066
552684
−2
−
1383
UDP-N-
Peptidoglycan
D23_1c0602
Neut_0651








acetylmuramate:L-
biosynthesis--gjo;










alanyl-gamma-D-
<br>Recycling of










glutamyl-meso-
Peptidoglycan Amino










diaminopimelate ligase
Acids










(EC 6.3.2.—)




fig|6666666.60966.peg.603
CDS
554191
555363
1
+
1173
NADH dehydrogenase
Respiratory
D23_1c0603
Neut_0652








(EC 1.6.99.3)
dehydrogenases 1;











<br>Riboflavin synthesis











cluster



fig|6666666.60966.peg.604
CDS
556325
555387
−2
−
939
Mutator mutT protein
Nudix proteins
D23_1c0604
Neut_0653








(7,8-dihydro-8-
(nucleoside triphosphate










oxoguanine-
hydrolases); <br>Nudix










triphosphatase) (EC
proteins (nucleoside










3.6.1.—)/Thiamin-
triphosphate hydrolases)










phosphate











pyrophosphorylase-like











protein




fig|6666666.60966.peg.605
CDS
557210
556338
−2
−
873
putative ATP/GTP-
-none-
D23_1c0605
Neut_0654








binding protein




fig|6666666.60966.peg.606
CDS
558441
557212
−3
−
1230
Glutamate N-
Arginine Biosynthesis--
D23_1c0607
Neut_0655








acetyltransferase (EC
gjo; <br>Arginine










2.3.1.35)/N-
Biosynthesis--gjo;










acetylglutamate
<br>Arginine










synthase (EC 2.3.1.1)
Biosynthesis extended;











<br>Arginine











Biosynthesis extended



fig|6666666.60966.peg.607
CDS
558602
559015
2
+
414
FIG136845: Rhodanese-
Glutaredoxin 3
D23_1c0608
Neut_0656








related
containing cluster










sulfurtransferase




fig|6666666.60966.peg.608
CDS
559045
559302
1
+
258
Glutaredoxin 3 (Grx3)
Glutaredoxin 3
D23_1c0609
Neut_0657









containing cluster;











<br>Glutaredoxins;











<br>Glutathione: Redox











cycle



fig|6666666.60966.peg.609
CDS
559377
559862
3
+
486
Protein export
Glutaredoxin 3
D23_1c0610
Neut_0658








cytoplasm chaperone
containing cluster










protein (SecB,











maintains protein to be











exported in unfolded











state)




fig|6666666.60966.peg.610
CDS
559866
560345
3
+
480
FIG00859406:
-none-
D23_1c0611
Neut_0659








hypothetical protein




fig|6666666.60966.peg.611
CDS
560342
561331
2
+
990
Glycerol-3-phosphate
Glutaredoxin 3
D23_1c0612
Neut_0660








dehydrogenase
containing cluster;










[NAD(P)+] (EC 1.1.1.94)
<br>Glycerol and











Glycerol-3-phosphate











Uptake and Utilization;











<br>Glycerolipid and











Glycerophospholipid











Metabolism in Bacteria



fig|6666666.60966.peg.612
CDS
561519
561791
3
+
273
DNA-binding protein
DNA structural proteins,
D23_1c0613
Neut_0661








HU-beta
bacterial



fig|6666666.60966.peg.614
CDS
562230
564023
3
+
1794
Peptidyl-prolyl cis-trans
Peptidyl-prolyl cis-trans
D23_1c0616
Neut_0662








isomerase PpiD (EC
isomerase










5.2.1.8)




fig|6666666.60966.peg.615
CDS
564844
564050
−1
−
795
Enoyl-[acyl-carrier-
Fatty Acid Biosynthesis
D23_1c0617
Neut_0663








protein] reductase
FASII










[NADH] (EC 1.3.1.9)




fig|6666666.60966.peg.616
CDS
565168
564959
−1
−
210
hypothetical protein
-none-
D23_1c0618
NA

fig|6666666.60966.peg.617
CDS
565170
567587
3
+
2418
Transcription accessory
CBSS-243265.1.peg.198;
D23_1c0619
Neut_0664








protein (S1 RNA-binding
<br>Transcription










domain)
factors bacterial



fig|6666666.60966.peg.618
CDS
567598
567975
1
+
378
hypothetical protein
-none-
D23_1c0620
Neut_0682

fig|6666666.60966.peg.619
CDS
567977
568255
2
+
279
hypothetical protein
-none-
D23_1c0621
Neut_0682

fig|6666666.60966.peg.621
CDS
568500
568871
3
+
372
hypothetical protein
-none-
D23_1c0622
Neut_0683

fig|6666666.60966.peg.622
CDS
569150
568989
−2
−
162
hypothetical protein
-none-
D23_1c0623
Neut_0684

fig|6666666.60966.peg.623
CDS
570485
569238
−2
−
1248
Mobile element protein
-none-
D23_1c0624
Neut_0357

fig|6666666.60966.peg.624
CDS
571236
570577
−3
−
660
N-hydroxyarylamine O-
-none-
D23_1c0626
Neut_0684








acetyltransferase (EC











2.3.1.118)




fig|6666666.60966.peg.625
CDS
572209
571295
−1
−
915
Permease of the
Queuosine-Archaeosine
D23_1c0627
Neut_0685








drug/metabolite
Biosynthesis










transporter (DMT)











superfamily




fig|6666666.60966.peg.626
CDS
573622
572339
−1
−
1284
TRAP dicarboxylate
TRAP Transporter
D23_1c0628
Neut_0686








transporter, DctM
unknown substrate 6










subunit, unknown











substrate 6




fig|6666666.60966.peg.627
CDS
574259
573705
−2
−
555
TRAP dicarboxylate
TRAP Transporter
D23_1c0629
Neut_0687








transporter, DctQ
unknown substrate 6










subunit, unknown











substrate 6




fig|6666666.60966.peg.628
CDS
575698
574334
−1
−
1365
TldE protein, part of
Putative TldE-TldD
D23_1c0630
Neut_0688








TldE/TldD proteolytic
proteolytic complex










complex




fig|6666666.60966.peg.629
CDS
575950
576474
1
+
525
FIG138315: Putative
Putative TldE-TldD
D23_1c0632
Neut_0689








alpha helix protein
proteolytic complex



fig|6666666.60966.peg.630
CDS
576475
576609
1
+
135
hypothetical protein
-none-
D23_1c0633
NA

fig|6666666.60966.peg.631
CDS
576740
577006
2
+
267
FIG00859002:
-none-
D23_1c0635
Neut_0690








hypothetical protein




fig|6666666.60966.peg.632
CDS
577046
577804
2
+
759
Exodeoxyribonuclease
DNA repair, bacterial
D23_1c0636
Neut_0691








III (EC 3.1.11.2)




fig|6666666.60966.peg.633
CDS
577801
579195
1
+
1395
AmpG permease
Recycling of
D23_1c0637
Neut_0692









Peptidoglycan Amino











Acids



fig|6666666.60966.peg.636
CDS
580217
579867
−2
−
351
Cytochrome O
Terminal cytochrome O
D23_1c0638
Neut_0694








ubiquinol oxidase
ubiquinol oxidase;










subunit IV (EC 1.10.3.—)
<br>Terminal











cytochrome oxidases



fig|6666666.60966.peg.637
CDS
580885
580214
−1
−
672
Cytochrome O
Terminal cytochrome O
D23_1c0639
Neut_0695








ubiquinol oxidase
ubiquinol oxidase;










subunit III (EC 1.10.3.—)
<br>Terminal











cytochrome oxidases



fig|6666666.60966.peg.638
CDS
582993
580882
−3
−
2112
Cytochrome O
Terminal cytochrome O
D23_1c0640
Neut_0696








ubiquinol oxidase
ubiquinol oxidase;










subunit 1 (EC 1.10.3.—)
<br>Terminal











cytochrome oxidases



fig|6666666.60966.peg.639
CDS
583998
582997
−3
−
1002
Cytochrome O
Terminal cytochrome O
D23_1c0641
Neut_0697








ubiquinol oxidase
ubiquinol oxidase;










subunit II (EC 1.10.3.—)
<br>Terminal











cytochrome oxidases



fig|6666666.60966.peg.640
CDS
585484
584237
−1
−
1248
Mobile element protein
-none-
D23_1c0642
Neut_0357

fig|6666666.60966.peg.641
CDS
585502
585633
1
+
132
patatin family protein
-none-
D23_1c0643
Neut_1317

fig|6666666.60966.peg.642
CDS
585643
586530
1
+
888
UTP--glucose-1-
-none-
D23_1c0644
Neut_0698








phosphate











uridylyltransferase (EC











2.7.7.9)




fig|6666666.60966.peg.643
CDS
586705
587817
1
+
1113
FIG00859666:
-none-
D23_1c0645
Neut_0699








hypothetical protein




fig|6666666.60966.peg.644
CDS
587837
589201
2
+
1365
Succinate-semialdehyde
-none-
D23_1c0646
Neut_0700








dehydrogenase [NAD]











(EC 1.2.1.24); Succinate-











semialdehyde











dehydrogenase











[NADP+] (EC 1.2.1.16)




fig|6666666.60966.peg.645
CDS
589224
590942
3
+
1719
InterPro IPR001440
-none-
D23_1c0647
Neut_0701








COGs COG0457




fig|6666666.60966.peg.646
CDS
592871
591033
−2
−
1839
Long-chain-fatty-acid--
Biotin biosynthesis;
D23_1c0648
Neut_0702








CoA ligase (EC 6.2.1.3)
<br>Biotin synthesis











cluster; <br>Fatty acid











metabolism cluster



fig|6666666.60966.peg.647
CDS
595204
592868
−1
−
2337
Butyryl-CoA
-none-
D23_1c0649
Neut_0703








dehydrogenase (EC











1.3.99.2)




fig|6666666.60966.peg.648
CDS
595489
595223
−1
−
267
hypothetical protein
-none-
D23_1c0650
Neut_0704

fig|6666666.60966.peg.649
CDS
596053
595673
−1
−
381
Putative membrane
-none-
D23_1c0651
Neut_0705








protein




fig|6666666.60966.peg.650
CDS
596962
596099
−1
−
864
Pirin
-none-
D23_1c0652
Neut_0706

fig|6666666.60966.peg.651
CDS
597098
598030
2
+
933
Transcriptional
-none-
D23_1c0653
Neut_0707








regulator, LysR family




fig|6666666.60966.peg.652
CDS
598202
599338
2
+
1137
hypothetical protein
-none-
D23_1c0655
Neut_0708

fig|6666666.60966.peg.653
CDS
599418
599657
3
+
240
Flavodoxin reductases
Anaerobic respiratory
D23_1c0656
Neut_0709








(ferredoxin-NADPH
reductases










reductases) family 1




fig|6666666.60966.peg.654
CDS
599689
600114
1
+
426
Flavodoxin reductases
Anaerobic respiratory
D23_1c0657
Neut_0709








(ferredoxin-NADPH
reductases










reductases) family 1




fig|6666666.60966.peg.655
CDS
601243
600251
−1
−
993
Multicopper oxidase
Copper homeostasis
D23_1c0658
Neut_0710

fig|6666666.60966.peg.656
CDS
602188
601454
−1
−
735
FIG00859807:
-none-
D23_1c0659
Neut_0711








hypothetical protein




fig|6666666.60966.peg.657
CDS
602534
602346
−2
−
189
hypothetical protein
-none-
D23_1c0660
Neut_0712

fig|6666666.60966.peg.658
CDS
602837
602700
−2
−
138
Putative NAD(P)-
-none-
D23_1c0661
Neut_0990








dependent











oxidoreductase EC-











YbbO




fig|6666666.60966.peg.659
CDS
603148
602882
−1
−
267
ABC-type multidrug
CBSS-196164.1.peg.1690
D23_1c0662
Neut_0713








transport system,











permease component




fig|6666666.60966.peg.660
CDS
603362
605239
2
+
1878
1,4-alpha-glucan
-none-
D23_1c0663
Neut_0714








branching enzyme (EC











2.4.1.18)




fig|6666666.60966.peg.661
CDS
605497
605619
1
+
123
Glutathione peroxidase
Glutathione: Redox cycle
D23_1c0664
Neut_0715








(EC 1.11.1.9)




fig|6666666.60966.peg.662
CDS
607768
605882
−1
−
1887
TonB-dependent hemin,
Ton and Tol transport
D23_1c0665
Neut_0716








ferrichrome receptor
systems



fig|6666666.60966.peg.663
CDS
609583
607862
−1
−
1722
hypothetical protein
-none-
D23_1c0666
Neut_0717

fig|6666666.60966.peg.664
CDS
610957
609656
−1
−
1302
Membrane protein
-none-
D23_1c0667
Neut_0718








involved in colicin











uptake




fig|6666666.60966.peg.665
CDS
611184
612413
3
+
1230
FIG00858430:
-none-
D23_1c0668
Neut_0719








hypothetical protein




fig|6666666.60966.peg.666
CDS
612533
615022
2
+
2490
TonB-dependent
Ton and Tol transport
D23_1c0669
Neut_0720








receptor
systems



fig|6666666.60966.peg.667
CDS
615143
615012
−2
−
132
hypothetical protein
-none-
D23_1c0670
NA

fig|6666666.60966.peg.668
CDS
615337
617457
1
+
2121
TonB-dependent
Ton and Tol transport
D23_1c0672
Neut_0721








receptor
systems



fig|6666666.60966.peg.669
CDS
617524
618762
1
+
1239
putative signal peptide
-none-
D23_1c0673
Neut_0722








protein




fig|6666666.60966.peg.670
CDS
618762
619262
3
+
501
InterPro IPR000063
-none-
D23_1c0674
Neut_0723








COGs COG0526




fig|6666666.60966.peg.671
CDS
619459
621978
1
+
2520
Enoyl-CoA hydratase
Acetyl-CoA fermentation
D23_1c0675
Neut_0724








(EC 4.2.1.17)/3,2-
to Butyrate; <br>Acetyl-










trans-enoyl-CoA
CoA fermentation to










isomerase (EC 5.3.3.8)/
Butyrate; <br>Butanol










3-hydroxyacyl-CoA
Biosynthesis;










dehydrogenase (EC
<br<Butyrate










1.1.1.35)
metabolism cluster;











<br>Butyrate











metabolism cluster;











<br>Fatty acid











metabolism cluster;











<br>Fatty acid











metabolism cluster;











<br>Polyhydroxybutyrate











metabolism;











<br>Polyhydroxybutyrate











metabolism



fig|6666666.60966.peg.672
CDS
622043
623245
2
+
1203
3-ketoacyl-CoA thiolase
Acetyl-CoA fermentation
D23_1c0676
Neut_0725








(EC 2.3.1.16) @ Acetyl-
to Butyrate; <br>Biotin










CoA acetyltransferase
biosynthesis; <br>Biotin










(EC 2.3.1.9)
synthesis cluster;











<br>Butanol











Biosynthesis;











<br>Butyrate











metabolism cluster;











<br>Fatty acid











metabolism cluster;











<br>Isoprenoid











Biosynthesis;











<br>Polyhydroxybutyrate











metabolism;











<br>Polyhydroxybutyrate











metabolism



fig|6666666.60966.peg.673
CDS
623639
623301
−2
−
339
FIG00859796:
-none-
D23_1c0677
Neut_0726








hypothetical protein




fig|6666666.60966.peg.674
CDS
623711
623827
2
+
117
hypothetical protein
-none-
D23_1c0678
NA

fig|6666666.60966.peg.675
CDS
624186
624479
3
+
294
Mobile element protein
-none-
D23_1c0680
Neut_1719

fig|6666666.60966.peg.676
CDS
624578
625456
2
+
879
Mobile element protein
-none-
D23_1c0681
Neut_1720

fig|6666666.60966.peg.677
CDS
626009
625605
−2
−
405
hypothetical protein
-none-
D23_1c0682
NA

fig|6666666.60966.peg.678
CDS
626270
628669
2
+
2400
Predicted hydrolase of
-none-
D23_1c0684
Neut_0728








the metallo-beta-











lactamase superfamily,











clustered with KDO2-











Lipid A biosynthesis











genes




fig|6666666.60966.peg.679
CDS
628866
629183
3
+
318
Flagellar transcriptional
Flagellum
D23_1c0685
Neut_0729








activator FlhD




fig|6666666.60966.peg.680
CDS
629210
629785
2
+
576
Flagellar transcriptional
Flagellum
D23_1c0686
Neut_0730








activator FlhC




fig|6666666.60966.peg.681
CDS
630020
631549
2
+
1530
Proposed peptidoglycan
Peptidoglycan lipid II
D23_1c0687
Neut_0731








lipid II flippase MurJ
flippase



fig|6666666.60966.peg.683
CDS
633437
632277
−2
−
1161
Outer membrane
Lipopolysaccharide
D23_1c0688
Neut_0732








protein NlpB,
assembly










lipoprotein component











of the protein assembly











complex (forms a











complex with YaeT,











YfiO, and YfgL);











Lipoprotein-34











precursor




fig|6666666.60966.peg.684
CDS
634289
633447
−2
−
843
Dihydrodipicolinate
-none-
D23_1c0689
Neut_0733








synthase (EC 4.2.1.52)




fig|6666666.60966.peg.685
CDS
637007
634416
−2
−
2592
ClpB protein
Protein chaperones;
D23_1c0690
Neut_0734








<br>Proteolysis in











bacteria, ATP-dependent




fig|6666666.60966.peg.686
CDS
637484
637326
−2
−
159
hypothetical protein
-none-
D23_1c0693
NA

fig|6666666.60966.peg.687
CDS
638994
637501
−3
−
1494
Ferredoxin-dependent
Ammonia assimilation;
D23_1c0694
Neut_0735








glutamate synthase (EC
<br>Glutamine,










1.4.7.1)
Glutamate, Aspartate











and Asparagine











Biosynthesis



fig|6666666.60966.peg.688
CDS
639034
639930
1
+
897
Quinolinate

Mycobacterium

D23_1c0695
NA








phosphoribosyltransferase
virulence operon










[decarboxylating]
possibly involved in










(EC 2.4.2.19)
quinolinate biosynthesis;











<br>NAD and NADP











cofactor biosynthesis











global



fig|6666666.60966.peg.689
CDS
641903
640635
−2
−
1269
Flagellar hook-length
Flagellum
D23_1c0696
Neut_0740








control protein FliK




fig|6666666.60966.peg.690
CDS
642413
641961
−2
−
453
Flagellar protein FliJ
Flagellum
D23_1c0697
Neut_0741

fig|6666666.60966.peg.691
CDS
643836
642430
−3
−
1407
Flagellum-specific ATP
Flagellar motility;
D23_1c0698
Neut_0742








synthase Flil
<br>Flagellum



fig|6666666.60966.peg.692
CDS
644577
643858
−3
−
720
Flagellar assembly
Flagellum
D23_1c0699
Neut_0743








protein FliH




fig|6666666.60966.peg.693
CDS
645764
644769
−2
−
996
Flagellar motor switch
Flagellum
D23_1c0700
Neut_0744








protein FliG




fig|6666666.60966.peg.694
CDS
647397
645754
−3
−
1644
Flagellar M-ring protein
Flagellum
D23_1C0701
Neut_0745








FliF




fig|6666666.60966.peg.695
CDS
647548
647402
−1
−
147
hypothetical protein
-none-
D23_1c0702
NA

fig|6666666.60966.peg.696
CDS
647628
648872
3
+
1245
Flagellar sensor
Flagellum
D23_1c0703
Neut_0746








histidine kinase FleS




fig|6666666.60966.peg.697
CDS
648876
650189
3
+
1314
InterPro
-none-
D23_1c0704
Neut_0747








IPR001789:IPR002078:IPR002197:











IPR003593











COGs COG2204




fig|6666666.60966.peg.698
CDS
650217
650546
3
+
330
Flagellar hook-basal
Flagellum; <br>Flagellum
D23_1c0705
Neut_0748








body complex protein
in Campylobacter










FliE




fig|6666666.60966.peg.699
CDS
650581
651390
1
+
810
FIG00858443:
-none-
D23_1c0706
Neut_0749








hypothetical protein




fig|6666666.60966.peg.700
CDS
651752
651411
−2
−
342
Flagellar biosynthesis
Flagellar motility;
D23_1c0707
Neut_0750








protein FlhB
<br>Flagellum



fig|6666666.60966.peg.701
CDS
652764
651739
−3
−
1026
FIG00726091:
-none-
D23_1c0708
Neut_0751








hypothetical protein




fig|6666666.60966.peg.702
CDS
652766
652948
2
+
183
hypothetical protein
-none-
D23_1c0709
NA

fig|6666666.60966.peg.703
CDS
653125
653517
1
+
393
hypothetical protein
-none-
D23_1c0710
Neut_2449

fig|6666666.60966.peg.704
CDS
653664
653810
3
+
147
Mobile element protein
-none-
D23_1c0711
Neut_1756

fig|6666666.60966.peg.705
CDS
654316
653858
−1
−
459
Cytochrome c family
-none-
D23_1c0712
Neut_0754








protein




fig|6666666.60966.peg.706
CDS
654869
654345
−2
−
525
CopG protein
Copper homeostasis
D23_1c0713
Neut_0755

fig|6666666.60966.peg.707
CDS
655268
656209
2
+
942
tRNA(Cytosine32)-2-
CBSS-
D23_1c0714
Neut_0756








thiocytidine synthetase
326442.4.peg.1852;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.708
CDS
657180
656236
−3
−
945
Lipoate synthase
Lipoic acid metabolism;
D23_1c0715
Neut_0757









<br>Lipoic acid synthesis











cluster; <br>Possible











RNA degradation cluster



fig|6666666.60966.peg.709
CDS
657847
657170
−1
−
678
Octanoate-[acyl-carrier-
Lipoic acid metabolism;
D23_1c0716
Neut_0758








protein]-protein-N-
<br>Lipoic acid synthesis










octanoyltransferase
cluster



fig|6666666.60966.peg.710
CDS
658198
657935
−1
−
264
Proposed lipoate
Lipoicacid metabolism;
D23_1c0717
Neut_0759








regulatory protein YbeD
<br>Lipoic acid synthesis











cluster



fig|6666666.60966.peg.711
CDS
659068
658208
−1
−
861
D-alanine
Pyruvate Alanine Serine
D23_1c0718
Neut_0760








aminotransferase (EC
Interconversions










2.6.1.21)




fig|6666666.60966.peg.712
CDS
660251
659088
−2
−
1164
D-alanyl-D-alanine
CBSS-84588.1.peg.1247;
D23_1c0719
Neut_0761








carboxypeptidase (EC
<br>Metallocarboxypeptidases










3.4.16.4)
(EC 3.4.17.—);











<br>Murein Hydrolases;











<br>Peptidoglycan











Biosynthesis



fig|6666666.60966.peg.713
CDS
660353
660787
2
+
435
LSU ribosomal protein
-none-
D23_1c0720
Neut_0762








L13p (L13Ae)




fig|6666666.60966.peg.714
CDS
660799
661191
1
+
393
SSU ribosomal protein
-none-
D23_1c0721
Neut_0763








S9p (S16e)




fig|6666666.60966.peg.715
CDS
661324
662352
1
+
1029
N-acetyl-gamma-
Arginine Biosynthesis--
D23_1c0722
Neut_0764








glutamyl-phosphate
gjo; <br>Arginine










reductase (EC 1.2.1.38)
Biosynthesis extended



fig|6666666.60966.peg.716
CDS
662454
663221
3
+
768
putative integral
-none-
D23_1c0723
Neut_0765








membrane protein




fig|6666666.60966.peg.717
CDS
663202
663627
1
+
426
Integral membrane
-none-
D23_1c0724
Neut_0766








protein CcmA involved











in cell shape











determination




fig|6666666.60966.peg.718
CDS
665316
663655
−3
−
1662
DNA repair protein
DNA repair, bacterial
D23_1c0725
Neut_0767








RecN




fig|6666666.60966.peg.719
CDS
666357
665326
−3
−
1032
NAD kinase (EC
NAD and NADP cofactor
D23_1c0726
Neut_0768








2.7.1.23)
biosynthesis global



fig|6666666.60966.peg.720
CDS
666433
667449
1
+
1017
Heat-inducible
GroEL GroES; <br>Heat
D23_1c0727
Neut_0769








transcription repressor
shock dnaK gene cluster










HrcA
extended



fig|6666666.60966.peg.721
CDS
667469
668566
2
+
1098
Ferrochelatase,
Heme and Siroheme
D23_1c0728
Neut_0770








protoheme ferro-lyase
Biosynthesis










(EC 4.99.1.1)




fig|6666666.60966.peg.722
CDS
668678
669469
2
+
792
Zn-dependent protease
-none-
D23_1c0729
Neut_0771








with chaperone











function PA4632




fig|6666666.60966.peg.723
CDS
669589
670461
1
+
873
Phosphoribulokinase
Calvin-Benson cycle
D23_1c0730
Neut_0772








(EC 2.7.1.19)




fig|6666666.60966.peg.724
CDS
670525
672771
1
+
2247
ATP-dependent DNA
DNA repair, bacterial
D23_1c0731
Neut_0773








helicase UvrD/PcrA
UvrD and related











helicases



fig|6666666.60966.peg.725
CDS
673569
672778
−3
−
792
Possible
-none-
D23_1c0732
Neut_0774








transmembrane protein




fig|6666666.60966.peg.726
CDS
674610
673660
−3
−
951
Homoserine kinase (EC
CBSS-
D23_1c0733
Neut_0775








2.7.1.39)
269482.1.peg.1294;











<br>Methionine











Biosynthesis;











<br>Threonine and











Homoserine











Biosynthesis



fig|6666666.60966.peg.727
CDS
674585
674716
2
+
132
hypothetical protein
-none-
D23_1c0734
NA

fig|6666666.60966.peg.728
CDS
675030
674704
−3
−
327
FIG00858562:
-none-
D23_1c0735
Neut_0776








hypothetical protein




fig|6666666.60966.peg.729
CDS
675190
674996
−1
−
195
hypothetical protein
-none-
D23_1c0736
NA

fig|6666666.60966.peg.730
CDS
675866
675147
−2
−
720
FIG00859241:
-none-
D23_1c0737
Neut_0777








hypothetical protein




fig|6666666.60966.peg.731
CDS
675882
678602
3
+
2721
DNA polymerase I (EC
DNA Repair Base
D23_1c0738
Neut_0778








2.7.7.7)
Excision



fig|6666666.60966.peg.732
CDS
678725
679912
2
+
1188
Fatty acid desaturase
-none-
D23_1c0739
Neut_0779








(EC 1.14.19.1); Delta-9











fatty acid desaturase











(EC 1.14.19.1)




fig|6666666.60966.peg.733
CDS
680149
679994
−1
−
156
LSU ribosomal protein
-none-
D23_1c0740
Neut_0780








L33p @ LSU ribosomal











protein L33p, zinc-











independent




fig|6666666.60966.peg.734
CDS
680390
680190
−2
−
201
LSU ribosomal protein
-none-
D23_1c0741
Neut_0781








L28p




fig|6666666.60966.peg.735
CDS
681169
680495
−1
−
675
DNA repair protein
Bacterial cell division
D23_1c0742
Neut_0782








RadC
cluster; <br>DNA repair,











bacterial



fig|6666666.60966.peg.736
CDS
681339
682508
3
+
1170
Phosphopantothenoylcysteine
Coenzyme A
D23_1c0743
Neut_0783








decarboxylase
Biosynthesis;










(EC 4.1.1.36)/
<br>Coenzyme A










Phosphopantothenoylcysteine
Biosynthesis










synthetase (EC











6.3.2.5)




fig|6666666.60966.peg.737
CDS
682518
682967
3
+
450
Deoxyuridine 5&#39;-
Housecleaning
D23_1c0744
Neut_0784








triphosphate
nucleoside triphosphate










nucleotidohydrolase (EC
pyrophosphatases;










3.6.1.23)
<br>Nudix proteins











(nucleoside triphosphate











hydrolases)



fig|6666666.60966.peg.738
CDS
682961
683386
2
+
426
exported protein
-none-
D23_1c0745
Neut_0785

fig|6666666.60966.peg.739
CDS
685816
683759
−1
−
2058
Pyrophosphate-
Phosphate metabolism
D23_1c0746
Neut_0786








energized proton pump











(EC 3.6.1.1)




fig|6666666.60966.peg.740
CDS
687229
685970
−1
−
1260
6-phosphofructokinase
Glycolysis and
D23_1c0747
Neut_0787








(EC 2.7.1.11)
Gluconeogenesis



fig|6666666.60966.peg.741
CDS
687933
687400
−3
−
534
Adenylate kinase (EC
Purine conversions
D23_1c0748
NA








2.7.4.3)




fig|6666666.60966.peg.742
CDS
688328
689359
2
+
1032
RecA protein
DNA repair, bacterial;
D23_1c0749
Neut_0789









<br>DNA repair system











including RecA, MutS











and a hypothetical











protein; <br>RecA and











RecX



fig|6666666.60966.peg.743
CDS
689362
689802
1
+
441
Regulatory protein RecX
DNA repair system
D23_1c0750
Neut_0790









including RecA, MutS











and a hypothetical











protein; <br>RecA and











RecX



fig|6666666.60966.peg.744
CDS
689820
692411
3
+
2592
Alanyl-tRNA synthetase
Cluster containing
D23_1c0751
Neut_0791








(EC 6.1.1.7)
Alanyl-tRNA synthetase;











<br>tRNA











aminoacylation, Ala



fig|6666666.60966.peg.745
CDS
692450
693403
2
+
954
Thioredoxin reductase
Thioredoxin-disulfide
D23_1c0752
Neut_0792








(EC 1.8.1.9)
reductase;











<br>pyrimidine











conversions



fig|6666666.60966.peg.746
CDS
693409
6939991
1
+
591
Smr domain
-none-
D23_1c0753
Neut_0793

fig|6666666.60966.peg.747
CDS
694203
694349
3
+
147
Carbonic anhydrase (EC
Zinc regulated enzymes
D23_1c0754
Neut_0794








4.2.1.1)




fig|6666666.60966.peg.750
CDS
695056
695208
1
+
153
hypothetical protein
-none-
D23_1c0755
Neut_1255

fig|6666666.60966.peg.751
CDS
695216
695383
2
+
168
hypothetical protein
-none-
D23_1c0756
Neut_2449

fig|6666666.60966.peg.752
CDS
695522
695986
2
+
465
Mobile element protein
-none-
D23_1c0758
Neut_1256

fig|6666666.60966.peg.753
CDS
696281
696072
−2
−
210
Chemotaxis regulator-
Flagellar motility
D23_1c0759
Neut_0796








transmits











chemoreceptor signals











to flagelllar motor











components CheY




fig|6666666.60966.peg.754
CDS
696491
696619
2
+
129
hypothetical protein
-none-
D23_1c0760
Neut_0797

fig|6666666.60966.peg.755
CDS
696639
696812
3
+
174
Mobile element protein
-none-
D23_1c0760
Neut_0797

fig|6666666.60966.peg.756
CDS
696806
696934
2
+
129
Mobile element protein
-none-
D23_1c0761
NA

fig|6666666.60966.peg.757
CDS
697179
698426
3
+
1248
Mobile element protein
-none-
D23_1c0762
Neut_0357

fig|6666666.60966.peg.758
CDS
698760
700454
3
+
1695
NADH dehydrogenase,
Respiratory Complex I
D23_1c0763
Neut_0799








subunit 5




fig|6666666.60966.peg.759
CDS
700473
701258
3
+
786
hypothetical protein
-none-
D23_1c0765
Neut_0800

fig|6666666.60966.peg.760
CDS
701243
704371
2
+
3129
Hypothetical
CO2 uptake,
D23_1c0766
Neut_0801








transmembrane protein
carboxysome;










coupled to NADH-
<br>Respiratory










ubiquinone
Complex I










oxidoreductase chain 5











homolog




fig|6666666.60966.peg.761
CDS
704368
704694
1
+
327
Nitrogen regulatory
Ammonia assimilation
D23_1c0767
Neut_0802








protein P-II




fig|6666666.60966.peg.762
CDS
704850
705059
3
+
210
hypothetical protein
-none-
D23_1c0768
Neut_0800

fig|6666666.60966.peg.763
CDS
705044
708184
2
+
3141
Hypothetical
CO2 uptake,
D23_1c0769
Neut_0801








transmembrane protein
carboxysome;










coupled to NADH-
<br>Respiratory










ubiquinone
Complex I










oxidoreductase chain 5











homolog




fig|6666666.60966.peg.764
CDS
708181
708507
1
+
327
Nitrogen regulatory
Ammonia assimilation
D23_1c0770
Neut_0802








protein P-II




fig|6666666.60966.peg.765
CDS
709429
708509
−1
−
921
RuBisCO operon
CO2 uptake,
D23_1c0771
Neut_0803








transcriptional
carboxysome










regulator CbbR




fig|6666666.60966.peg.766
CDS
709628
711049
2
+
1422
Ribulose bisphosphate
CO2 uptake,
D23_1c0772
Neut_0804








carboxylase large chain
carboxysome;










(EC 4.1.1.39)
<br>Calvin-Benson cycle;











<br>Photorespiration











(oxidative C2 cycle)



fig|6666666.60966.peg.767
CDS
711134
711460
2
+
327
Ribulose bisphosphate
CO2 uptake,
D23_1c0773
Neut_0805








carboxylase small chain
carboxysome;










(EC 4.1.1.39)
<br>Calvin-Benson cycle;











<br>Photorespiration











(oxidative C2 cycle)



fig|6666666.60966.peg.768
CDS
711860
711645
−2
−
216
hypothetical protein
-none-
D23_1c0774
Neut_0806

fig|6666666.60966.peg.769
CDS
711868
714264
1
+
2397
carboxysome shell
CO2 uptake,
D23_1c0774
Neut_0806








protein CsoS2
carboxysome



fig|6666666.60966.peg.770
CDS
714275
715804
2
+
1530
carboxysome shell
CO2 uptake,
D23_1c0775
Neut_0807








protein CsoS3
carboxysome



fig|6666666.60966.peg.771
CDS
715825
716082
1
+
258
putative carboxysome
CO2 uptake,
D23_1c0776
Neut_0808








peptide A
carboxysome



fig|6666666.60966.peg.772
CDS
716082
716330
3
+
249
putative carboxysome
CO2 uptake,
D23_1c0777
Neut_0809








peptide B
carboxysome



fig|6666666.60966.peg.773
CDS
716439
716735
3
+
297
carboxysome shell
CO2 uptake,
D23_1c0778
Neut_0810








protein CsoS1
carboxysome



fig|6666666.60966.peg.774
CDS
716777
717124
2
+
348
carboxysome shell
CO2 uptake,
D23_1c0779
Neut_0811








protein CsoS1
carboxysome



fig|6666666.60966.peg.775
CDS
717145
717567
1
+
423
bacterioferritin possible
-none-
D23_1c0780
Neut_0812








associated with











carboxysome




fig|6666666.60966.peg.776
CDS
717576
717842
3
+
267
Possible pterin-4 alpha-
CO2 uptake,
D23_1c0781
Neut_0813








carbinolamine
carboxysome










dehydratase-like











protein




fig|6666666.60966.peg.777
CDS
717911
718483
2
+
573
Chromosome (plasmid)
Bacterial Cell Division;
D23_1c0782
Neut_0814








partitioning protein
<br>Bacterial










ParA
Cytoskeleton; <br>Cell











Division Subsystem











including YidCD;











<br>RNA modification











and chromosome











partitioning cluster



fig|6666666.60966.peg.778
CDS
718480
718674
1
+
195
hypothetical protein
-none-
D23_1c0783
NA

fig|6666666.60966.peg.779
CDS
718681
719631
1
+
951
Rubisco activation
CO2 uptake,
D23_1c0784
Neut_0815








protein CbbQ
carboxysome



fig|6666666.60966.peg.780
CDS
719654
722014
2
+
2361
Rubisco activation
CO2 uptake,
D23_1c0785
Neut_0816








protein CbbO
carboxysome



fig|6666666.60966.peg.781
CDS
722027
722659
2
+
633
FIG00852745:
-none-
D23_1c0786
Neut_0817








hypothetical protein




fig|6666666.60966.peg.782
CDS
722704
723528
1
+
825
FIG00853400:
-none-
D23_1c0787
Neut_0818








hypothetical protein




fig|6666666.60966.peg.783
CDS
723822
723676
−3
−
147
Mobile element protein
-none-
D23_1c0788
NA

fig|6666666.60966.peg.784
CDS
723900
724055
3
+
156
hypothetical protein
-none-
D23_1c0790
NA

fig|6666666.60966.peg.785
CDS
724125
724304
3
+
180
Rubisco activation
CO2 uptake,
D23_1c0791
NA








protein CbbO
carboxysome



fig|6666666.60966.peg.786
CDS
724415
724621
2
+
207
Rubisco activation
CO2 uptake,
D23_1c0792
Neut_0816








protein CbbO
carboxysome



fig|6666666.60966.peg.787
CDS
724700
724975
2
+
276
Nitric oxide reductase
Denitrification;
D23_1c0793
Neut_0816








activation protein NorD
<br>Denitrifying











reductase gene clusters



fig|6666666.60966.peg.788
CDS
724985
725104
2
+
120
hypothetical protein
-none-
D23_1c0794
Neut_0816

fig|6666666.60966.peg.789
CDS
725079
725336
3
+
258
Nitric oxide reductase
Denitrification;
D23_1c0794
Neut_0816








activation protein NorD
<br>Denitrifying











reductase gene clusters



fig|6666666.60966.peg.790
CDS
725493
725657
3
+
165
hypothetical protein
-none-
D23_1c0795
Neut_0821

fig|6666666.60966.peg.791
CDS
727182
725782
−3
−
1401
FIG00861154:
-none-
D23_1c0796
Neut_1550








hypothetical protein




fig|6666666.60966.peg.792
CDS
727830
727411
−3
−
420
FIG00859219:
-none-
D23_1c0797
Neut_0823








hypothetical protein




fig|6666666.60966.peg.793
CDS
729449
728481
−2
−
969
Octaprenyl diphosphate
Isoprenoid Biosynthesis;
D23_1c0800
Neut_0825








synthase (EC 2.5.1.90)/
<br>Isoprenoid










Dimethylallyltransferase
Biosynthesis;










(EC 2.5.1.1)/(2E,6E)-
<br>Isoprenoid










farnesyl diphosphate
Biosynthesis:










synthase (EC 2.5.1.10)/
Interconversions;










Geranylgeranyl
<br>Isoprenoinds for










diphosphate synthase
Quinones;










(EC 2.5.1.29)
<br>Isoprenoinds for











Quinones;











<br>Isoprenoinds for











Quinones;











<br>Isoprenoinds for











Quinones;











<br>Polyprenyl











Diphosphate











Biosynthesis;











<br>Polyprenyl











Diphosphate











Biosynthesis;











<br>Polyprenyl











Diphosphate











Biosynthesis



fig|6666666.60966.peg.795
CDS
729633
730886
3
+
1254
Glutamyl-tRNA
A Gammaproteobacteria
D23_1c0801
Neut_0826








reductase (EC 1.2.1.70)
Cluster Relating to











Translation; <br>Heme











and Siroheme











Biosynthesis



fig|6666666.60966.peg.796
CDS
730883
731962
2
+
1080
Peptide chain release
A Gammaproteobacteria
D23_1c0802
Neut_0827








factor 1
Cluster Relating to











Translation; <br>CBSS-











216600.3.peg.802;











<br>Translation











termination factors











bacterial



fig|6666666.60966.peg.797
CDS
731959
732840
1
+
882
Protein-N(5)-glutamine
A Gammaproteobacteria
D23_1c0803
Neut_0828








methyltransferase
Cluster Relating to










PrmC, methylates
Translation; <br>CBSS-










polypeptide chain
216600.3.peg.802;










release factors RF1 and
<br>Translation










RF2
termination factors











bacterial



fig|6666666.60966.peg.798
CDS
732995
733303
2
+
309
Glutaredoxin-related
Glutaredoxins
D23_1c0805
Neut_0829








protein




fig|6666666.60966.peg.799
CDS
733743
733324
−3
−
420
Putative membrane
-none-
D23_1c0806
Neut_0830








protein




fig|6666666.60966.peg.800
CDS
734018
734161
2
+
144
hypothetical protein
-none-
D23_1c0807
NA

fig|6666666.60966.peg.801
CDS
734194
734826
1
+
633
Glutathione S-
Glutathione: Non-redox
D23_1c0808
Neut_0831








transferase (EC
reactions










2.5.1.18)




fig|6666666.60966.peg.802
CDS
735097
735381
1
+
285
conserved hypothetical
-none-
D23_1c0809
Neut_0832








protein




fig|6666666.60966.peg.803
CDS
735730
736488
1
+
759
hypothetical protein
-none-
D23_1c0810
Neut_0833

fig|6666666.60966.peg.804
CDS
737600
736485
−2
−
1116
COGs COG1502
-none-
D23_1c0811
Neut_0834

fig|6666666.60966.peg.805
CDS
738943
737585
−1
−
1359
hypothetical protein
-none-
D23_1c0812
Neut_0835

fig|6666666.60966.peg.806
CDS
739386
739240
−3
−
147
hypothetical protein
-none-
D23_1c0813
NA

fig|6666666.60966.peg.807
CDS
740790
739585
−3
−
1206
DnaJ domain protein
-none-
D23_1c0814
Neut_0836

fig|6666666.60966.peg.809
CDS
742340
741159
−2
−
1182
Putative
-none-
D23_1c0815
Neut_0837








aminotransferase




fig|6666666.60966.peg.810
CDS
744454
742337
−1
−
2118
Conserved domain
-none-
D23_1c0816
Neut_0838








protein




fig|6666666.60966.peg.811
CDS
744823
744647
−1
−
177
hypothetical protein
-none-
D23_1c0817
NA

fig|6666666.60966.peg.812
CDS
745953
745228
−3
−
726
hypothetical protein
-none-
D23_1c0818
Neut_0840

fig|6666666.60966.peg.814
CDS
748473
746350
−3
−
2124
InterPro IPR000209
-none-
D23_1c0820
Neut_0841








COGs COG1404




fig|6666666.60966.peg.815
CDS
748862
749245
2
+
384
ApaG protein
EC49-61
D23_1c0822
Neut_0842

fig|6666666.60966.peg.816
CDS
749258
749992
2
+
735
Tetrapyrrole methylase
-none-
D23_1c0823
Neut_0843








family protein




fig|6666666.60966.peg.817
CDS
751297
750077
−1
−
1221
Proton/glutamate
Glutamate and
D23_1c0824
Neut_0844








symport protein @
Aspartate uptake in










Sodium/glutamate
Bacteria










symport protein




fig|6666666.60966.peg.818
CDS
752156
751611
−2
−
546
Cytochrome c-type
Biogenesis of c-type
D23_1c0825
Neut_0845








biogenesis protein ResA
cytochromes



fig|6666666.60966.peg.819
CDS
754247
752304
−2
−
1944
Cytochrome c-type
Biogenesis of c-type
D23_1c0826
Neut_0846








biogenesis protein
cytochromes;










DsbD, protein-disulfide
<br>Periplasmic disulfide










reductase (EC 1.8.1.8)
interchange



fig|6666666.60966.peg.820
CDS
754631
754260
−2
−
372
Periplasmic divalent
Copper homeostasis:
D23_1c0827
Neut_0847








cation tolerance protein
copper tolerance










CutA




fig|6666666.60966.peg.821
CDS
754715
754909
2
+
195
FIG00859483:
-none-
D23_1c0828
Neut_0848








hypothetical protein




fig|6666666.60966.peg.822
CDS
754952
755695
2
+
744
FIG00859295:
-none-
D23_1c0829
Neut_0849








hypothetical protein




fig|6666666.60966.peg.823
CDS
756608
755733
−2
−
876
Staphylococcus
-none-
D23_1c0830
Neut_0850








nuclease (SNase)











domain




fig|6666666.60966.peg.824
CDS
756650
757549
2
+
900
Methionine ABC
Methionine
D23_1c0831
Neut_0851








transporter ATP-binding
Biosynthesis;










protein
<br>Methionine











Degradation



fig|6666666.60966.peg.825
CDS
757674
758384
3
+
711
Uncharacterized ABC
Lipopolysaccharide
D23_1c0832
Neut_0852








transporter, permease
assembly










component YrbE




fig|6666666.60966.peg.826
CDS
758396
758863
2
+
468
Uncharacterized ABC
Lipopolysaccharide
D23_1c0833
Neut_0853








transporter, periplasmic
assembly










component YrbD




fig|6666666.60966.peg.827
CDS
758879
759496
2
+
618
Uncharacterized ABC
Lipopolysaccharide
D23_1c0834
Neut_0854








transporter, auxiliary
assembly










component YrbC




fig|6666666.60966.peg.828
CDS
759503
759817
2
+
315
STAS domain
-none-
D23_1c0835
Neut_0855

fig|6666666.60966.peg.829
CDS
759879
760793
3
+
915
ABC-type multidrug
CBSS-196164.1.peg.1690
D23_1c0836
Neut_0856








transport system,











ATPase component




fig|6666666.60966.peg.830
CDS
760790
761545
2
+
756
ABC-type multidrug
CBSS-196164.1.peg.1690
D23_1c0837
Neut_0857








transport system,











permease component




fig|6666666.60966.peg.831
CDS
761590
761844
1
+
255
YrbA protein
Broadly distributed
D23_1c0838
Neut_0858









proteins not in











subsystems



fig|6666666.60966.peg.832
CDS
763192
761900
−1
−
1293
Dihydrolipoamide
Dehydrogenase
D23_1c0839
Neut_0859








succinyltransferase
complexes; <br>TCA










component (E2) of 2-
Cycle










oxoglutarate











dehydrogenase











complex (EC 2.3.1.61)




fig|6666666.60966.peg.833
CDS
766072
763214
−1
−
2859
2-oxoglutarate
Dehydrogenase
D23_1c0840
Neut_0860








dehydrogenase E1
complexes; <br>TCA










component (EC 1.2.4.2)
Cycle



fig|6666666.60966.peg.834
CDS
767529
766234
−3
−
1296
Citrate synthase (si) (EC
TCA Cycle
D23_1c0841
Neut_0861








2.3.3.1)




fig|6666666.60966.peg.835
CDS
767808
767575
−3
−
234
YgfY COG2938
-none-
D23_1c0842
Neut_0862

fig|6666666.60966.peg.836
CDS
768500
767805
−2
−
696
Succinate
5-FCL-like protein;
D23_1c0843
Neut_0863








dehydrogenase iron-
<br>Succinate










sulfur protein (EC
dehydrogenase;










1.3.99.1)
<br>TCA Cycle



fig|6666666.60966.peg.837
CDS
770059
768629
−1
−
1431
Threonine synthase (EC
Threonine and
D23_1c0844
Neut_0864








4.2.3.1)
Homoserine











Biosynthesis



fig|6666666.60966.peg.839
CDS
771500
770184
−2
−
1317
Homoserine
Methionine
D23_1c0845
Neut_0865








dehydrogenase (EC
Biosynthesis;










1.1.1.3)
<br>Threonine and











Homoserine











Biosynthesis



fig|6666666.60966.peg.840
CDS
772833
771607
−3
−
1227
Aspartate
CBSS-216591.1.peg.168;
D23_1c0846
Neut_0866








aminotransferase (EC
<br>Glutamine,










2.6.1.1)
Glutamate, Aspartate











and Asparagine











Biosynthesis;











<br>Threonine and











Homoserine











Biosynthesis



fig|6666666.60966.peg.841
CDS
773025
773147
3
+
123
hypothetical protein
-none-
D23_1c0847
NA

fig|6666666.60966.peg.842
CDS
773125
773508
1
+
384
Membrane protein
-none-
D23_1c0848
Neut_0867

fig|6666666.60966.peg.843
CDS
773605
775980
1
+
2376
Phosphoenolpyruvate
A Hypothetical that
D23_1c0849
Neut_0868








synthase (EC 2.7.9.2)
Clusters with PEP











Synthase; <br>Glycolysis











and Gluconeogenesis;











<br>Pyruvate











metabolism I:











anaplerotic reactions,











PEP



fig|6666666.60966.peg.844
CDS
775985
776812
2
+
828
FIG137360:
A Hypothetical that
D23_1c0850
Neut_0869








hypothetical protein
Clusters with PEP











Synthase



fig|6666666.60966.peg.845
CDS
777372
776854
−3
−
519
NLP/P60
-none-
D23_1c0851
Neut_0870

fig|6666666.60966.peg.846
CDS
779204
777507
−2
−
1698
Glutaminyl-tRNA
tRNA aminoacylation,
D23_1c0852
Neut_0871








synthetase (EC 6.1.1.18)
Glu and Gln



fig|6666666.60966.peg.847
CDS
779394
779245
−3
−
150
hypothetical protein
-none-
D23_1c0853
NA

fig|6666666.60966.peg.848
CDS
779393
780991
2
+
1599
Lysyl-tRNA synthetase
tRNA aminoacylation,
D23_1c0854
Neut_0872








(class II) (EC 6.1.1.6)
Lys



fig|6666666.60966.peg.849
CDS
781093
781749
1
+
657
FIG00858849:
-none-
D23_1c0855
Neut_0873








hypothetical protein




fig|6666666.60966.peg.850
CDS
781999
782385
1
+
387
hypothetical protein
-none-
D23_1c0856
NA

fig|6666666.60966.peg.851
CDS
782415
782747
3
+
333
Mobile element protein
-none-
D23_1c0857
NA

fig|6666666.60966.peg.852
CDS
782952
783485
3
+
534
hypothetical protein
-none-
D23_1c0858
Neut_0875

fig|6666666.60966.peg.853
CDS
783597
783767
3
+
171
hypothetical protein
-none-
D23_1c0859
NA

fig|6666666.60966.peg.854
CDS
784671
784048
−3
−
624
Trp repressor binding
-none-
D23_1c0860
Neut_0876








protein




fig|6666666.60966.peg.855
CDS
785041
784757
−1
−
285
Mobile element protein
-none-
D23_1c0861
NA

fig|6666666.60966.peg.857
CDS
787300
785558
−1
−
1743
Beta-glucosidase (EC
-none-
D23_1c0862
Neut_0879








3.2.1.21)




fig|6666666.60966.peg.858
CDS
788430
787327
−3
−
1104
Mobile element protein
-none-
D23_1c0863
Neut_1278

fig|6666666.60966.peg.859
CDS
789557
789045
−2
−
513
Mobile element protein
-none-
D23_1c0864
Neut_1624

fig|6666666.60966.peg.860
CDS
789894
789589
−3
−
306
Mobile element protein
-none-
D23_1c0865
Neut_1371

fig|6666666.60966.peg.861
CDS
790136
789951
−2
−
186
Mobile element protein
-none-
D23_1c0866
Neut_2500

fig|6666666.60966.peg.863
CDS
792236
790869
−2
−
1368
ATP-dependent RNA
ATP-dependent RNA
D23_1c0869
Neut_0889








helicase RhlE
helicases, bacterial



fig|6666666.60966.peg.865
CDS
794169
792502
−3
−
1668
ATPase components of
-none-
D23_1c0871
Neut_0890








ABC transporters with











duplicated ATPase











domains




fig|6666666.60966.peg.867
CDS
794389
794568
1
+
180
hypothetical protein
-none-
D23_1c0872
NA

fig|6666666.60966.peg.868
CDS
795019
795636
1
+
618
FIG123464:
Cell wall related cluster
D23_1c0873
Neut_0891








Polysaccharide export











protein




fig|6666666.60966.peg.869
CDS
795679
797223
1
+
1545
Lipopolysaccharide
Cell wall related cluster
D23_1c0874
Neut_0892








biosynthesis chain











length determinant











protein




fig|6666666.60966.peg.870
CDS
797305
798243
1
+
939
Protein-tyrosine kinase
Cell wall related cluster
D23_1c0875
Neut_0893








(EC 2.7.1.112)




fig|6666666.60966.peg.871
CDS
798243
799823
3
+
1581
Glycine-rich cell wall
Cell wall related cluster
D23_1c0876
Neut_0894








structural protein











precursor




fig|6666666.60966.peg.872
CDS
799837
800670
1
+
834
FIG022606: AAA ATPase
Cell wall related cluster
D23_1c0877
Neut_0895

fig|6666666.60966.peg.873
CDS
800676
801515
3
+
840
FIG004655:
Cell wall related cluster
D23_1c0878
Neut_0896








Polysaccharide











deacetylase




fig|6666666.60966.peg.875
CDS
801827
802591
2
+
765
FIG070318:
Cell wall related cluster
D23_1c0879
Neut_0897








hypothetical protein




fig|6666666.60966.peg.876
CDS
802597
803808
1
+
1212
FIG137776:
Cell wall related cluster
D23_1c0880
Neut_0898








Glycosyltransferase




fig|6666666.60966.peg.877
CDS
803877
805457
3
+
1581
Eight transmembrane
Cell wall related cluster;
D23_1c0881
Neut_0899








protein EpsH/EpsI
<br>Cell wall related










protein
cluster



fig|6666666.60966.peg.878
CDS
805493
806635
2
+
1143
FIG040338: Glycosyl
Cell wall related cluster
D23_1c0882
Neut_0900








transferase




fig|6666666.60966.peg.879
CDS
806677
808611
1
+
1935
Asparagine synthetase
Cell wall related cluster;
D23_1c0884
Neut_0901








[glutamine-hydrolyzing]
<br>Glutamine,










(EC 6.3.5.4) AsnH
Glutamate, Aspartate











and Asparagine











Biosynthesis



fig|6666666.60966.peg.880
CDS
808662
809654
3
+
993
FIG00859061:
-none-
D23_1c0885
Neut_0902








hypothetical protein




fig|6666666.60966.peg.881
CDS
809654
810592
2
+
939
FIG00859041:
-none-
D23_1c0886
Neut_0903








hypothetical protein




fig|6666666.60966.peg.882
CDS
810623
811849
2
+
1227
hypothetical protein
-none-
D23_1c0887
Neut_0903

fig|6666666.60966.peg.883
CDS
812814
811852
−3
−
963
Mobile element protein
-none-
D23_1c0888
Neut_1746

fig|6666666.60966.peg.884
CDS
813957
813094
−3
−
864
Mobile element protein
-none-
D23_1c0889
Neut_2192

fig|6666666.60966.peg.885
CDS
814250
813954
−2
−
297
hypothetical protein
-none-
D23_1c0890
Neut_2193

fig|6666666.60966.peg.887
CDS
814624
815706
1
+
1083
glycosyltransferase
-none-
D23_1c0891
NA

fig|6666666.60966.peg.888
CDS
817016
816339
−2
−
678
hypothetical protein
-none-
D23_1c0892
NA

fig|6666666.60966.peg.889
CDS
818253
817114
−3
−
1140
hypothetical protein
-none-
D23_1c0893
Neut_0906

fig|6666666.60966.peg.890
CDS
819313
818282
−1
−
1032
hypothetical protein
-none-
D23_1c0894
Neut_2116

fig|6666666.60966.peg.891
CDS
820446
819313
−3
−
1134
hypothetical protein
-none-
D23_1c0895
Neut_0905

fig|6666666.60966.peg.892
CDS
821935
820481
−1
−
1455
hypothetical protein
-none-
D23_1c0896
Neut_0909

fig|6666666.60966.peg.893
CDS
823840
822074
−1
−
1767
Asparagine synthetase
Cyanophycin
D23_1c0897
Neut_0910








[glutamine-hydrolyzing]
Metabolism;










(EC 6.3.5.4)
<br>Glutamate and











Aspartate uptake in











Bacteria; <br>Glutamine,











Glutamate, Aspartate











and Asparagine











Biosynthesis



fig|6666666.60966.peg.895
CDS
824361
825170
3
+
810
hypothetical protein
-none-
D23_1c0898
Neut_0911

fig|6666666.60966.peg.896
CDS
825186
826454
3
+
1269
hypothetical protein
-none-
D23_1c0899
Neut_0912

fig|6666666.60966.peg.897
CDS
827356
826457
−1
−
900
hypothetical protein
-none-
D23_1c0900
Neut_0913

fig|6666666.60966.peg.898
CDS
827907
827404
−3
−
504
Low molecular weight
LMPTP YfkJ cluster;
D23_1c0901
Neut_0914








protein tyrosine
<br>Protein deglycation










phosphatase (EC











3.1.3.48)




fig|6666666.60966.peg.899
CDS
828032
829777
2
+
1746
ABC transporter, fused
-none-
D23_1c0902
Neut_0915








permease and ATPase











domains




fig|6666666.60966.peg.900
CDS
830559
829798
−3
−
762
Sulfur carrier protein
Thiamin biosynthesis
D23_1c0903
Neut_0916








adenylyltransferase











ThiF




fig|6666666.60966.peg.901
CDS
832018
830588
−1
−
1431
Carboxyl-terminal
Phosphoglycerate
D23_1c0904
Neut_0917








protease (EC
mutase protein family










3.4.21.102)




fig|6666666.60966.peg.902
CDS
833380
832100
−1
−
1281
Lipoprotein NlpD
Stationary phase repair
D23_1c0905
Neut_0918









cluster



fig|6666666.60966.peg.903
CDS
834129
833380
−3
−
750
Phosphoglycerate
Glycolysis and
D23_1c0906
Neut_0919








mutase (EC 5.4.2.1)
Gluconeogenesis;











<br>Phosphoglycerate











mutase protein family



fig|6666666.60966.peg.904
CDS
834328
835086
1
+
759
Triosephosphate
CBSS-
D23_1c0907
Neut_0920








isomerase (EC 5.3.1.1)
331978.3.peg.2915;











<br>Calvin-Benson cycle;











<br>Glycolysis and











Gluconeogenesis



fig|6666666.60966.peg.905
CDS
835105
835470
1
+
366
Preprotein translocase
CBSS-331978.3.peg.2915
D23_1c0908
Neut_0921








subunit SecG (TC











3.A.5.1.1)




fig|6666666.60966.peg.906
CDS
835677
836045
3
+
369
NADH ubiquinone
NADH ubiquinone
D23_1c0910
Neut_0922








oxidoreductase chain A
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.907
CDS
836049
836525
3
+
477
NADH-ubiquinone
NADH ubiquinone
D23_1c0911
Neut_0923








oxidoreductase chain B
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.908
CDS
836535
837155
3
+
621
NADH-ubiquinone
NADH ubiquinone
D23_1c0912
Neut_0924








oxidoreductase chain C
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.909
CDS
837213
838466
3
+
1254
NADH-ubiquinone
NADH ubiquinone
D23_1c0913
Neut_0925








oxidoreductase chain D
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.910
CDS
838475
838951
2
+
477
NADH-ubiquinone
NADH ubiquinone
D23_1c0914
Neut_0926








oxidoreductase chain E
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.911
CDS
838948
840225
1
+
1278
NADH-ubiquinone
NADH ubiquinone
D23_1c0915
Neut_0927








oxidoreductase chain F
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.912
CDS
840287
842692
2
+
2406
NADH-ubiquinone
NADH ubiquinone
D23_1c0917
Neut_0928








oxidoreductase chain G
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.913
CDS
842717
843814
2
+
1098
NADH-ubiquinone
NADH ubiquinone
D23_1c0918
Neut_0929








oxidoreductase chain H
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.914
CDS
843832
844320
1
+
489
NADH-ubiquinone
NADH ubiquinone
D23_1c0919
Neut_0930








oxidoreductase chain I
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.915
CDS
844339
844944
1
+
606
NADH-ubiquinone
NADH ubiquinone
D23_1c0920
Neut_0931








oxidoreductase chain J
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.916
CDS
845000
845305
2
+
306
NADH-ubiquinone
NADH ubiquinone
D23_1c0921
Neut_0932








oxidoreductase chain K
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.917
CDS
845366
847312
2
+
1947
NADH-ubiquinone
NADH ubiquinone
D23_1c0922
Neut_0933








oxidoreductase chain L
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.918
CDS
847401
848882
3
+
1482
NADH-ubiquinone
NADH ubiquinone
D23_1c0923
Neut_0934








oxidoreductase chain M
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.919
CDS
848945
850390
2
+
1446
NADH-ubiquinone
NADH ubiquinone
D23_1c0924
Neut_0935








oxidoreductase chain N
oxidoreductase;










(EC 1.6.5.3)
<br>Respiratory











Complex I



fig|6666666.60966.peg.920
CDS
851362
850412
−1
−
951
L-sorbosone
-none-
D23_1c0925
Neut_0936








dehydrogenase




fig|6666666.60966.peg.921
CDS
851619
853541
3
+
1923
Chaperone protein
Protein chaperones
D23_1c0926
Neut_0937








HtpG




fig|6666666.60966.peg.922
CDS
853878
854918
3
+
1041
WD40 domain protein
-none-
D23_1c0927
Neut_0938








beta Propeller




fig|6666666.60966.peg.924
CDS
855176
855598
2
+
423
Mobile element protein
-none-
D23_1c0929
Neut_0939

fig|6666666.60966.peg.925
CDS
855805
858447
1
+
2643
Hopanoid-associated
Hopanes
D23_1c0930
Neut_0940








RND transporter, HpnN




fig|6666666.60966.peg.926
CDS
859079
858483
−2
−
597
DedA protein
Colicin V and Bacteriocin
D23_1c0931
Neut_0941









Production Cluster;











<br>DedA family of inner











membrane proteins;











<br>Uptake of selenate











and selenite



fig|6666666.60966.peg.928
CDS
861652
859424
−1
−
2229
Probable
-none-
D23_1c0933
Neut_0942








transmembrane protein




fig|6666666.60966.peg.929
CDS
861629
861754
2
+
126
hypothetical protein
-none-
D23_1c0934
NA

fig|6666666.60966.peg.930
CDS
861857
861720
−2
−
138
hypothetical protein
-none-
D23_1c0935
NA

fig|6666666.60966.peg.931
CDS
861928
862341
1
+
414
Protoporphyrinogen IX
Heme and Siroheme
D23_1c0936
Neut_0943








oxidase, novel form,
Biosynthesis










HemJ (EC 1.3.—.—)




fig|6666666.60966.peg.932
CDS
862893
862363
−3
−
531
Peptide deformylase
Bacterial RNA-
D23_1c0937
Neut_0944








(EC 3.5.1.88)
metabolizing Zn-











dependent hydrolases;











<br>Translation











termination factors











bacterial



fig|6666666.60966.peg.933
CDS
863632
862886
−1
−
747
5&#39;-
-none-
D23_1c0938
Neut_0945








methylthioadenosine











phosphorylase (EC











2.4.2.28)




fig|6666666.60966.peg.934
CDS
865800
863752
−3
−
2049
DNA ligase (EC 6.5.1.2)
DNA Repair Base
D23_1c0939
Neut_0946









Excision



fig|6666666.60966.peg.935
CDS
865959
866654
3
+
696
hypothetical protein
-none-
D23_1c0940
Neut_0947

fig|6666666.60966.peg.936
CDS
867392
867021
−2
−
372
Flagellar biosynthesis
Flagellum
D23_1c0941
Neut_0948








protein FliT




fig|6666666.60966.peg.937
CDS
867859
867389
−1
−
471
Flagellar biosynthesis
Flagellum
D23_1c0942
Neut_0949








protein FliS




fig|6666666.60966.peg.938
CDS
869359
867917
−1
−
1443
Flagellar hook-
Flagellum
D23_1c0943
Neut_0950








associated protein FliD




fig|6666666.60966.peg.939
CDS
870186
869716
−3
−
471
hypothetical protein
-none-
D23_1c0944
Neut_0951

fig|6666666.60966.peg.940
CDS
870616
870891
1
+
276
hypothetical protein
-none-
D23_1c0945
Neut_0952

fig|6666666.60966.peg.941
CDS
871905
870955
−3
−
951
Glutathione synthetase
Glutathione:
D23_1c0946
Neut_0953








(EC 6.3.2.3)
Biosynthesis and











gamma-glutamyl cycle;











<br>Heat shock dnaK











gene cluster extended



fig|6666666.60966.peg.942
CDS
873212
871902
−2
−
1311
Glutamate--cysteine
Glutathione:
D23_1c0947
Neut_0954








ligase (EC 6.3.2.2),
Biosynthesis and










divergent, of Alpha- and
gamma-glutamyl cycle










Beta-proteobacteria











type




fig|6666666.60966.peg.944
CDS
873411
873722
3
+
312
LSU ribosomal protein
CBSS-176279.3.peg.868
D23_1c0949
Neut_0955








L21p




fig|6666666.60966.peg.945
CDS
873734
873991
2
+
258
LSU ribosomal protein
CBSS-176279.3.peg.868
D23_1c0950
Neut_0956








L27p




fig|6666666.60966.peg.946
CDS
873991
874104
1
+
114
hypothetical protein
-none-
D23_1c0951
NA

fig|6666666.60966.peg.947
CDS
874121
875152
2
+
1032
GTP-binding protein
CBSS-176279.3.peg.868;
D23_1c0952
Neut_0957








Obg
<br>Universal GTPases



fig|6666666.60966.peg.948
CDS
875158
876279
1
+
1122
Glutamate 5-kinase (EC
Proline Synthesis;
D23_1c0953
Neut_0958








2.7.2.11)/RNA-binding
<br>Proline Synthesis










C-terminal domain PUA




fig|6666666.60966.peg.949
CDS
876330
877331
3
+
1002
InterPro IPR000379
-none-
D23_1c0954
Neut_0959








COGs COG0429




fig|6666666.60966.peg.950
CDS
877428
878744
3
+
1317
Phosphate regulon
High affinity phosphate
D23_1c0955
Neut_0960








sensor protein PhoR
transporter and control










(SphS) (EC 2.7.13.3)
of PHO regulon;











<br>PhoR-PhoB two-











component regulatory











system; <br>Phosphate











metabolism



fig|6666666.60966.peg.951
CDS
879101
879343
2
+
243
RNA-binding protein
Hfl operon;
D23_1c0957
Neut_0961








Hfq
<br>Polyadenylation











bacterial; <br>Possible











RNA degradation cluster



fig|6666666.60966.peg.952
CDS
879345
880478
3
+
1134
GTP-binding protein
Hfl operon; <br>Possible
D23_1c0958
Neut_0962








HflX
RNA degradation cluster;











<br>Universal GTPases



fig|6666666.60966.peg.953
CDS
880535
881725
2
+
1191
HflK protein
Hfl operon; <br>Scaffold
D23_1c0959
Neut_0963









proteins for [4Fe—4S]











cluster assembly (MRP











family)



fig|6666666.60966.peg.954
CDS
881725
882603
1
+
879
HflC protein
Hfl operon; <br>Scaffold
D23_1c0960
Neut_0964









proteins for [4Fe—4S]











cluster assembly (MRP











family)



fig|6666666.60966.peg.955
CDS
882732
882917
3
+
186
Putative inner
Hfl operon
D23_1c0961
Neut_0965








membrane protein YjeT











(clustered with HflC)




fig|6666666.60966.peg.956
CDS
882992
884164
2
+
1173
ATP
Histidine Biosynthesis
D23_1c0962
Neut_0966








phosphoribosyltransferase











regulatory subunit











(EC 2.4.2.17)




fig|6666666.60966.peg.957
CDS
884298
885596
3
+
1299
Adenylosuccinate
Purine conversions
D23_1c0963
Neut_0967








synthetase (EC 6.3.4.4)




fig|6666666.60966.peg.958
CDS
885982
885665
−1
−
318
FIG00858510:
-none-
D23_1c0964
Neut_0968








hypothetical protein




fig|6666666.60966.peg.959
CDS
886361
886164
−2
−
198
FIG00859475:
-none-
D23_1c0966
Neut_0969








hypothetical protein




fig|6666666.60966.peg.961
CDS
889010
886635
−2
−
2376
ATP-dependent
Proteasome bacterial;
D23_1c0967
Neut_0970








protease La (EC
<br>Proteolysis in










3.4.21.53) Type I
bacteria, ATP-dependent



fig|6666666.60966.peg.962
CDS
889609
889160
−1
−
450
CBS domain protein
-none-
D23_1c0968
Neut_0971

fig|6666666.60966.peg.963
CDS
890160
889657
−3
−
504
hypothetical protein
-none-
D23_1c0969
Neut_0972

fig|6666666.60966.peg.964
CDS
890193
890345
3
+
153
hypothetical protein
-none-
D23_1c0970
NA

fig|6666666.60966.peg.965
CDS
890326
890442
1
+
117
hypothetical protein
-none-
D23_1c0971
NA

fig|6666666.60966.peg.966
CDS
890503
891663
1
+
1161
ABC-transporter
-none-
D23_1c0972
Neut_0973








permease protein




fig|6666666.60966.peg.967
CDS
891663
892352
3
+
690
ABC transporter, ATP-
-none-
D23_1c0973
Neut_0974








binding protein




fig|6666666.60966.peg.968
CDS
892533
893492
3
+
960
Membrane protein
-none-
D23_1c0974
Neut_0975

fig|6666666.60966.peg.969
CDS
895517
893706
−2
−
1812
Sodium/hydrogen
-none-
D23_1c0976
Neut_0976








exchanger family











protein




fig|6666666.60966.peg.970
CDS
895888
896574
1
+
687
FIG00859851:
-none-
D23_1c0978
Neut_0977








hypothetical protein




fig|6666666.60966.peg.971
CDS
897991
897029
−1
−
963
Mobile element protein
-none-
D23_1c0979
Neut_0978

fig|6666666.60966.peg.972
CDS
899539
898112
−1
−
1428
Pyruvate kinase (EC
Glycerate metabolism;
D23_1c0980
Neut_0979








2.7.1.40)
<br>Glycolysis and











Gluconeogenesis;











<br>Pyruvate











metabolism I:











anaplerotic reactions,











PEP



fig|6666666.60966.peg.973
CDS
899838
899563
−3
−
276
hypothetical protein
-none-
D23_1c0981
Neut_0980

fig|6666666.60966.peg.974
CDS
900234
900398
3
+
165
hypothetical protein
-none-
D23_1c0982
NA

fig|6666666.60966.peg.975
CDS
903871
900686
−1
−
3186
TonB-dependent
Ton and Tol transport
D23_1c0983
Neut_1076








receptor
systems



fig|6666666.60966.peg.976
CDS
904856
903873
−2
−
984
hypothetical protein
-none-
D23_1c0984
Neut_1077

fig|6666666.60966.peg.977
CDS
906168
904861
−3
−
1308
putative helicase
-none-
D23_1c0985
Neut_1078

fig|6666666.60966.peg.978
CDS
908497
906392
−1
−
2106
sucrose synthase
-none-
D23_1c0988
Neut_1079

fig|6666666.60966.peg.979
CDS
910925
908787
−2
−
2139
Sucrose phosphate
-none-
D23_1c0989
Neut_1080








synthase




fig|6666666.60966.peg.980
CDS
911865
910936
−3
−
930
Fructokinase (EC
-none-
D23_1c0990
Neut_1081








2.7.1.4)




fig|6666666.60966.peg.981
CDS
914147
912060
−2
−
2088
Excinuclease ABC
DNA repair, UvrABC
D23_1c0991
Neut_1082








subunit B
system



fig|6666666.60966.peg.982
CDS
914226
915419
3
+
1194
Aspartate
CBSS-216591.1.peg.168;
D23_1c0992
Neut_1083








aminotransferase (EC
<br>Glutamine,










2.6.1.1)
Glutamate, Aspartate











and Asparagine











Biosynthesis;











<br>Threonine and











Homoserine











Biosynthesis



fig|6666666.60966.peg.983
CDS
915551
915688
2
+
138
hypothetical protein
-none-
D23_1c0993
NA

fig|6666666.60966.peg.984
CDS
915891
916277
3
+
387
Mobile element protein
-none-
D23_1c0994
Neut_0884

fig|6666666.60966.peg.985
CDS
916240
916695
1
+
456
Mobile element protein
-none-
D23_1c0995
Neut_2502

fig|6666666.60966.peg.986
CDS
916764
917726
3
+
963
Mobile element protein
-none-
D23_1c0996
Neut_1862

fig|6666666.60966.peg.987
CDS
918535
918419
−1
−
117
hypothetical protein
-none-
D23_1c0997
NA

fig|6666666.60966.peg.988
CDS
919358
918504
−2
−
855
DNA-directed RNA
RNA polymerase
D23_1c0998
NA








polymerase alpha
bacterial










subunit (EC 2.7.7.6)




fig|6666666.60966.peg.989
CDS
919525
919409
−1
−
117
hypothetical protein
-none-
D23_1c0999
Neut_1085

fig|6666666.60966.peg.990
CDS
919587
919787
3
+
201
Glutathione synthetase
Glutathione:
D23_1c0999
Neut_1085








(EC 6.3.2.3)
Biosynthesis and











gamma-glutamyl cycle;











<br>Heat shock dnaK











gene cluster extended



fig|6666666.60966.peg.991
CDS
919919
920287
2
+
369
FIG00858546:
-none-
D23_1c1000
Neut_1086








hypothetical protein




fig|6666666.60966.peg.992
CDS
920496
921119
3
+
624
bacteriocin resistance
-none-
D23_1c1001
Neut_1087








protein, putative




fig|6666666.60966.peg.993
CDS
921168
921644
3
+
477
FIG00859915:
-none-
D23_1c1002
Neut_1088








hypothetical protein




fig|6666666.60966.peg.994
CDS
921659
923050
2
+
1392
FIG00858837:
-none-
D23_1c1003
Neut_1089








hypothetical protein




fig|6666666.60966.peg.995
CDS
923533
923105
−1
−
429
Zn-dependent
-none-
D23_1c1004
Neut_1090








hydrolases, including











glyoxylases




fig|6666666.60966.peg.996
CDS
923845
924936
1
+
1092
Diaminohydroxyphosphoribosylaminopyrimidine
Riboflavin, FMN and FAD
D23_1c1005
Neut_1091








deaminase (EC
metabolism;










3.5.4.26)/5-amino-6-
<br>Riboflavin, FMN and










(5-
FAD metabolism;










phosphoribosylamino)uracil
<br>Riboflavin, FMN and










reductase (EC
FAD metabolism in










1.1.1.193)
plants; <br>Riboflavin,











FMN and FAD











metabolism in plants;











<br>Riboflavin synthesis











cluster; <br>Riboflavin











synthesis cluster



fig|6666666.60966.peg.997
CDS
925042
926262
1
+
1221
Glycosyl transferase,
-none-
D23_1c1006
Neut_1092








group 1




fig|6666666.60966.peg.998
CDS
926363
927685
2
+
1323
UDP-glucose
-none-
D23_1c1007
Neut_1093








dehydrogenase (EC











1.1.1.22)




fig|6666666.60966.peg.999
CDS
928127
928318
2
+
192
hypothetical protein
-none-
D23_1c1009
Neut_1095

fig|6666666.60966.peg.1000
CDS
928500
928315
−3
−
186
hypothetical protein
-none-
D23_1c1010
NA

fig|6666666.60966.peg.1002
CDS
929085
930362
3
+
1278
InterPro IPR001296
-none-
D23_1c1011
Neut_1096








COGs COG0438




fig|6666666.60966.peg.1003
CDS
930467
931729
2
+
1263
Coenzyme F390
-none-
D23_1c1012
Neut_1097








synthetase




fig|6666666.60966.peg.1004
CDS
932351
931731
−2
−
621
exopolysaccharide
-none-
D23_1c1013
Neut_1098








synthesis protein ExoD-











related protein




fig|6666666.60966.peg.1005
CDS
932631
933110
3
+
480
FIG00859304:
-none-
D23_1c1014
Neut_1099








hypothetical protein




fig|6666666.60966.peg.1006
CDS
933200
934357
2
+
1158
FIG010505:
-none-
D23_1c1015
Neut_1100








hypothetical protein




fig|6666666.60966.peg.1007
CDS
934409
935224
2
+
816
FIG00858774:
-none-
D23_1c1016
Neut_1101








hypothetical protein




fig|6666666.60966.peg.1008
CDS
935243
936316
2
+
1074
Probable
-none-
D23_1c1017
Neut_1102








transmembrane protein




fig|6666666.60966.peg.1009
CDS
936361
937383
1
+
1023
FIG000906: Predicted
-none-
D23_1c1018
Neut_1103








Permease




fig|6666666.60966.peg.1010
CDS
937391
938608
2
+
1218
CDP-alcohol
-none-
D23_1c1019
Neut_1104








phosphatidyltransferase




fig|6666666.60966.peg.1011
CDS
938637
939593
3
+
957
FIG00480695:
-none-
D23_1c1020
Neut_1105








hypothetical protein




fig|6666666.60966.peg.1012
CDS
939607
940575
1
+
969
FIG00859274:
-none-
D23_1c1021
Neut_1106








hypothetical protein




fig|6666666.60966.peg.1013
CDS
940636
941283
1
+
648
FIG00859276:
-none-
D23_1c1022
Neut_1107








hypothetical protein




fig|6666666.60966.peg.1014
CDS
941749
941294
−1
−
456
Zn-ribbon-containing,
DNA replication cluster 1
D23_1c1023
Neut_1108








possibly RNA-binding











protein and truncated











derivatives




fig|6666666.60966.peg.1016
CDS
942037
942186
1
+
150
hypothetical protein
-none-
D23_1c1024
NA

fig|6666666.60966.peg.1017
CDS
942242
944971
2
+
2730
Protein export
-none-
D23_1c1025
Neut_1109








cytoplasm protein SecA











ATPase RNA helicase











(TC 3.A.5.1.1)




fig|6666666.60966.peg.1018
CDS
945151
945756
1
+
606
Ubiquinol-cytochrome C
Ubiquinone
D23_1c1026
Neut_1110








reductase iron-sulfur
Menaquinone-










subunit (EC 1.10.2.2)
cytochrome c reductase











complexes



fig|6666666.60966.peg.1019
CDS
945758
947005
2
+
1248
Ubiquinol--cytochrome
Ubiquinone
D23_1c1027
Neut_1111








c reductase,
Menaquinone-










cytochrome B subunit
cytochrome c reductase










(EC 1.10.2.2)
complexes



fig|6666666.60966.peg.1020
CDS
947002
947706
1
+
705
ubiquinol cytochrome C
Ubiquinone
D23_1c1028
Neut_1112








oxidoreductase,
Menaquinone-










cytochrome C1 subunit
cytochrome c reductase











complexes



fig|6666666.60966.peg.1021
CDS
947758
948357
1
+
600
Stringent starvation
Carbon Starvation
D23_1c1029
Neut_1113








protein A




fig|6666666.60966.peg.1023
CDS
949015
949215
1
+
201
hypothetical protein
-none-
D23_1c1031
Neut_2449

fig|6666666.60966.peg.1024
CDS
949203
949682
3
+
480
Mobile element protein
-none-
D23_1c1032
Neut_2417

fig|6666666.60966.peg.1025
CDS
950361
950651
3
+
291
Mobile element protein
-none-
D23_1c1034
Neut_2190

fig|6666666.60966.peg.1026
CDS
951943
950696
−1
−
1248
Mobile element protein
-none-
D23_1c1035
Neut_0357

fig|6666666.60966.peg.1027
CDS
952378
952208
−1
−
171
hypothetical protein
-none-
D23_1c1036
NA

fig|6666666.60966.peg.1028
CDS
953114
952689
−2
−
426
C4-type zinc finger
Zinc regulated enzymes
D23_1c1037
Neut_1117








protein, DksA/TraR











family




fig|6666666.60966.peg.1029
CDS
955194
953479
−3
−
1716
Adenylate cyclase (EC
cAMP signaling in
D23_1c1038
Neut_1118








4.6.1.1)
bacteria



fig|6666666.60966.peg.1030
CDS
956008
955157
−1
−
852
HD domain
-none-
D23_1c1039
Neut_1119

fig|6666666.60966.peg.1032
CDS
956563
957111
1
+
549
InterPro IPR000345
-none-
D23_1c1042
Neut_1126

fig|6666666.60966.peg.1033
CDS
958663
957200
−1
−
1464
3-polyprenyl-4-
Ubiquinone
D23_1c1043
Neut_1127








hydroxybenzoate
Biosynthesis;










carboxy-lyase (EC
<br>Ubiquinone










4.1.1.—)
Biosynthesis-gjo



fig|6666666.60966.peg.1034
CDS
959616
958756
−3
−
861
4-hydroxybenzoate
Ubiquinone
D23_1c1045
Neut_1128








polyprenyltransferase
Biosynthesis;










(EC 2.5.1.39)
<br>Ubiquinone











Biosynthesis-gjo



fig|6666666.60966.peg.1035
CDS
960159
959695
−3
−
465
Chorismate--pyruvate
Ubiquinone
D23_1c1046
Neut_1129








lyase (EC 4.1.3.40)
Biosynthesis;











<br>Ubiquinone











Biosynthesis-gjo



fig|6666666.60966.peg.1036
CDS
960706
960299
−1
−
408
twitching motility
-none-
D23_1c1047
Neut_1130








protein PilG




fig|6666666.60966.peg.1037
CDS
962283
960874
−3
−
1410
Potassium uptake
Hyperosmotic potassium
D23_1c1048
Neut_1131








protein TrkH
uptake; <br>Potassium











homeostasis;











<br>Potassium











homeostasis



fig|6666666.60966.peg.1038
CDS
963803
962355
−2
−
1449
Trk system potassium
Bacterial RNA-
D23_1c1049
Neut_1132








uptake protein TrkA
metabolizing Zn-











dependent hydrolases;











<br>Hyperosmotic











potassium uptake;











<br>Possible RNA











degradation cluster;











<br>Potassium











homeostasis;











<br>Potassium











homeostasis



fig|6666666.60966.peg.1039
CDS
965344
964070
−1
−
1275
FIG00858490:
-none-
D23_1c1050
Neut_1133








hypothetical protein




fig|6666666.60966.peg.1040
CDS
965355
965495
3
+
141
hypothetical protein
-none-
D23_1c1051
NA

fig|6666666.60966.peg.1041
CDS
965968
965477
−1
−
492
Starvation lipoprotein
Carbon Starvation
D23_1c1052
Neut_1134








Slp paralog




fig|6666666.60966.peg.1042
CDS
966371
967021
2
+
651
Septum site-
Bacterial Cell Division;
D23_1c1054
Neut_1135








determining protein
<br>Bacterial










MinC
Cytoskeleton;











<br>Bacterial cell











division cluster;











<br>Septum site-











determining cluster Min



fig|6666666.60966.peg.1043
CDS
967047
967856
3
+
810
Septum site-
Bacterial Cell Division;
D23_1c1055
Neut_1136








determining protein
<br>Bacterial










MinD
Cytoskeleton;











<br>Bacterial cell











division cluster;











<br>Septum site-











determining cluster Min



fig|6666666.60966.peg.1044
CDS
967856
968152
2
+
297
Cell division topological
Bacterial Cell Division;
D23_1c1056
Neut_1137








specificity factor MinE
<br>Bacterial











Cytoskeleton;











<br>Bacterial cell











division cluster;











<br>Septum site-











determining cluster Min



fig|6666666.60966.peg.1045
CDS
968284
968895
1
+
612
Outer membrane
A Gammaproteobacteria
D23_1c1057
Neut_1138








lipoprotein LolB
Cluster Relating to











Translation;











<br>Lipopolysaccharide











assembly;











<br>Lipoprotein sorting











system



fig|6666666.60966.peg.1046
CDS
968920
969756
1
+
837
4-diphosphocytidyl-2-C-
A Gammaproteobacteria
D23_1c1058
Neut_1139








methyl-D-erythritol
Cluster Relating to










kinase (EC 2.7.1.148)
Translation;











<br>Isoprenoid











Biosynthesis;











<br>Nonmevalonate











Branch of Isoprenoid











Biosynthesis



fig|6666666.60966.peg.1047
CDS
969932
970882
2
+
951
Ribose-phosphate
A Gammaproteobacteria
D23_1c1060
Neut_1140








pyrophosphokinase (EC
Cluster Relating to










2.7.6.1)
Translation; <br>De











Novo Purine











Biosynthesis;











<br>Pentose phosphate











pathway;











<br>Transcription repair











cluster



fig|6666666.60966.peg.1048
CDS
970936
971544
1
+
609
LSU ribosomal protein
Transcription repair
D23_1c1061
Neut_1141








L25p
cluster



fig|6666666.60966.peg.1049
CDS
971667
972236
3
+
570
Peptidyl-tRNA
Sporulation-associated
D23_1c1062
Neut_1142








hydrolase (EC 3.1.1.29)
proteins with broader











functions;











<br>Transcription repair











cluster; <br>Translation











termination factors











bacterial



fig|6666666.60966.peg.1050
CDS
972291
973382
3
+
1092
GTP-binding and nucleic
Universal GTPases
D23_1c1063
Neut_1143








acid-binding protein











YchF




fig|6666666.60966.peg.1051
CDS
973589
973461
−2
−
129
hypothetical protein
-none-
D23_1c1064
NA

fig|6666666.60966.peg.1052
CDS
973891
975303
1
+
1413
3-isopropylmalate
Branched-Chain Amino
D23_1c1066
Neut_1144








dehydratase large
Acid Biosynthesis;










subunit (EC 4.2.1.33)
<br>Leucine











Biosynthesis



fig|6666666.60966.peg.1053
CDS
975336
975464
3
+
129
FIG00858504:
-none-
D23_1c1067
Neut_1145








hypothetical protein




fig|6666666.60966.peg.1054
CDS
975470
976108
2
+
639
3-isopropylmalate
Branched-Chain Amino
D23_1c1068
Neut_1146








dehydratase small
Acid Biosynthesis;










subunit (EC 4.2.1.33)
<br>Leucine











Biosynthesis



fig|6666666.60966.peg.1055
CDS
976133
977203
2
+
1071
3-isopropylmalate
Branched-Chain Amino
D23_1c1069
Neut_1147








dehydrogenase (EC
Acid Biosynthesis;










1.1.1.85)
<br>Leucine











Biosynthesis



fig|6666666.60966.peg.1056
CDS
977333
978457
2
+
1125
Aspartate-
Lysine Biosynthesis DAP
D23_1c1070
Neut_1148








semialdehyde
Pathway, GJO scratch;










dehydrogenase (EC
<br>Threonine and










1.2.1.11)
Homoserine











Biosynthesis



fig|6666666.60966.peg.1057
CDS
978574
980970
1
+
2397
hypothetical protein
-none-
D23_1c1071
Neut_1149

fig|6666666.60966.peg.1058
CDS
981084
981917
3
+
834
tRNA pseudouridine
Colicin V and Bacteriocin
D23_1c1072
Neut_1150








synthase A (EC 4.2.1.70)
Production Cluster;











<br>RNA pseudouridine











syntheses; <br>tRNA











modification Bacteria;











<br>tRNA processing



fig|6666666.60966.peg.1059
CDS
981929
982555
2
+
627
Phosphoribosylanthranilate
Auxin biosynthesis;
D23_1c1073
Neut_1151








isomerase (EC
<br>Chorismate:










5.3.1.24)
Intermediate for











synthesis of Tryptophan,











PAPA antibiotics, PABA,











3-hydroxyanthranilate











and more.;











<br>Tryptophan











synthesis



fig|6666666.60966.peg.1060
CDS
982542
983741
3
+
1200
Tryptophan synthase
Auxin biosynthesis;
D23_1c1074
Neut_1152








beta chain (EC 4.2.1.20)
<br>Chorismate:











Intermediate for











synthesis of Tryptophan,











PAPA antibiotics, PABA,











3-hydroxyanthranilate











and more.;











<br>Tryptophan











synthesis



fig|6666666.60966.peg.1061
CDS
983794
984618
1
+
825
Tryptophan synthase
Auxin biosynthesis;
D23_1c1075
Neut_1153








alpha chain (EC
<br>Chorismate:










4.2.1.20)
Intermediate for











synthesis of Tryptophan,











PAPA antibiotics, PABA,











3-hydroxyanthranilate











and more.;











<br>Tryptophan











synthesis



fig|6666666.60966.peg.1062
CDS
984623
985513
2
+
891
Acetyl-coenzyme A
Colicin V and Bacteriocin
D23_1c1076
Neut_1154








carboxyl transferase
Production Cluster;










beta chain (EC 6.4.1.2)
<br>Fatty Acid











Biosynthesis FASII



fig|6666666.60966.peg.1063
CDS
985642
986925
1
+
1284
Dihydrofolate synthase
Colicin V and Bacteriocin
D23_1c1077
Neut_1155








(EC 6.3.2.12)/
Production Cluster;










Folylpolyglutamate
<br>Colicin V and










synthase (EC 6.3.2.17)
Bacteriocin Production











Cluster; <br>Folate











Biosynthesis; <br>Folate











Biosynthesis



fig|6666666.60966.peg.1064
CDS
986945
987616
2
+
672
DedD protein
Colicin V and Bacteriocin
D23_1c1078
Neut_1156









Production Cluster



fig|6666666.60966.peg.1065
CDS
987613
988107
1
+
495
Colicin V production
Colicin V and Bacteriocin
D23_1c1079
Neut_1157








protein
Production Cluster



fig|6666666.60966.peg.1066
CDS
988214
989731
2
+
1518
Amidophosphoribosyltransferase
Colicin V and Bacteriocin
D23_1c1080
Neut_1158








(EC 2.4.2.14)
Production Cluster;











<br>De Novo Purine











Biosynthesis



fig|6666666.60966.peg.1067
CDS
989748
990923
3
+
1176
O-acetylhomoserine
Methionine
D23_1c1081
Neut_1159








sulfhydrylase (EC
Biosynthesis;










2.5.1.49)/O-
<br>Methionine










succinylhomoserine
Biosynthesis










sulfhydrylase (EC











2.5.1.48)




fig|6666666.60966.peg.1068
CDS
991043
992554
2
+
1512
Threonine dehydratase
Branched-Chain Amino
D23_1c1082
Neut_1160








biosynthetic (EC
Acid Biosynthesis










4.3.1.19)




fig|6666666.60966.peg.1069
CDS
992670
992536
−3
−
135
hypothetical protein
-none-
D23_1c1083
NA

fig|6666666.60966.peg.1070
CDS
993016
994950
1
+
1935
twitching motility
-none-
D23_1c1084
Neut_1161








protein PilJ




fig|6666666.60966.peg.1071
CDS
995179
995054
−1
−
126
hypothetical protein
-none-
D23_1c1085
Neut_1162

fig|6666666.60966.peg.1072
CDS
995174
1000177
2
+
5004
Signal transduction
Flagellar motility
D23_1c1085
Neut_1162








histidine kinase CheA











(EC 2.7.3.—)




fig|6666666.60966.peg.1073
CDS
1000248
1002095
3
+
1848
ParB-like nuclease
-none-
D23_1c1086
Neut_1163








domain




fig|6666666.60966.peg.1074
CDS
1003717
1002203
−1
−
1515
Ubiquinone
Ubiquinone
D23_1c1087
Neut_1164








biosynthesis
Biosynthesis;










monooxygenase UbiB
<br>Ubiquinone











Biosynthesis-gjo



fig|6666666.60966.peg.1075
CDS
1004439
1003807
−3
−
633
Protein YigP (COG3165)
Ubiquinone
D23_1c1088
Neut_1165








clustered with
Biosynthesis;










ubiquinone biosynthetic
<br>Ubiquinone










genes
Biosynthesis-gjo



fig|6666666.60966.peg.1076
CDS
1004959
1004528
−1
−
432
FIG00858586:
-none-
D23_1c1089
Neut_1166








hypothetical protein




fig|6666666.60966.peg.1077
CDS
1005165
1004962
−3
−
204
hypothetical protein
-none-
D23_1c1090
NA

fig|6666666.60966.peg.1078
CDS
1005185
1007323
2
+
2139
Signal transduction
Flagellar motility
D23_1c1091
Neut_1167








histidine kinase CheA











(EC 2.7.3.—)




fig|6666666.60966.peg.1079
CDS
1007395
1007916
1
+
522
Positive regulator of
-none-
D23_1c1092
Neut_1168








CheA protein activity











(CheW)




fig|6666666.60966.peg.1080
CDS
1008003
1010258
3
+
2256
Methyl-accepting
-none-
D23_1c1093
Neut_1169








chemotaxis protein I











(serine chemoreceptor











protein)




fig|6666666.60966.peg.1082
CDS
1010399
1012744
2
+
2346
Methyl-accepting
-none-
D23_1c1094
Neut_1170








chemotaxis protein I











(serine chemoreceptor











protein)




fig|6666666.60966.peg.1083
CDS
1012932
1013807
3
+
876
Chemotaxis protein
-none-
D23_1c1095
Neut_1171








methyltransferase CheR











(EC 2.1.1.80)




fig|6666666.60966.peg.1084
CDS
1013887
1014471
1
+
585
Chemotaxis protein
-none-
D23_1c1096
Neut_1172








CheD




fig|6666666.60966.peg.1085
CDS
1014502
1015569
1
+
1068
Chemotaxis response
-none-
D23_1c1097
Neut_1173








regulator protein-











glutamate











methylesterase CheB











(EC 3.1.1.61)




fig|6666666.60966.peg.1087
CDS
1017858
1016338
−3
−
1521
Ferredoxin reductase
Anaerobic respiratory
D23_1c1099
Neut_1175









reductases



fig|6666666.60966.peg.1088
CDS
1018141
1019145
1
+
1005
Fructose-1,6-
Calvin-Benson cycle;
D23_1c1100
Neut_1176








bisphosphatase, type I
<br>Glycolysis and










(EC 3.1.3.11)
Gluconeogenesis



fig|6666666.60966.peg.1089
CDS
1020142
1019183
−1
−
960
Glutathione S-
Glutathione: Non-redox
D23_1c1101
Neut_1177








transferase, omega (EC
reactions










2.5.1.18)




fig|6666666.60966.peg.1090
CDS
1020604
1020146
−1
−
459
Membrane protein,
-none-
D23_1c1102
Neut_1178








distant similarity to











thiosulphate:quinone











oxidoreductase DoxD




fig|6666666.60966.peg.1091
CDS
1020710
1020862
2
+
153
hypothetical protein
-none-
D23_1c1103
NA

fig|6666666.60966.peg.1092
CDS
1022088
1021138
−3
−
951
COGs COG0726
-none-
D23_1c1104
Neut_1179

fig|6666666.60966.peg.1093
CDS
1022664
1022212
−3
−
453
Phosphohistidine
-none-
D23_1c1105
Neut_1180








phosphatase SixA




fig|6666666.60966.peg.1094
CDS
1023442
1022753
−1
−
690
COGs COG1814
-none-
D23_1c1106
Neut_1181

fig|6666666.60966.peg.1095
CDS
1024149
1023445
−3
−
705
probable
-none-
D23_1c1107
Neut_1182








carboxylesterase




fig|6666666.60966.peg.1096
CDS
1024228
1025334
1
+
1107
InterPro IPR002931
-none-
D23_1c1108
Neut_1183








COGs COG1305




fig|6666666.60966.peg.1097
CDS
1027262
1025541
−2
−
1722
Sulfite reductase
Cysteine Biosynthesis;
D23_1c1109
Neut_1184








[NADPH] hemoprotein
<br>Inorganic Sulfur










beta-component (EC
Assimilation










1.8.1.2)




fig|6666666.60966.peg.1098
CDS
1029106
1027271
−1
−
1836
Sulfite reductase
Cysteine Biosynthesis;
D23_1c1110
Neut_1185








[NADPH] flavoprotein
<br>Inorganic Sulfur










alpha-component (EC
Assimilation










1.8.1.2)




fig|6666666.60966.peg.1100
CDS
1030580
1029651
−2
−
930
Cys regulon
Cysteine Biosynthesis;
D23_1c1111
Neut_1186








transcriptional activator
<br>LysR-family proteins










CysB
in Escherichia coli



fig|6666666.60966.peg.1101
CDS
1030815
1031513
3
+
699
Phosphoadenylyl-
Cysteine Biosynthesis;
D23_1c1112
Neut_1187








sulfate reductase
<br>Inorganic Sulfur










[thioredoxin] (EC
Assimilation;










1.8.4.8)/Adenylyl-
<br>Inorganic Sulfur










sulfate reductase
Assimilation










[thioredoxin] (EC











1.8.4.10)




fig|6666666.60966.peg.1102
CDS
1031599
1032447
1
+
849
Sulfate
Cysteine Biosynthesis;
D23_1c1113
Neut_1188








adenylyltransferase
<br>Inorganic Sulfur










subunit 2 (EC 2.7.7.4)
Assimilation



fig|6666666.60966.peg.1103
CDS
1032508
1033791
1
+
1284
Sulfate
Cysteine Biosynthesis;
D23_1c1114
Neut_1189








adenylyltransferase
<br>Inorganic Sulfur










subunit 1 (EC 2.7.7.4)
Assimilation



fig|6666666.60966.peg.1105
CDS
1033967
1037446
2
+
3480
Glutamate synthase
Ammonia assimilation;
D23_1c1115
Neut_1190








[NADPH] small chain
<br>Glutamine,










(EC 1.4.1.13)
Glutamate, Aspartate











and Asparagine











Biosynthesis



fig|6666666.60966.peg.1106
CDS
1037596
1038723
1
+
1128
NAD(P)
Phosphate metabolism
D23_1c1116
Neut_1191








transhydrogenase alpha











subunit (EC 1.6.1.2)




fig|6666666.60966.peg.1107
CDS
1038778
1039086
1
+
309
NAD(P)
Phosphate metabolism
D23_1c1117
Neut_1192








transhydrogenase alpha











subunit (EC 1.6.1.2)




fig|6666666.60966.peg.1108
CDS
1039087
1040466
1
+
1380
NAD(P)
Phosphate metabolism
D23_1c1118
Neut_1193








transhydrogenase











subunit beta (EC











1.6.1.2)




fig|6666666.60966.peg.1109
CDS
1041147
1040488
−3
−
660
FIG00858826:
-none-
D23_1c1119
Neut_1194








hypothetical protein




fig|6666666.60966.peg.1110
CDS
1042046
1041582
−2
−
465
Bacterioferritin
-none-
D23_1c1120
Neut_1195

fig|6666666.60966.peg.1112
CDS
1043119
1043253
1
+
135
hypothetical protein
-none-
D23_1c1121
NA

fig|6666666.60966.peg.1113
CDS
1043368
1043511
1
+
144
hypothetical protein
-none-
D23_1c1122
NA

fig|6666666.60966.peg.1115
CDS
1043900
1043736
−2
−
165
hypothetical protein
-none-
D23_1c1123
NA

fig|6666666.60966.peg.1116
CDS
1043900
1044847
2
+
948
2,3-
-none-
D23_1c1124
Neut_1198








bisphosphoglycerate-











independent











phosphoglycerate











mutase




fig|6666666.60966.peg.1117
CDS
1044958
1045530
1
+
573
InterPro
-none-
D23_1c1125
Neut_1199








IPR000014:IPR001633











COGs COG2200




fig|6666666.60966.peg.1118
CDS
1045566
1045859
3
+
294
Mobile element protein
-none-
D23_1c1126
Neut_1719

fig|6666666.60966.peg.1119
CDS
1045958
1046836
2
+
879
Mobile element protein
-none-
D23_1c1127
Neut_1720

fig|6666666.60966.peg.1120
CDS
1046891
1047784
2
+
894
InterPro
-none-
D23_1c1128
Neut_1199








IPR000014:IPR001633











COGs COG2200




fig|6666666.60966.peg.1121
CDS
1048688
1047801
−2
−
888
Phosphoribosylaminoimidazole-
De Novo Purine
D23_1c1129
Neut_1200








succinocarboxamide
Biosynthesis










synthase (EC 6.3.2.6)




fig|6666666.60966.peg.1122
CDS
1049856
1048726
−3
−
1131
Phosphoribosylaminoimidazole
De Novo Purine
D23_1c1130
Neut_1201








carboxylase
Biosynthesis










ATPase subunit (EC











4.1.1.21)




fig|6666666.60966.peg.1123
CDS
1050317
1049847
−2
−
471
Phosphoribosylaminoimidazole
De Novo Purine
D23_1c1131
Neut_1202








carboxylase
Biosynthesis










catalytic subunit (EC











4.1.1.21)




fig|6666666.60966.peg.1124
CDS
1050521
1050955
2
+
435
Biopolymer transport
Ton and Tol transport
D23_1c1133
Neut_1203








protein ExbD/TolR
systems



fig|6666666.60966.peg.1125
CDS
1050942
1051664
3
+
723
Superoxide dismutase
Oxidative stress;
D23_1c1134
Neut_1204








[Fe] (EC 1.15.1.1)
<br>Protection from











Reactive Oxygen Species



fig|6666666.60966.peg.1126
CDS
1051674
1052324
3
+
651
ATP
Histidine Biosynthesis;
D23_1c1135
Neut_1205








phosphoribosyltransferase
<br>Riboflavin synthesis










(EC 2.4.2.17)
cluster



fig|6666666.60966.peg.1127
CDS
1052409
1053644
3
+
1236
Histidinol
Histidine Biosynthesis
D23_1c1136
Neut_1206








dehydrogenase (EC











1.1.1.23)




fig|6666666.60966.peg.1128
CDS
1053708
1054883
3
+
1176
2-octaprenyl-6-
CBSS-87626.3.peg.3639;
D23_1c1137
Neut_1207








methoxyphenol
<br>Ubiquinone










hydroxylase (EC
Biosynthesis;










1.14.13.—)
<br>Ubiquinone











Biosynthesis-gjo



fig|6666666.60966.peg.1129
CDS
1055047
1056060
1
+
1014
tRNA dihydrouridine
Possible RNA
D23_1c1138
Neut_1208








synthase B (EC 1.—.—.—)
degradation cluster;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1130
CDS
1056057
1056299
3
+
243
DNA-binding protein Fis
DNA structural proteins,
D23_1c1139
Neut_1209









bacterial



fig|6666666.60966.peg.1131
CDS
1056309
1057871
3
+
1563
IMP cyclohydrolase (EC
5-FCL-like protein;
D23_1c1140
Neut_1210








3.5.4.10)/
<br>De Novo Purine










Phosphoribosylaminoimidazolecarboxamide
Biosynthesis; <br>De










formyltransferase (EC
Novo Purine










2.1.2.3)
Biosynthesis



fig|6666666.60966.peg.1132
CDS
1057947
1059233
3
+
1287
Phosphoribosylamine-
De Novo Purine
D23_1c1141
Neut_1211








glycine ligase (EC
Biosynthesis










6.3.4.13)




fig|6666666.60966.peg.1133
CDS
1059226
1060497
1
+
1272
FIG00858582:
-none-
D23_1c1142
Neut_1213








hypothetical protein




fig|6666666.60966.peg.1134
CDS
1061025
1060582
−3
−
444
TPR repeat precursor
-none-
D23_1c1143
Neut_1214

fig|6666666.60966.peg.1135
CDS
1061496
1061041
−3
−
456
Mobile element protein
-none-
D23_1c1144
Neut_2502

fig|6666666.60966.peg.1136
CDS
1061839
1061459
−1
−
381
Mobile element protein
-none-
D23_1c1145
Neut_0884

fig|6666666.60966.peg.1137
CDS
1062885
1061836
−3
−
1050
TPR repeat precursor
-none-
D23_1c1146
Neut_0701

fig|6666666.60966.peg.1138
CDS
1064906
1062960
−2
−
1947
DinG family ATP-
DNA repair, bacterial
D23_1c1148
Neut_1215








dependent helicase
DinG and relatives










YoaA




fig|6666666.60966.peg.1139
CDS
1065051
1064932
−3
−
120
hypothetical protein
-none-
D23_1c1149
NA

fig|6666666.60966.peg.1140
CDS
1065126
1067303
3
+
2178
Outer membrane
EC49-61; <br>ECSIG4-
D23_1c1150
Neut_1216








protein Imp, required
SIG7;










for envelope biogenesis/
<br>Lipopolysaccharide










Organic solvent
assembly










tolerance protein











precursor




fig|6666666.60966.peg.1141
CDS
1067300
1068643
2
+
1344
Survival protein SurA
EC49-61; <br>ECSIG4-
D23_1c1151
Neut_1217








precursor (Peptidyl-
SIG7;










prolyl cis-trans
<br>Lipopolysaccharide










isomerase SurA) (EC
assembly; <br>Peptidyl-










5.2.1.8)
prolyl cis-trans











isomerase;











<br>Periplasmic Stress











Response



fig|6666666.60966.peg.1142
CDS
1068713
1069750
2
+
1038
4-hydroxythreonine-4-
EC49-61; <br>ECSIG4-
D23_1c1152
Neut_1218








phosphate
SIG7; <br>Pyridoxin










dehydrogenase (EC
(Vitamin B6)










1.1.1.262)
Biosynthesis



fig|6666666.60966.peg.1143
CDS
1069754
1070524
2
+
771
SSU rRNA
EC49-61; <br>ECSIG4-
D23_1c1153
Neut_1219








(adenine(1518)-
SIG7; <br>RNA










N(6)/adenine(1519)-
methylation;










N(6))-
<br>Ribosome










dimethyltransferase (EC
biogenesis bacterial










2.1.1.182) ## SSU rRNA











m6,m6-A1518-1519




fig|6666666.60966.peg.1144
CDS
1071020
1070517
−2
−
504
Methylated-DNA--
DNA repair, bacterial
D23_1c1154
Neut_1220








protein-cysteine











methyltransferase (EC











2.1.1.63)




fig|6666666.60966.peg.1145
CDS
1071346
1071080
−1
−
267
ADA regulatory protein/
DNA repair, bacterial;
D23_1c1155
Neut_1221








Methylated-DNA--
<br>DNA repair,










protein-cysteine
bacterial










methyltransferase (EC











2.1.1.63)




fig|6666666.60966.peg.1146
CDS
1072448
1071324
−2
−
1125
ADA regulatory protein/
DNA repair, bacterial;
D23_1c1156
Neut_1221








Methylated-DNA--
<br>DNA repair,










protein-cysteine
bacterial










methyltransferase (EC











2.1.1.63)




fig|6666666.60966.peg.1149
CDS
1073291
1073809
2
+
519
Helix-turn-helix motif
-none-
D23_1c1157
Neut_1223

fig|6666666.60966.peg.1150
CDS
1075783
1074353
−1
−
1431
Siroheme synthase/
Heme and Siroheme
D23_1c1159
Neut_1002








Precorrin-2 oxidase (EC
Biosynthesis; <br>Heme










1.3.1.76)/
and Siroheme










Sirohydrochlorin
Biosynthesis; <br>Heme










ferrochelatase (EC
and Siroheme










4.99.1.4)/
Biosynthesis










Uroporphyrinogen-III











methyltransferase (EC











2.1.1.107)




fig|6666666.60966.peg.1151
CDS
1076939
1075926
−2
−
1014
Phosphate ABC
High affinity phosphate
D23_1c1160
Neut_1001








transporter, periplasmic
transporter and control










phosphate-binding
of PHO regulon;










protein PstS (TC
<br>PhoR-PhoB two-










3.A.1.7.1)
component regulatory











system; <br>Phosphate











metabolism



fig|6666666.60966.peg.1152
CDS
1078435
1077059
−1
−
1377
Phosphoglucosamine
Sialic Acid Metabolism;
D23_1c1161
Neut_1000








mutase (EC 5.4.2.10)
<br>UDP-N-











acetylmuramate from











Fructose-6-phosphate











Biosynthesis



fig|6666666.60966.peg.1153
CDS
1079505
1078603
−3
−
903
Dihydropteroate
Folate Biosynthesis
D23_1c1162
Neut_0999








synthase (EC 2.5.1.15)




fig|6666666.60966.peg.1154
CDS
1081457
1079529
−2
−
1929
Cell division protein
Bacterial Cell Division
D23_1c1163
Neut_0998








FtsH (EC 3.4.24.—)




fig|6666666.60966.peg.1155
CDS
1082161
1081541
−1
−
621
Cell division protein FtsJ/
Bacterial Cell Division;
D23_1c1164
Neut_0997








Ribosomal RNA large
<br>RNA methylation










subunit











methyltransferase E (EC











2.1.1.—) ## LSU rRNA











Um2552




fig|6666666.60966.peg.1156
CDS
1082195
1082575
2
+
381
FIG004454: RNA
-none-
D23_1c1165
Neut_0996








binding protein




fig|6666666.60966.peg.1157
CDS
1082674
1083084
1
+
411
CBS domain
-none-
D23_1c1166
Neut_0995

fig|6666666.60966.peg.1158
CDS
1083081
1083464
3
+
384
tRNA
A cluster relating to
D23_1c1167
Neut_0994








nucleotidyltransferase,
Tryptophanyl-tRNA










A-adding (EC 2.7.7.25)
synthetase;











<br>Polyadenylation











bacterial; <br>tRNA











nucleotidyltransferase



fig|6666666.60966.peg.1159
CDS
1084218
1083646
−3
−
573
DNA-3-methyladenine
DNA Repair Base
D23_1c1168
Neut_0993








glycosylase II (EC
Excision










3.2.2.21)




fig|6666666.60966.peg.1160
CDS
1084717
1084241
−1
−
477
Glutathione peroxidase
Glutathione: Redox cycle
D23_1c1169
Neut_0992








(EC 1.11.1.9)




fig|6666666.60966.peg.1161
CDS
1084748
1085341
2
+
594
Carbonic anhydrase,
Zinc regulated enzymes
D23_1c1170
Neut_0991








gamma class (EC











4.2.1.1)




fig|6666666.60966.peg.1162
CDS
1085402
1086241
2
+
840
Putative NAD(P)-
-none-
D23_1c1171
Neut_0990








dependent











oxidoreductase EC-











YbbO




fig|6666666.60966.peg.1163
CDS
1086401
1087885
2
+
1485
alpha amylase, catalytic
-none-
D23_1c1172
Neut_0989








region




fig|6666666.60966.peg.1164
CDS
1090985
1087899
−2
−
3087
RND multidrug efflux
Multidrug Resistance
D23_1c1173
Neut_0988








transporter; Acriflavin
Efflux Pumps










resistance protein




fig|6666666.60966.peg.1165
CDS
1092079
1090982
−1
−
1098
Membrane fusion
Multidrug Resistance
D23_1c1174
Neut_0987








protein of RND family
Efflux Pumps










multidrug efflux pump




fig|6666666.60966.peg.1168
CDS
1092982
1092851
−1
−
132
hypothetical protein
-none-
D23_1c1175
NA

fig|6666666.60966.peg.1169
CDS
1094042
1093413
−2
−
630
Nicotinamidase family
NAD and NADP cofactor
D23_1c1176
NA








protein YcaC
biosynthesis global



fig|6666666.60966.peg.1170
CDS
1094408
1094223
−2
−
186
Mobile element protein
-none-
D23_1c1178
Neut_1984

fig|6666666.60966.peg.1171
CDS
1094750
1094514
−2
−
237
Mobile element protein
-none-
D23_1c1179
Neut_1353

fig|6666666.60966.peg.1172
CDS
1095334
1094984
−1
−
351
hypothetical protein
-none-
D23_1c1180
NA

fig|6666666.60966.peg.1173
CDS
1095854
1095486
−2
−
369
Mobile element protein
-none-
D23_1c1181
Neut_2502

fig|6666666.60966.peg.1175
CDS
1096049
1095933
−2
−
117
Mobile element protein
-none-
D23_1c1182
Neut_0884

fig|6666666.60966.peg.1176
CDS
1096623
1096288
−3
−
336
putative (AJ245540)
-none-
D23_1c1183
Neut_1054








NrfJ [ Wolinella











succinogenes ]




fig|6666666.60966.peg.1177
CDS
1098408
1096669
−3
−
1740
FIG00859793:
-none-
D23_1c1184
Neut_1053








hypothetical protein




fig|6666666.60966.peg.1178
CDS
1098651
1100255
3
+
1605
Multicopper oxidase
Copper homeostasis
D23_1c1185
Neut_1052

fig|6666666.60966.peg.1179
CDS
1101152
1100349
−2
−
804
Inositol-1-
-none-
D23_1c1186
Neut_1051








monophosphatase (EC











3.1.3.25)




fig|6666666.60966.peg.1180
CDS
1101712
1101155
−1
−
558
Alkyl hydroperoxide
-none-
D23_1c1187
Neut_1050








reductase and/or thiol-











specific antioxidant











family (AhpC/TSA)











protein




fig|6666666.60966.peg.1181
CDS
1101810
1102571
3
+
762
Ribosomal RNA small
Heat shock dnaK gene
D23_1c1188
Neut_1049








subunit
cluster extended;










methyltransferase E (EC
<br>RNA methylation










2.1.1.—)




fig|6666666.60966.peg.1182
CDS
1102595
1103929
2
+
1335
N-acetylglutamate
Arginine Biosynthesis--
D23_1c1189
Neut_1048








synthase (EC 2.3.1.1)
gjo; <br>Arginine











Biosynthesis extended



fig|6666666.60966.peg.1183
CDS
1104924
1104208
−3
−
717
FIG002842:
-none-
D23_1c1190
Neut_1046








hypothetical protein




fig|6666666.60966.peg.1184
CDS
1105647
1105036
−3
−
612
Dephospho-CoA kinase
Coenzyme A
D23_1c1191
Neut_1045








(EC 2.7.1.24)
Biosynthesis



fig|6666666.60966.peg.1185
CDS
1106511
1105651
−3
−
861
Leader peptidase
-none-
D23_1c1192
Neut_1044








(Prepilin peptidase) (EC











3.4.23.43)/N-











methyltransferase (EC











2.1.1.—)




fig|6666666.60966.peg.1186
CDS
1107775
1106555
−1
−
1221
Type IV fimbrial
-none-
D23_1c1193
Neut_1043








assembly protein PilC




fig|6666666.60966.peg.1187
CDS
1108692
1107835
−3
−
858
Nucleoside-
CBSS-296591.1.peg.2330
D23_1c1194
Neut_1042








diphosphate-sugar











epimerases




fig|6666666.60966.peg.1189
CDS
1108961
1109818
2
+
858
2-polyprenylphenol
-none-
D23_1c1195
Neut_1041








hydroxylase and related











flavodoxin











oxidoreductases/CDP-











6-deoxy-delta-3,4-











glucoseen reductase-











like




fig|6666666.60966.peg.1190
CDS
1111006
1109825
−1
−
1182
Homolog of E. coli
-none-
D23_1c1196
Neut_1040








HemY protein




fig|6666666.60966.peg.1191
CDS
1112031
1111003
−3
−
1029
Uroporphyrinogen-III
Heme and Siroheme
D23_1c1197
Neut_1039








methyltransferase (EC
Biosynthesis










2.1.1.107)




fig|6666666.60966.peg.1192
CDS
1112828
1112046
−2
−
783
Uroporphyrinogen-III
Heme and Siroheme
D23_1c1198
Neut_1038








synthase (EC 4.2.1.75)
Biosynthesis



fig|6666666.60966.peg.1193
CDS
1113852
1112848
−3
−
1005
Porphobilinogen
Heme and Siroheme
D23_1c1199
Neut_1037








deaminase (EC 2.5.1.61)
Biosynthesis



fig|6666666.60966.peg.1194
CDS
1113898
1116699
1
+
2802
Phosphoenolpyruvate
Pyruvate metabolism I:
D23_1c1200
Neut_1036








carboxylase (EC
anaplerotic reactions,










4.1.1.31)
PEP



fig|6666666.60966.peg.1195
CDS
1116922
1118904
1
+
1983
FIG00858706:
-none-
D23_1c1201
Neut_1035








hypothetical protein




fig|6666666.60966.peg.1196
CDS
1120329
1118899
−3
−
1431
probable integral
-none-
D23_1c1202
Neut_1034








membrane protein











NMA1898




fig|6666666.60966.peg.1197
CDS
1121723
1120329
−2
−
1395
FIG00859415:
-none-
D23_1c1203
Neut_1033








hypothetical protein




fig|6666666.60966.peg.1198
CDS
1121909
1121763
−2
−
147
hypothetical protein
-none-
D23_1c1204
NA

fig|6666666.60966.peg.1199
CDS
1121985
1122698
3
+
714
COGs COG0518
-none-
D23_1c1205
Neut_1032

fig|6666666.60966.peg.1200
CDS
1123590
1122748
−3
−
843
RNA polymerase sigma
Heat shock Cell division
D23_1c1206
Neut_1031








factor RpoH
Proteases and a











Methyltransferase;











<br>Heat shock dnaK











gene cluster extended;











<br>Transcription











initiation, bacterial











sigma factors



fig|6666666.60966.peg.1201
CDS
1124005
1124823
1
+
819
Cytochrome c family
-none-
D23_1c1207
NA








protein




fig|6666666.60966.peg.1203
CDS
1125802
1127289
1
+
1488
FIG00858881:
-none-
D23_1c1209
Neut_1029








hypothetical protein




fig|6666666.60966.peg.1204
CDS
1127318
1128325
2
+
1008
Sulfate-binding protein
Inorganic Sulfur
D23_1c1210
Neut_1028








Sbp
Assimilation



fig|6666666.60966.peg.1205
CDS
1128452
1128580
2
+
129
hypothetical protein
-none-
D23_1c1211
NA

fig|6666666.60966.peg.1206
CDS
1128661
1129494
1
+
834
Sulfate transport
Cysteine Biosynthesis;
D23_1c1212
Neut_1026








system permease
<br>Inorganic Sulfur










protein CysT
Assimilation



fig|6666666.60966.peg.1207
CDS
1129502
1130371
2
+
870
Sulfate transport
Cysteine Biosynthesis;
D23_1c1213
Neut_1025








system permease
<br>Inorganic Sulfur










protein CysW
Assimilation



fig|6666666.60966.peg.1208
CDS
1130383
1131471
1
+
1089
Sulfate and thiosulfate
Cysteine Biosynthesis;
D23_1c1214
Neut_1024








import ATP-binding
<br>Inorganic Sulfur










protein CysA (EC
Assimilation;










3.6.3.25)
<br>Uptake of selenate











and selenite



fig|6666666.60966.peg.1209
CDS
1131827
1131510
−2
−
318
possible lipase
-none-
D23_1c1215
Neut_1023

fig|6666666.60966.peg.1210
CDS
1133403
1131859
−3
−
1545
Aminopeptidase PepA-
-none-
D23_1c1216
Neut_1022








related protein




fig|6666666.60966.peg.1211
CDS
1133455
1134249
1
+
795
Thymidylate synthase
Folate Biosynthesis;
D23_1c1217
Neut_1021








(EC 2.1.1.45)
<br>pyrimidine











conversions



fig|6666666.60966.peg.1212
CDS
1134246
1134776
3
+
531
Dihydrofolate reductase
5-FCL-like protein;
D23_1c1218
Neut_1020








(EC 1.5.1.3)
<br>EC49-61; <br>Folate











Biosynthesis



fig|6666666.60966.peg.1213
CDS
1136053
1134809
−1
−
1245
Response regulator
-none-
D23_1c1219
Neut_1019

fig|6666666.60966.peg.1215
CDS
1136321
1136785
2
+
465
Mobile element protein
-none-
D23_1c1220
Neut_0357

fig|6666666.60966.peg.1216
CDS
1136808
1137512
3
+
705
Mobile element protein
-none-
D23_1c1221
Neut_1318

fig|6666666.60966.peg.1217
CDS
1137576
1138703
3
+
1128
Catalase (EC 1.11.1.6)
Oxidative stress;
D23_1c1222
NA









<br>Photorespiration











(oxidative C2cycle);











<br>Protection from











Reactive Oxygen Species



fig|6666666.60966.peg.1218
CDS
1139453
1138773
−2
−
681
Mobile element protein
-none-
D23_1c1223
Neut_1318

fig|6666666.60966.peg.1219
CDS
1139703
1139837
3
+
135
Mobile element protein
-none-
D23_1c1224
Neut_2500

fig|6666666.60966.peg.1220
CDS
1139894
1140238
2
+
345
Mobile element protein
-none-
D23_1c1225
Neut_1375

fig|6666666.60966.peg.1221
CDS
1141157
1140195
−2
−
963
Mobile element protein
-none-
D23_1c1226
Neut_1278

fig|6666666.60966.peg.1222
CDS
1141250
1141762
2
+
513
Mobile element protein
-none-
D23_1c1227
Neut_1624

fig|6666666.60966.peg.1223
CDS
1142310
1141846
−3
−
465
Mobile element protein
-none-
D23_1c1228
Neut_0357

fig|6666666.60966.peg.1224
CDS
1142882
1142409
−2
−
474
Mobile element protein
-none-
D23_1c1229
Neut_0883

fig|6666666.60966.peg.1225
CDS
1144087
1143419
−1
−
669
hypothetical protein
-none-
D23_1c1230
NA

fig|6666666.60966.peg.1226
CDS
1144329
1144078
−3
−
252
ABC-type antimicrobial
-none-
D23_1c1231
NA








peptide transport











system, permease











component




fig|6666666.60966.peg.1227
CDS
1144623
1145231
3
+
609
Transcriptional
-none-
D23_1c1232
Neut_1011








regulator, TetR family




fig|6666666.60966.peg.1228
CDS
1145317
1146351
1
+
1035
Predicted membrane
ATP-dependent efflux
D23_1c1233
Neut_1010








fusion protein (MFP)
pump transporter Ybh










component of efflux











pump, membrane











anchor protein YbhG




fig|6666666.60966.peg.1229
CDS
1146341
1148125
2
+
1785
ABC transporter
ATP-dependent efflux
D23_1c1234
Neut_1009








multidrug efflux pump,
pump transporter Ybh










fused ATP-binding











domains




fig|6666666.60966.peg.1230
CDS
1148122
1149270
1
+
1149
ABC transport system,
ATP-dependent efflux
D23_1c1235
Neut_1008








permease component
pump transporter Ybh










YbhS




fig|6666666.60966.peg.1231
CDS
1149276
1150400
3
+
1125
ABC transport system,
ATP-dependent efflux
D23_1c1236
Neut_1007








permease component
pump transporter Ybh










YbhR




fig|6666666.60966.peg.1232
CDS
1150415
1150546
2
+
132
hypothetical protein
-none-
D23_1c1237
NA

fig|6666666.60966.peg.1233
CDS
1150719
1150507
−3
−
213
hypothetical protein
-none-
D23_1c1238
NA

fig|6666666.60966.peg.1234
CDS
1150690
1150875
1
+
186
hypothetical protein
-none-
D23_1c1239
Neut_1006

fig|6666666.60966.peg.1235
CDS
1150882
1151043
1
+
162
hypothetical protein
-none-
D23_1c1240
NA

fig|6666666.60966.peg.1236
CDS
1151054
1151923
2
+
870
hypothetical protein
-none-
D23_1c1241
Neut_1006

fig|6666666.60966.peg.1237
CDS
1151916
1152278
3
+
363
hypothetical protein
-none-
D23_1c1242
NA

fig|6666666.60966.peg.1239
CDS
1152362
1152703
2
+
342
hypothetical protein
-none-
D23_1c1243
Neut_1005

fig|6666666.60966.peg.1240
CDS
1153760
1152756
−2
−
1005
Mobile element protein
-none-
D23_1c1244
Neut_1862

fig|6666666.60966.peg.1241
CDS
1153821
1154177
3
+
357
Putative transport
-none-
D23_1c1245
Neut_1004








system permease











protein




fig|6666666.60966.peg.1242
CDS
1154289
1154441
3
+
153
FIG00626672:
-none-
D23_1c1246
Neut_1003








hypothetical protein




fig|6666666.60966.peg.1243
CDS
1154607
1154476
−3
−
132
hypothetical protein
-none-
D23_1c1247
Neut_1226

fig|6666666.60966.peg.1244
CDS
1156287
1154728
−3
−
1560
amino acid transporter
-none-
D23_1c1248
Neut_1227

fig|6666666.60966.peg.1245
CDS
1157495
1156611
−2
−
885
DNA recombination-
DNA repair, bacterial
D23_1c1250
Neut_1228








dependent growth











factor C




fig|6666666.60966.peg.1246
CDS
1158541
1157738
−1
−
804
Probable component of
Lipopolysaccharide
D23_1c1252
Neut_1229








the lipoprotein
assembly










assembly complex











(forms a complex with











YaeT, YfgL, and NlpB)




fig|6666666.60966.peg.1247
CDS
1158543
1159571
3
+
1029
Ribosomal large subunit
RNA pseudouridine
D23_1c1253
Neut_1230








pseudouridine synthase
syntheses;










D (EC 4.2.1.70)
<br>Ribosome











biogenesis bacterial



fig|6666666.60966.peg.1248
CDS
1159795
1161201
1
+
1407
Glutamine synthetase
Ammonia assimilation;
D23_1c1254
Neut_1231








type I (EC 6.3.1.2)
<br>Glutamine,











Glutamate, Aspartate











and Asparagine











Biosynthesis;











<br>Glutamine











synthetases;











<br>Peptidoglycan











Biosynthesis



fig|6666666.60966.peg.1249
CDS
1161356
1161826
2
+
471
FIG00858905:
-none-
D23_1c1256
Neut_1232








hypothetical protein




fig|6666666.60966.peg.1250
CDS
1161926
1161813
−2
−
114
hypothetical protein
-none-
D23_1c1257
NA

fig|6666666.60966.peg.1251
CDS
1162096
1162263
1
+
168
hypothetical protein
-none-
D23_1c1258
NA

fig|6666666.60966.peg.1252
CDS
1162260
1162415
3
+
156
hypothetical protein
-none-
D23_1c1259
NA

fig|6666666.60966.peg.1253
CDS
1162412
1163191
2
+
780
Putative sulfate
Inorganic Sulfur
D23_1c1260
Neut_1235








permease
Assimilation



fig|6666666.60966.peg.1254
CDS
1163827
1163267
−1
−
561
Iron-sulfur cluster
-none-
D23_1c1261
Neut_1236








assembly scaffold











protein IscU/NifU-like











for SUF system, SufE3




fig|6666666.60966.peg.1255
CDS
1164319
1163837
−1
−
483
Putative iron-sulfur
-none-
D23_1c1262
Neut_1237








cluster assembly











scaffold protein for SUF











system, SufE2




fig|6666666.60966.peg.1256
CDS
1165584
1164316
−3
−
1269
Cysteine desulfurase
Alanine biosynthesis;
D23_1c1263
Neut_1238








(EC 2.8.1.7), SufS
<br>mnm5U34










subfamily
biosynthesis bacteria;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1257
CDS
1166895
1165588
−3
−
1308
Iron-sulfur cluster
CBSS-
D23_1c1264
Neut_1239








assembly protein SufD
196164.1.peg.1690;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1258
CDS
1167683
1166892
−2
−
792
Iron-sulfur cluster
CBSS-
D23_1c1265
Neut_1240








assembly ATPase
196164.1.peg.1690;










protein SufC
<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1259
CDS
1169116
1167680
−1
−
1437
Iron-sulfur cluster
CBSS-
D23_1c1266
Neut_1241








assembly protein SufB
196164.1.peg.1690;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1260
CDS
1169465
1169136
−2
−
330
Iron binding protein
Alanine biosynthesis;
D23_1c1267
Neut_1242








IscA for iron-sulfur
<br>tRNA modification










cluster assembly
Bacteria



fig|6666666.60966.peg.1261
CDS
1169958
1169491
−3
−
468
Iron-sulfur cluster
Alanine biosynthesis;
D23_1c1268
Neut_1243








regulator IscR
<br>Rrf2 family











transcriptional











regulators



fig|6666666.60966.peg.1262
CDS
1170306
1171838
3
+
1533
2-isopropylmalate
Branched-Chain Amino
D23_1c1270
Neut_1244








synthase (EC 2.3.3.13)
Acid Biosynthesis;











<br>Leucine











Biosynthesis



fig|6666666.60966.peg.1263
CDS
1171964
1172467
2
+
504
Cytochrome c-type
Biogenesis of c-type
D23_1c1271
Neut_1245








biogenesis protein ResA
cytochromes



fig|6666666.60966.peg.1264
CDS
1173081
1172488
−3
−
594
FIG016425: Soluble lytic
-none-
D23_1c1272
Neut_1246








murein transglycosylase











and related regulatory











proteins (some contain











LysM/invasin domains)




fig|6666666.60966.peg.1265
CDS
1174775
1173069
−2
−
1707
Prolyl-tRNA synthetase
tRNA aminoacylation,
D23_1c1273
Neut_1247








(EC 6.1.1.15), bacterial
Pro










type




fig|6666666.60966.peg.1266
CDS
1175004
1175567
3
+
564
Adenosine (5&#39;)-
CBSS-
D23_1c1274
Neut_1248








pentaphospho-
364106.7.peg.3204;










(5&#39;&#39;)-
<br>Nudix proteins










adenosine
(nucleoside triphosphate










pyrophosphohydrolase
hydrolases);










(EC 3.6.1.—)
<br>Phosphoglycerate











mutase protein family



fig|6666666.60966.peg.1267
CDS
1175673
1176677
3
+
1005
Cytochrome c551
Protection from Reactive
D23_1c1275
Neut_1249








peroxidase (EC 1.11.1.5)
Oxygen Species



fig|6666666.60966.peg.1269
CDS
1176892
1178190
1
+
1299
Sensor histidine kinase
Global Two-component
D23_1c1276
Neut_1250








PrrB (RegB) (EC 2.7.3.—)
Regulator PrrBA in











Proteobacteria



fig|6666666.60966.peg.1270
CDS
1178205
1178750
3
+
546
Dna binding response
Global Two-component
D23_1c1277
Neut_1251








regulator PrrA (RegA)
Regulator PrrBA in











Proteobacteria



fig|6666666.60966.peg.1271
CDS
1181021
1178853
−2
−
2169
Ferrichrome-iron
-none-
D23_1c1278
Neut_1252








receptor




fig|6666666.60966.peg.1272
CDS
1181355
1181558
3
+
204
hypothetical protein
-none-
D23_1c1279
NA

fig|6666666.60966.peg.1273
CDS
1181609
1181776
2
+
168
hypothetical protein
-none-
D23_1c1280
NA

fig|6666666.60966.peg.1274
CDS
1181748
1181981
3
+
234
Mobile element protein
-none-
D23_1c1281
NA

fig|6666666.60966.peg.1275
CDS
1182136
1181990
−1
−
147
hypothetical protein
-none-
D23_1c1282
NA

fig|6666666.60966.peg.1277
CDS
1182799
1182386
−1
−
414
hypothetical protein
-none-
D23_1c1283
Neut_1254

fig|6666666.60966.peg.1278
CDS
1182892
1183920
1
+
1029
Mobile element protein
-none-
D23_1c1284
Neut_1746

fig|6666666.60966.peg.1280
CDS
1185348
1184569
−3
−
780
CDP-diacylglycerol--
Glycerolipid and
D23_1c1285
Neut_1258








serine O-
Glycerophospholipid










phosphatidyltransferase
Metabolism in Bacteria










(EC 2.7.8.8)




fig|6666666.60966.peg.1281
CDS
1186028
1185378
−2
−
651
Phosphatidylserine
Glycerolipid and
D23_1c1286
Neut_1259








decarboxylase (EC
Glycerophospholipid










4.1.1.65)
Metabolism in Bacteria



fig|6666666.60966.peg.1282
CDS
1187049
1186033
−3
−
1017
Ketol-acid
Branched-Chain Amino
D23_1c1287
Neut_1260








reductoisomerase (EC
Acid Biosynthesis;










1.1.1.86)
<br>Coenzyme A











Biosynthesis



fig|6666666.60966.peg.1283
CDS
1187629
1187138
−1
−
492
Acetolactate synthase
Acetolactate synthase
D23_1c1288
Neut_1261








small subunit (EC
subunits; <br>Branched-










2.2.1.6)
Chain Amino Acid











Biosynthesis



fig|6666666.60966.peg.1284
CDS
1189337
1187634
−2
−
1704
Acetolactate synthase
Acetolactate synthase
D23_1c1289
Neut_1262








large subunit (EC
subunits; <br>Branched-










2.2.1.6)
Chain Amino Acid











Biosynthesis



fig|6666666.60966.peg.1285
CDS
1189440
1189327
−3
−
114
hypothetical protein
-none-
D23_1c1290
NA

fig|6666666.60966.peg.1287
CDS
1191111
1189663
−3
−
1449
TldD protein, part of
CBSS-316057.3.peg.563;
D23_1c1292
Neut_1263








TldE/TldD proteolytic
<br>CBSS-










complex
354.1.peg.2917;











<br>Putative TldE-TldD











proteolytic complex



fig|6666666.60966.peg.1288
CDS
1192101
1191238
−3
−
864
FIG003879: Predicted
CBSS-354.1.peg.2917
D23_1c1293
Neut_1264








amidohydrolase/











Aliphatic amidase AmiE











(EC 3.5.1.4)




fig|6666666.60966.peg.1289
CDS
1196193
1192303
−3
−
3891
FIG005080: Possible
CBSS-354.1.peg.2917
D23_1c1294
Neut_1265








exported protein




fig|6666666.60966.peg.1290
CDS
1196421
1199210
3
+
2790
Glutamate-ammonia-
Ammonia assimilation;
D23_1c1295
Neut_1266








ligase
<br>CBSS-










adenylyltransferase (EC
316057.3.peg.3521










2.7.7.42)




fig|6666666.60966.peg.1291
CDS
1200720
1200058
−3
−
663
FIG00859512:
-none-
D23_1c1300
Neut_1268








hypothetical protein




fig|6666666.60966.peg.1292
CDS
1200901
1200761
−1
−
141
hypothetical protein
-none-
D23_1c1301
NA

fig|6666666.60966.peg.1293
CDS
1200921
1202306
3
+
1386
Argininosuccinate lyase
Arginine Biosynthesis--
D23_1c1302
Neut_1269








(EC 4.3.2.1)
gjo; <br>Arginine











Biosynthesis extended



fig|6666666.60966.peg.1294
CDS
1202336
1203241
2
+
906
Ribulosamine/erythrulosamine
Protein deglycation
D23_1c1303
Neut_1270








3-kinase











potentially involved in











protein deglycation




fig|6666666.60966.peg.1295
CDS
1203386
1204876
2
+
1491
FIG00807778:
-none-
D23_1c1304
Neut_1271








hypothetical protein




fig|6666666.60966.peg.1297
CDS
1205984
1205553
−2
−
432
hypothetical protein
-none-
D23_1c1305
Neut_1272

fig|6666666.60966.peg.1298
CDS
1206313
1205987
−1
−
327
hypothetical protein
-none-
D23_1c1306
Neut_1273

fig|6666666.60966.peg.1299
CDS
1206643
1206329
−1
−
315
CrcB protein
-none-
D23_1c1307
Neut_1274

fig|6666666.60966.peg.1300
CDS
1206663
1206902
3
+
240
hypothetical protein
-none-
D23_1c1308
NA

fig|6666666.60966.peg.1301
CDS
1207586
1206945
−2
−
642
Chemotaxis response-
-none-
D23_1c1309
Neut_1275








phosphatase CheZ




fig|6666666.60966.peg.1302
CDS
1208030
1207635
−2
−
396
Chemotaxis regulator-
Flagellar motility
D23_1c1310
Neut_1276








transmits











chemoreceptor signals











to flagelllar motor











components CheY




fig|6666666.60966.peg.1303
CDS
1209139
1208375
−1
−
765
Mobile element protein
-none-
D23_1c1311
NA

fig|6666666.60966.peg.1305
CDS
1210466
1210134
−2
−
333
hypothetical protein
-none-
D23_1c1313
NA

fig|6666666.60966.peg.1306
CDS
1210482
1210661
3
+
180
hypothetical protein
-none-
D23_1c1314
Neut_1280

fig|6666666.60966.peg.1307
CDS
1212693
1210768
−3
−
1926
Cytochrome c, class I
-none-
D23_1c1315
Neut_1281

fig|6666666.60966.peg.1308
CDS
1213523
1213044
−2
−
480
FIG00858481:
-none-
D23_1c1317
Neut_1282








hypothetical protein




fig|6666666.60966.peg.1309
CDS
1213544
1214608
2
+
1065
Folate-dependent
-none-
D23_1c1318
Neut_1283








protein for Fe/S cluster











synthesis/repair in











oxidative stress




fig|6666666.60966.peg.1310
CDS
1215290
1214631
−2
−
660
FOG: Ankyrin repeat
-none-
D23_1c1319
Neut_1284

fig|6666666.60966.peg.1311
CDS
1215984
1215292
−3
−
693
Putative
YcfH
D23_1c1320
Neut_1285








deoxyribonuclease YcfH




fig|6666666.60966.peg.1313
CDS
1216517
1216125
−2
−
393
Queuosine biosynthesis
Queuosine-Archaeosine
D23_1c1321
Neut_1286








QueD, PTPS-I
Biosynthesis; <br>Zinc











regulated enzymes;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1315
CDS
1216624
1217484
1
+
861
Radical SAM domain
-none-
D23_1c1322
Neut_1287








protein




fig|6666666.60966.peg.1316
CDS
1217801
1217514
−2
−
288
FIG00858571:
-none-
D23_1c1323
Neut_1288








hypothetical protein




fig|6666666.60966.peg.1318
CDS
1219170
1218214
−3
−
957
Cobalt-zinc-cadmium
Cobalt-zinc-cadmium
D23_1c1325
Neut_1289








resistance protein CzcD
resistance



fig|6666666.60966.peg.1319
CDS
1221684
1219195
−3
−
2490
Lead, cadmium, zinc
Copper Transport
D23_1c1326
Neut_1290








and mercury
System; <br>Copper










transporting ATPase (EC
homeostasis










3.6.3.3) (EC 3.6.3.5);











Copper-translocating P-











type ATPase (EC 3.6.3.4)




fig|6666666.60966.peg.1320
CDS
1223842
1221797
−1
−
2046
1,4-alpha-glucan
Glycogen metabolism
D23_1c1327
Neut_1291








(glycogen) branching











enzyme, GH-13-type (EC











2.4.1.18)




fig|6666666.60966.peg.1321
CDS
1223815
1224054
1
+
240
hypothetical protein
-none-
D23_1c1328
NA

fig|6666666.60966.peg.1322
CDS
1224141
1225418
3
+
1278
Glucose-1-phosphate
Glycogen metabolism
D23_1c1329
Neut_1292








adenylyltransferase (EC











2.7.7.27)




fig|6666666.60966.peg.1323
CDS
1225484
1227202
2
+
1719
Amylopullulanase (EC
-none-
D23_1c1330
Neut_1293








3.2.1.1)/(EC 3.2.1.41)




fig|6666666.60966.peg.1324
CDS
1227268
1229292
1
+
2025
Alpha-amylase (EC
-none-
D23_1c1331
Neut_1294








3.2.1.1)




fig|6666666.60966.peg.1325
CDS
1229324
1232014
2
+
2691
hypothetical protein
-none-
D23_1c1332
Neut_1295

fig|6666666.60966.peg.1326
CDS
1232973
1232236
−3
−
738
Uracil-DNA glycosylase,
Uracil-DNA glycosylase
D23_1c1334
Neut_1296








family 4




fig|6666666.60966.peg.1327
CDS
1233520
1233032
−1
−
489
Ribosomal-protein-
Bacterial RNA-
D23_1c1335
Neut_1297








S18p-alanine
metabolizing Zn-










acetyltransferase (EC
dependent hydrolases;










2.3.1.—)
<br>Ribosome











biogenesis bacterial



fig|6666666.60966.peg.1328
CDS
1234194
1233523
−3
−
672
Inactive homolog of
-none-
D23_1c1336
Neut_1298








metal-dependent











proteases, putative











molecular chaperone




fig|6666666.60966.peg.1329
CDS
1234742
1234209
−2
−
534
2&#39;-5&#39; RNA
RNA processing orphans
D23_1c1337
Neut_1299








ligase




fig|6666666.60966.peg.1330
CDS
1235245
1234742
−1
−
504
2-C-methyl-D-erythritol
Isoprenoid Biosynthesis;
D23_1c1338
Neut_1300








2,4-cyclodiphosphate
<br>Nonmevalonate










synthase (EC 4.6.1.12)
Branch of Isoprenoid











Biosynthesis;











<br>Possible RNA











degradation cluster;











<br>Stationary phase











repair cluster



fig|6666666.60966.peg.1331
CDS
1235544
1235356
−3
−
189
hypothetical protein
-none-
D23_1c1339
Neut_0314

fig|6666666.60966.peg.1332
CDS
1235706
1235566
−3
−
141
hypothetical protein
-none-
D23_1c1340
Neut_0314

fig|6666666.60966.peg.1335
CDS
1236565
1236008
−1
−
558
Translation elongation
Translation elongation
D23_1c1341
Neut_1302








factor P
factors bacterial



fig|6666666.60966.peg.1336
CDS
1237794
1236640
−3
−
1155
hypothetical protein
-none-
D23_1c1342
Neut_1303

fig|6666666.60966.peg.1337
CDS
1237927
1238928
1
+
1002
D-lactate
Fermentations: Lactate
D23_1c1343
Neut_1304








dehydrogenase (EC











1.1.1.28)




fig|6666666.60966.peg.1338
CDS
1240296
1239037
−3
−
1260
putative membrane
-none-
D23_1c1344
Neut_1315








protein




fig|6666666.60966.peg.1339
CDS
1241400
1240354
−3
−
1047
Peptide chain release
Programmed frameshift;
D23_1c1345
Neut_1316








factor 2; programmed
<br>Programmed










frameshift-containing
frameshift;











<br>Translation











termination factors











bacterial



fig|6666666.60966.peg.1340
CDS
1243378
1241576
−1
−
1803
patatin family protein
-none-
D23_1c1346
Neut_1317

fig|6666666.60966.peg.1341
CDS
1244736
1243531
−3
−
1206
Catalase (EC 1.11.1.6)
Oxidative stress;
D23_1c1348
NA









<br>Photorespiration











(oxidative C2 cycle);











<br>Protection from











Reactive Oxygen Species



fig|6666666.60966.peg.1342
CDS
1246268
1244739
−2
−
1530
Peroxidase (EC 1.11.1.7)
Oxidative stress;
D23_1c1349
NA









<br>Protection from











Reactive Oxygen Species



fig|6666666.60966.peg.1343
CDS
1247585
1246281
−2
−
1305
Peroxidase (EC 1.11.1.7)
Oxidative stress;
D23_1c1350
NA









<br>Protection from











Reactive Oxygen Species



fig|6666666.60966.peg.1344
CDS
1248078
1247623
−3
−
456
hypothetical protein
-none-
D23_1c1351
NA

fig|6666666.60966.peg.1345
CDS
1248448
1251117
1
+
2670
FIG00860108:
-none-
D23_1c1352
Neut_0141








hypothetical protein




fig|6666666.60966.peg.1346
CDS
1251218
1253155
2
+
1938
Choline dehydrogenase
-none-
D23_1c1353
NA








(EC 1.1.99.1)




fig|6666666.60966.peg.1347
CDS
1256051
1253184
−2
−
2868
Peroxidase (EC 1.11.1.8)
-none-
D23_1c1354
NA

fig|6666666.60966.peg.1348
CDS
1257505
1256081
−1
−
1425
Hemagglutinin
-none-
D23_1c1355
NA

fig|6666666.60966.peg.1349
CDS
1258257
1257547
−3
−
711
hypothetical protein
-none-
D23_1c1356
NA

fig|6666666.60966.peg.1350
CDS
1259233
1258262
−1
−
972
hypothetical protein
-none-
D23_1c1357
NA

fig|6666666.60966.peg.1351
CDS
1261078
1259246
−1
−
1833
hypothetical protein
-none-
D23_1c1358
NA

fig|6666666.60966.peg.1352
CDS
1262776
1261109
−1
−
1668
Arachidonate 15-
-none-
D23_1c1359
NA








lipoxygenase (EC











1.13.11.33)




fig|6666666.60966.peg.1353
CDS
1264449
1262845
−3
−
1605
putative
-none-
D23_1c1360
NA








cyclooxygenase-2




fig|6666666.60966.peg.1354
CDS
1266134
1264638
−2
−
1497
hypothetical protein
-none-
D23_1c1361
NA

fig|6666666.60966.peg.1355
CDS
1266382
1266167
−1
−
216
hypothetical protein
-none-
D23_1c1362
NA

fig|6666666.60966.peg.1356
CDS
1266704
1266444
−2
−
261
hypothetical protein
-none-
D23_1c1363
NA

fig|6666666.60966.peg.1357
CDS
1267804
1266983
−1
−
822
Kazal-type serine
-none-
D23_1c1364
NA








protease inhibitor











domain




fig|6666666.60966.peg.1358
CDS
1268650
1267970
−1
−
681
Kazal-type serine
-none-
D23_1c1365
NA








protease inhibitor











domain




fig|6666666.60966.peg.1359
CDS
1268913
1268800
−3
−
114
hypothetical protein
-none-
D23_1c1366
NA

fig|6666666.60966.peg.1360
CDS
1269830
1269126
−2
−
705
Mobile element protein
-none-
D23_1c1367
Neut_1318

fig|6666666.60966.peg.1361
CDS
1270083
1269853
−3
−
231
Mobile element protein
-none-
D23_1c1368
Neut_1318

fig|6666666.60966.peg.1362
CDS
1270317
1270111
−3
−
207
Mobile element protein
-none-
D23_1c1369
Neut_2405

fig|6666666.60966.peg.1363
CDS
1271332
1270409
−1
−
924
alpha/beta hydrolase
-none-
D23_1c1370
NA








fold




fig|6666666.60966.peg.1364
CDS
1271721
1271329
−3
−
393
hypothetical protein
-none-
D23_1c1371
NA

fig|6666666.60966.peg.1365
CDS
1272160
1273251
1
+
1092
Putrescine transport
Polyamine Metabolism
D23_1c1372
Neut_1328








ATP-binding protein











PotA (TC 3.A.1.11.1)




fig|6666666.60966.peg.1366
CDS
1273248
1274150
3
+
903
Spermidine Putrescine
Polyamine Metabolism
D23_1c1373
Neut_1329








ABC transporter











permease component











PotB (TC 3.A.1.11.1)




fig|6666666.60966.peg.1367
CDS
1274170
1274955
1
+
786
Spermidine Putrescine
Polyamine Metabolism
D23_1c1374
Neut_1330








ABC transporter











permease component











potC (TC_3.A.1.11.1)




fig|6666666.60966.peg.1368
CDS
1274952
1276061
3
+
1110
ABC transporter,
Polyamine Metabolism
D23_1c1375
Neut_1331








periplasmic spermidine











putrescine-binding











protein PotD (TC











3.A.1.11.1)




fig|6666666.60966.peg.1369
CDS
1276066
1276374
1
+
309
Ferredoxin, 2Fe—2S
Alanine biosynthesis;
D23_1c1376
Neut_1332









<br>Soluble











cytochromes and











functionally related











electron carriers;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1370
CDS
1278030
1276423
−3
−
1608
Type I restriction-
Restriction-Modification
D23_1c1377
Neut_0541








modification system,
System; <br>Type I










DNA-methyltransferase
Restriction-Modification










subunit M (EC 2.1.1.72)




fig|6666666.60966.peg.1371
CDS
1279031
1278027
−2
−
1005
Putative DNA-binding
Restriction-Modification
D23_1c1378
NA








protein in cluster with
System










Type I restriction-











modification system




fig|6666666.60966.peg.1372
CDS
1282963
1279028
−1
−
3936
Type I restriction-
Restriction-Modification
D23_1c1379
Neut_0537








modification system,
System; <br>Type I










restriction subunit R (EC
Restriction-Modification










3.1.21.3)




fig|6666666.60966.peg.1373
CDS
1283272
1282982
−1
−
291
Type I restriction-
Restriction-Modification
D23_1c1380
NA








modification system,
System; <br>Type I










restriction subunit R (EC
Restriction-Modification










3.1.21.3)




fig|6666666.60966.peg.1374
CDS
1287342
1283581
−3
−
3762
macromolecule
-none-
D23_1c1381
Neut_1336








metabolism;











macromolecule











synthesis, modification;











dna-replication, repair,











restr./modif.




fig|6666666.60966.peg.1375
CDS
1287828
1287349
−3
−
480
FIG00858549:
-none-
D23_1c1382
Neut_1337








hypothetical protein




fig|6666666.60966.peg.1376
CDS
1288968
1287859
−3
−
1110
2-keto-3-deoxy-D-
Chorismate Synthesis;
D23_1c1383
Neut_1338








arabino-heptulosonate-
<br>Common Pathway










7-phosphate synthase I
For Synthesis of










alpha (EC 2.5.1.54)
Aromatic Compounds











(DAHP synthase to











chorismate)



fig|6666666.60966.peg.1377
CDS
1290768
1289113
−3
−
1656
MutS domain protein,
DNA repair, bacterial
D23_1c1384
Neut_1339








family 6
MutL-MutS system



fig|6666666.60966.peg.1378
CDS
1290915
1291493
3
+
579
FIG00858435:
-none-
D23_1c1385
Neut_1340








hypothetical protein




fig|6666666.60966.peg.1379
CDS
1291506
1292660
3
+
1155
Probable Co/Zn/Cd
Cobalt-zinc-cadmium
D23_1c1386
Neut_1341








efflux system
resistance










membrane fusion











protein




fig|6666666.60966.peg.1380
CDS
1292693
1293328
2
+
636
ABC transporter ATP-
-none-
D23_1c1387
Neut_1342








binding protein YvcR




fig|6666666.60966.peg.1381
CDS
1293325
1294527
1
+
1203
ABC transporter
-none-
D23_1c1388
Neut_1343








permease protein




fig|6666666.60966.peg.1382
CDS
1294533
1295732
3
+
1200
putative ABC
-none-
D23_1c1389
Neut_1344








transporter protein




fig|6666666.60966.peg.1383
CDS
1296266
1295742
−2
−
525
FIG00859169:
-none-
D23_1c1390
Neut_1345








hypothetical protein




fig|6666666.60966.peg.1385
CDS
1296862
1297086
1
+
225
ADA regulatory protein/
DNA repair, bacterial;
D23_1c1391
Neut_1346








Methylated-DNA--
<br>DNA repair,










protein-cysteine
bacterial










methyltransferase (EC











2.1.1.63)




fig|6666666.60966.peg.1386
CDS
1297089
1297802
3
+
714
hypothetical protein
-none-
D23_1c1392
Neut_1347

fig|6666666.60966.peg.1387
CDS
1298101
1297967
−1
−
135
hypothetical protein
-none-
D23_1c1393
NA

fig|6666666.60966.peg.1389
CDS
1298212
1298838
1
+
627
Alkylated DNA repair
-none-
D23_1c1395
Neut_1349








protein




fig|6666666.60966.peg.1390
CDS
1300170
1298923
−3
−
1248
Mobile element protein
-none-
D23_1c1396
Neut_0357

fig|6666666.60966.peg.1391
CDS
1300681
1300355
−1
−
327
hypothetical protein
-none-
D23_1c1397
Neut_1350

fig|6666666.60966.peg.1392
CDS
1301157
1300963
−3
−
195
Glutaredoxin
Glutaredoxins;
D23_1c1398
Neut_1351









<br>Glutathione: Redox











cycle; <br>Phage DNA











synthesis



fig|6666666.60966.peg.1393
CDS
1302170
1301697
−2
−
474
Mobile element protein
-none-
D23_1c1399
Neut_1353

fig|6666666.60966.peg.1394
CDS
1303008
1302400
−3
−
609
Glutathione S-
Glutathione: Non-redox
D23_1c1400
Neut_1354








transferase (EC
reactions










2.5.1.18)




fig|6666666.60966.peg.1395
CDS
1303729
1303556
−1
−
174
hypothetical protein
-none-
D23_1c1402
NA

fig|6666666.60966.peg.1396
CDS
1303948
1307514
1
+
3567
Exodeoxyribonuclease V
DNA repair, bacterial
D23_1c1403
Neut_1355








gamma chain (EC
RecBCD pathway










3.1.11.5)




fig|6666666.60966.peg.1397
CDS
1307530
1311216
1
+
3687
Exodeoxyribonuclease V
DNA repair, bacterial
D23_1c1404
Neut_1356








beta chain (EC 3.1.11.5)
RecBCD pathway



fig|6666666.60966.peg.1398
CDS
1311213
1313258
3
+
2046
Exodeoxyribonuclease V
DNA repair, bacterial
D23_1c1405
Neut_1357








alpha chain (EC
RecBCD pathway










3.1.11.5)




fig|6666666.60966.peg.1399
CDS
1314581
1313277
−2
−
1305
Aspartyl
-none-
D23_1c1406
Neut_1358








aminopeptidase




fig|6666666.60966.peg.1400
CDS
1315032
1314604
−3
−
429
PIN domain family
-none-
D23_1c1407
Neut_1359








protein




fig|6666666.60966.peg.1401
CDS
1315334
1315032
−2
−
303
DNA-binding protein,
-none-
D23_1c1408
Neut_1360








CopG family




fig|6666666.60966.peg.1402
CDS
1316699
1315362
−2
−
1338
Sensor protein PhoQ
-none-
D23_1c1409
Neut_1361








(EC 2.7.13.3)




fig|6666666.60966.peg.1403
CDS
1317382
1316696
−1
−
687
DNA-binding response
-none-
D23_1c1410
Neut_1362








regulator




fig|6666666.60966.peg.1404
CDS
1317741
1317451
−3
−
291
hypothetical protein
-none-
D23_1c1411
Neut_1363

fig|6666666.60966.peg.1405
CDS
1318192
1317827
−1
−
366
Putative metal
G3E family of P-loop
D23_1c1412
NA








chaperone, involved in
GTPases (metallocenter










Zn homeostasis, GTPase
biosynthesis); <br>Zinc










of COG0523 family
regulated enzymes



fig|6666666.60966.peg.1406
CDS
1318485
1319036
3
+
552
Protein of unknown
-none-
D23_1c1413
Neut_1365








function DUF924




fig|6666666.60966.peg.1407
CDS
1320160
1319171
−1
−
990
Integron integrase
Integrons
D23_1c1414
Neut_1366








IntlPac




fig|6666666.60966.peg.1408
CDS
1320314
1321651
2
+
1338
DNA modification
-none-
D23_1c1415
NA








methyltransferase




fig|6666666.60966.peg.1409
CDS
1321654
1322532
1
+
879
hypothetical protein
-none-
D23_1c1416
NA

fig|6666666.60966.peg.1410
CDS
1322665
1322880
1
+
216
hypothetical protein
-none-
D23_1c1417
NA

fig|6666666.60966.peg.1411
CDS
1323474
1324154
3
+
681
ThiJ/Pfpl family protein
-none-
D23_1c1418
NA

fig|6666666.60966.peg.1412
CDS
1324808
1324990
2
+
183
hypothetical protein
-none-
D23_1c1419
NA

fig|6666666.60966.peg.1413
CDS
1325941
1324979
−1
−
963
Mobile element protein
-none-
D23_1c1420
Neut_1746

fig|6666666.60966.peg.1415
CDS
1326558
1328531
3
+
1974
Monoamine oxidase
Auxin biosynthesis;
D23_1c1421
NA








(1.4.3.4)
<br>Glycine and Serine











Utilization;











<br>Threonine











degradation



fig|6666666.60966.peg.1417
CDS
1328848
1328711
−1
−
138
Mobile element protein
-none-
D23_1c1422
Neut_2501

fig|6666666.60966.peg.1418
CDS
1329144
1328821
−3
−
324
Mobile element protein
-none-
D23_1c1423
Neut_1624

fig|6666666.60966.peg.1419
CDS
1329566
1329129
−2
−
438
Mobile element protein
-none-
D23_1c1424
Neut_1888

fig|6666666.60966.peg.1420
CDS
1330200
1329892
−3
−
309
Death on curing
Phd-Doc, YdcE-YdcD
D23_1c1425
NA








protein, Doc toxin
toxin-antitoxin











(programmed cell death)











systems



fig|6666666.60966.peg.1421
CDS
1330677
1330231
−3
−
447
Prevent host death
Phd-Doc, YdcE-YdcD
D23_1c1426
NA








protein, Phd antitoxin
toxin-antitoxin











(programmed cell death)











systems



fig|6666666.60966.peg.1423
CDS
1331253
1331387
3
+
135
Mobile element protein
-none-
D23_1c1427
Neut_2500

fig|6666666.60966.peg.1424
CDS
1331444
1332292
2
+
849
Mobile element protein
-none-
D23_1c1428
Neut_1888

fig|6666666.60966.peg.1425
CDS
1332744
1333214
3
+
471
3-demethylubiquinone-
-none-
D23_1c1429
Neut_1376








9 3-methyltransferase




fig|6666666.60966.peg.1426
CDS
1333410
1335026
3
+
1617
Dihydroxyacetone
Dihydroxyacetone
D23_1c1431
Neut_1377








kinase, ATP-dependent
kinases










(EC 2.7.1.29)




fig|6666666.60966.peg.1427
CDS
1335644
1335210
−2
−
435
hypothetical protein
-none-
D23_1c1432
Neut_1378

fig|6666666.60966.peg.1428
CDS
1339065
1335670
−3
−
3396
PDZ domain
-none-
D23_1c1433
Neut_1379

fig|6666666.60966.peg.1429
CDS
1339241
1340350
2
+
1110
COGs COG0823
-none-
D23_1c1435
Neut_1380

fig|6666666.60966.peg.1430
CDS
1341715
1340438
−1
−
1278
Putative diheme
Soluble cytochromes
D23_1c1436
Neut_1381








cytochrome c-553
and functionally related











electron carriers



fig|6666666.60966.peg.1431
CDS
1342431
1341712
−3
−
720
Probable cytochrome c2
Soluble cytochromes
D23_1c1437
Neut_1382









and functionally related











electron carriers



fig|6666666.60966.peg.1432
CDS
1342445
1342963
2
+
519
FIG00859968:
-none-
D23_1c1438
Neut_1383








hypothetical protein




fig|6666666.60966.peg.1433
CDS
1344805
1342952
−1
−
1854
Cell division protein
Bacterial Cell Division
D23_1c1439
Neut_1384








FtsH (EC 3.4.24.—)




fig|6666666.60966.peg.1434
CDS
1345012
1346118
1
+
1107
S-
Glutathione-dependent
D23_1c1440
Neut_1385








(hydroxymethyl)glutathione
pathway of










dehydrogenase (EC
formaldehyde










1.1.1.284)
detoxification



fig|6666666.60966.peg.1435
CDS
1346131
1347000
1
+
870
S-formylglutathione
Glutathione-dependent
D23_1c1441
Neut_1386








hydrolase (EC 3.1.2.12)
pathway of











formaldehyde











detoxification



fig|6666666.60966.peg.1436
CDS
1348436
1347264
−2
−
1173
Ornithine
Arginine and Ornithine
D23_1c1442
Neut_1387








decarboxylase (EC
Degradation;










4.1.1.17)/Arginine
<br>Arginine and










decarboxylase (EC
Ornithine Degradation;










4.1.1.19)
<br>Polyamine











Metabolism;











<br>Polyamine











Metabolism



fig|6666666.60966.peg.1437
CDS
1348961
1349230
2
+
270
FIG00858492:
-none-
D23_1c1443
Neut_1388








hypothetical protein




fig|6666666.60966.peg.1438
CDS
1349336
1349214
−2
−
123
hypothetical protein
-none-
D23_1c1444
NA

fig|6666666.60966.peg.1439
CDS
1349660
1350622
2
+
963
Mobile element protein
-none-
D23_1c1446
Neut_1862

fig|6666666.60966.peg.1440
CDS
1350742
1352079
1
+
1338
Ribosomal protein S12p
Methylthiotransferases;
D23_1c1447
Neut_1389








Asp88 ( E. coli )
<br>Ribosomal protein










methylthiotransferase
S12p Asp











methylthiotransferase



fig|6666666.60966.peg.1441
CDS
1353046
1352255
−1
−
792
hypothetical protein
-none-
D23_1c1448
Neut_1390

fig|6666666.60966.peg.1442
CDS
1353301
1353618
1
+
318
Cell division protein
Bacterial Cell Division
D23_1c1449
Neut_1391








BolA




fig|6666666.60966.peg.1443
CDS
1353569
1354282
2
+
714
LemA family protein
-none-
D23_1c1450
Neut_1392

fig|6666666.60966.peg.1444
CDS
1354309
1355193
1
+
885
Beta-propeller domains
-none-
D23_1c1451
Neut_1393








of methanol











dehydrogenase type




fig|6666666.60966.peg.1445
CDS
1355207
1355710
2
+
504
FIG004694:
-none-
D23_1c1452
Neut_1394








Hypothetical protein




fig|6666666.60966.peg.1446
CDS
1356010
1356513
1
+
504
DNA-directed RNA
-none-
D23_1c1454
Neut_1395








polymerase specialized











sigma subunit, sigma24-











like




fig|6666666.60966.peg.1447
CDS
1356510
1357232
3
+
723
FIG00859011:
-none-
D23_1c1455
Neut_1396








hypothetical protein




fig|6666666.60966.peg.1448
CDS
1357326
1359644
3
+
2319
ABC transporter,
-none-
D23_1c1456
Neut_1397








transmembrane











region: ABC transporter











related




fig|6666666.60966.peg.1449
CDS
1359641
1360108
2
+
468
DUF1854 domain-
-none-
D23_1c1457
Neut_1398








containing protein




fig|6666666.60966.peg.1451
CDS
1360927
1362021
1
+
1095
hypothetical protein
-none-
D23_1c1458
Neut_1860

fig|6666666.60966.peg.1452
CDS
1362049
1362342
1
+
294
Mobile element protein
-none-
D23_1c1459
Neut_1719

fig|6666666.60966.peg.1453
CDS
1362441
1363319
3
+
879
Mobile element protein
-none-
D23_1c1460
Neut_1720

fig|6666666.60966.peg.1454
CDS
1363397
1365250
2
+
1854
hypothetical protein
-none-
D23_1c1461
NA

fig|6666666.60966.peg.1455
CDS
1365453
1365262
−3
−
192
Mobile element protein
-none-
D23_1c1462
Neut_2502

fig|6666666.60966.peg.1456
CDS
1365648
1367945
3
+
2298
Cyanophycin synthase
Cyanophycin
D23_1c1463
Neut_1401








(EC 6.3.2.29)(EC
Metabolism










6.3.2.30)




fig|6666666.60966.peg.1457
CDS
1367966
1370572
2
+
2607
Cyanophycin synthase
Cyanophycin
D23_1c1464
Neut_1402








(EC 6.3.2.29)(EC
Metabolism










6.3.2.30)




fig|6666666.60966.peg.1458
CDS
1371664
1370720
−1
−
945
Copper-containing
Denitrification;
D23_1c1465
Neut_1403








nitrite reductase (EC
<br>Denitrifying










1.7.2.1)
reductase gene clusters



fig|6666666.60966.peg.1459
CDS
1372091
1371708
−2
−
384
cytochrome c, class IC
-none-
D23_1c1466
Neut_1404

fig|6666666.60966.peg.1460
CDS
1372789
1372091
−1
−
699
Cytochrome c, class I
-none-
D23_1c1467
Neut_1405

fig|6666666.60966.peg.1461
CDS
1373888
1372827
−2
−
1062
Multicopper oxidase
Copper homeostasis
D23_1c1468
Neut_1406

fig|6666666.60966.peg.1462
CDS
1374021
1374137
3
+
117
hypothetical protein
-none-
D23_1c1469
NA

fig|6666666.60966.peg.1463
CDS
1374189
1374653
3
+
465
Nitrite-sensitive
Nitrosative stress;
D23_1c1470
Neut_1407








transcriptional
<br>Oxidative stress;










repressor NsrR
<br>Rrf2 family











transcriptional











regulators



fig|6666666.60966.peg.1464
CDS
1378537
1374641
−1
−
3897
FIG00858660:
-none-
D23_1c1471
Neut_1408








hypothetical protein




fig|6666666.60966.peg.1465
CDS
1380248
1378539
−2
−
1710
Outer membrane
-none-
D23_1c1472
Neut_1409








protein




fig|6666666.60966.peg.1466
CDS
1380471
1380340
−3
−
132
hypothetical protein
-none-
D23_1c1473
NA

fig|6666666.60966.peg.1467
CDS
1380491
1381141
2
+
651
Uracil-DNA glycosylase,
Uracil-DNA glycosylase
D23_1c1474
Neut_1410








family 5




fig|6666666.60966.peg.1468
CDS
1381162
1381350
1
+
189
putative isomerase
-none-
D23_1c1475
Neut_1411

fig|6666666.60966.peg.1469
CDS
1381364
1383178
2
+
1815
Excinuclease ABC
DNA repair, UvrABC
D23_1c1476
Neut_1412








subunit C
system



fig|6666666.60966.peg.1470
CDS
1383321
1384283
3
+
963
Mobile element protein
-none-
D23_1c1477
Neut_1746

fig|6666666.60966.peg.1471
CDS
1384401
1384814
3
+
414
ABC-type multidrug
CBSS-196164.1.peg.1690
D23_1c1478
NA








transport system,











permease component




fig|6666666.60966.peg.1472
CDS
1384811
1385149
2
+
339
ABC-type multidrug
CBSS-196164.1.peg.1690
D23_1c1479
NA








transport system,











permease component




fig|6666666.60966.peg.1474
CDS
1385894
1388275
2
+
2382
Penicillin acylase II
-none-
D23_1c1480
Neut_1415

fig|6666666.60966.peg.1475
CDS
1388559
1388395
−3
−
165
hypothetical protein
-none-
D23_1c1481
NA

fig|6666666.60966.peg.1476
CDS
1388615
1389973
2
+
1359
Response regulatory
-none-
D23_1c1482
Neut_1416








protein




fig|6666666.60966.peg.1477
CDS
1390014
1391603
3
+
1590
Long-chain-fatty-acid--
Biotin biosynthesis;
D23_1c1483
Neut_1417








CoAligase (EC 6.2.1.3)
<br>Biotin synthesis











cluster; <br>Fatty acid











metabolism cluster



fig|6666666.60966.peg.1478
CDS
1391630
1392835
2
+
1206
Diaminopimelate
Lysine Biosynthesis DAP
D23_1c1484
Neut_1418








decarboxylase (EC
Pathway, GJO scratch










4.1.1.20)




fig|6666666.60966.peg.1479
CDS
1392996
1394843
3
+
1848
Asparagine synthetase
Cyanophycin
D23_1c1485
Neut_1419








[glutamine-hydrolyzing]
Metabolism;










(EC 6.3.5.4)
<br>Glutamate and











Aspartate uptake in











Bacteria; <br>Glutamine,











Glutamate, Aspartate











and Asparagine











Biosynthesis



fig|6666666.60966.peg.1480
CDS
1394795
1394911
2
+
117
hypothetical protein
-none-
D23_1c1486
NA

fig|6666666.60966.peg.1482
CDS
1395163
1395975
1
+
813
FIG00858746:
-none-
D23_1c1488
Neut_1420








hypothetical protein




fig|6666666.60966.peg.1483
CDS
1397102
1396140
−2
−
963
Mobile element protein
-none-
D23_1c1490
Neut_1746

fig|6666666.60966.peg.1484
CDS
1397178
1397462
3
+
285
COGs COG0226
-none-
D23_1c1491
Neut_1423

fig|6666666.60966.peg.1485
CDS
1397455
1398681
1
+
1227
FIG00859800:
-none-
D23_1c1492
Neut_1424








hypothetical protein




fig|6666666.60966.peg.1486
CDS
1398693
1401635
3
+
2943
diguanylate
-none-
D23_1c1493
Neut_1425








cyclase/phosphodiesterase











(GGDEF & EAL











domains) with PAS/PAC











sensor(s)




fig|6666666.60966.peg.1488
CDS
1402082
1401924
−2
−
159
hypothetical protein
-none-
D23_1c1494
NA

fig|6666666.60966.peg.1489
CDS
1402531
1402115
−1
−
417
OsmC/Ohr family
-none-
D23_1c1495
Neut_1426








protein




fig|6666666.60966.peg.1490
CDS
1403584
1402532
−1
−
1053
DNA polymerase III
CBSS-208964.1.peg.3988
D23_1c1496
Neut_1427








delta subunit (EC











2.7.7.7)




fig|6666666.60966.peg.1491
CDS
1404106
1403612
−1
−
495
LPS-assembly
CBSS-
D23_1c1497
Neut_1428








lipoprotein RlpB
208964.1.peg.3988;










precursor (Rare
<br>Lipopolysaccharide










lipoprotein B)
assembly



fig|6666666.60966.peg.1492
CDS
1406732
1404126
−2
−
2607
Leucyl-tRNA synthetase
CBSS-
D23_1c1498
Neut_1429








(EC 6.1.1.4)
208964.1.peg.3988;











<br>tRNA











aminoacylation, Leu



fig|6666666.60966.peg.1493
CDS
1406756
1407925
2
+
1170
S-
CBSS-
D23_1c1499
Neut_1430








adenosylmethionine:tRNA
211586.1.peg.2832;










ribosyltransferase-
<br>Queuosine-










isomerase (EC 5.—.—.—)
Archaeosine











Biosynthesis;











<br>Scaffold proteins for











[4Fe—4S] cluster











assembly (MRP family);











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1494
CDS
1407922
1409007
1
+
1086
tRNA-guanine
CBSS-
D23_1c1500
Neut_1431








transglycosylase (EC
211586.1.peg.2832;










2.4.2.29)
<br>Queuosine-











Archaeosine











Biosynthesis;











<br>Scaffold proteins for











[4Fe—4S] cluster











assembly (MRP family);











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1495
CDS
1409072
1409536
2
+
465
Preprotein translocase
CBSS-211586.1.peg.2832
D23_1c1501
Neut_1432








subunit YajC (TC











3.A.5.1.1)




fig|6666666.60966.peg.1496
CDS
1409575
1411470
1
+
1896
Protein-export
CBSS-211586.1.peg.2832
D23_1c1502
Neut_1433








membrane protein











SecD (TC 3.A.5.1.1)




fig|6666666.60966.peg.1497
CDS
1411495
1412427
1
+
933
Protein-export
CBSS-211586.1.peg.2832
D23_1c1503
Neut_1434








membrane protein SecF











(TC 3.A.5.1.1)




fig|6666666.60966.peg.1498
CDS
1412467
1412844
1
+
378
FIG028220:
-none-
D23_1c1504
Neut_1435








hypothetical protein co-











occurring with HEAT











repeat protein




fig|6666666.60966.peg.1499
CDS
1412897
1413628
2
+
732
Ubiquinone/menaquinone
Menaquinone and
D23_1c1505
Neut_1436








biosynthesis
Phylloquinone










methyltransferase UbiE
Biosynthesis;










(EC 2.1.1.—)
<br>Ubiquinone











Biosynthesis;











<br>Ubiquinone











Biosynthesis-gjo



fig|6666666.60966.peg.1500
CDS
1413802
1413680
−1
−
123
Agmatinase (EC
Arginine and Ornithine
D23_1c1506
Neut_1437








3.5.3.11)
Degradation;











<br>Polyamine











Metabolism



fig|6666666.60966.peg.1501
CDS
1414650
1413808
−3
−
843
Agmatinase (EC
Arginine and Ornithine
D23_1c1507
Neut_1437








3.5.3.11)
Degradation;











<br>Polyamine











Metabolism



fig|6666666.60966.peg.1502
CDS
1415255
1414815
−2
−
441
Lipoprotein signal
Lipoprotein Biosynthesis;
D23_1c1509
Neut_1438








peptidase (EC 3.4.23.36)
<br>Signal peptidase



fig|6666666.60966.peg.1503
CDS
1415346
1415224
−3
−
123
hypothetical protein
-none-
D23_1c1510
NA

fig|6666666.60966.peg.1504
CDS
1418173
1415339
−1
−
2835
Isoleucyl-tRNA
tRNA aminoacylation, Ile
D23_1c1511
Neut_1439








synthetase (EC 6.1.1.5)




fig|6666666.60966.peg.1505
CDS
1418945
1418148
−2
−
798
Riboflavin kinase (EC
Riboflavin, FMN and FAD
D23_1c1512
Neut_1440








2.7.1.26)/FMN
metabolism;










adenylyltransferase (EC
<br>Riboflavin, FMN and










2.7.7.2)
FAD metabolism;











<br>Riboflavin, FMN and











FAD metabolism in











plants; <br>Riboflavin,











FMN and FAD











metabolism in plants;











<br>riboflavin to FAD;











<br>riboflavin to FAD



fig|6666666.60966.peg.1506
CDS
1419539
1419237
−2
−
303
possible sec-
-none-
D23_1c1513
Neut_1441








independent protein











translocase protein











TatC




fig|6666666.60966.peg.1507
CDS
1420011
1419886
−3
−
126
hypothetical protein
-none-
D23_1c1514
Neut_1442

fig|6666666.60966.peg.1508
CDS
1420112
1422079
2
+
1968
Dipeptide-binding ABC
ABC transporter
D23_1c1514
Neut_1442








transporter, periplasmic
dipeptide (TC 3.A.1.5.2)










substrate-binding











component (TC











3.A.1.5.2)




fig|6666666.60966.peg.1509
CDS
1422089
1423066
2
+
978
Oligopeptide transport
ABC transporter
D23_1c1515
Neut_1443








system permease
oligopeptide (TC










protein OppB (TC
3.A.1.5.1)










3.A.1.5.1)




fig|6666666.60966.peg.1511
CDS
1423196
1424851
2
+
1656
DnaJ-class molecular
Protein chaperones
D23_1c1516
Neut_1444








chaperone CbpA




fig|6666666.60966.peg.1512
CDS
1424900
1425844
2
+
945
DnaJ-class molecular
Protein chaperones
D23_1c1517
Neut_1445








chaperone CbpA




fig|6666666.60966.peg.1513
CDS
1425856
1426152
1
+
297
InterPro IPR000551
-none-
D23_1c1518
Neut_1446

fig|6666666.60966.peg.1514
CDS
1426240
1427103
1
+
864
FIG00858431:
-none-
D23_1c1519
Neut_1447








hypothetical protein




fig|6666666.60966.peg.1515
CDS
1427120
1427659
2
+
540
FAD pyrophosphatase
-none-
D23_1c1520
Neut_1448








(EC 3.6.1.18), projected











from PMID:18815383




fig|6666666.60966.peg.1516
CDS
1428946
1428491
−1
−
456
Mobile element protein
-none-
D23_1c1522
Neut_2502

fig|6666666.60966.peg.1517
CDS
1429295
1428909
−2
−
387
Mobile element protein
-none-
D23_1c1523
Neut_0884

fig|6666666.60966.peg.1518
CDS
1430487
1429300
−3
−
1188
Mobile element protein
-none-
D23_1c1524
Neut_2405

fig|6666666.60966.peg.1519
CDS
1430505
1430621
3
+
117
patatin family protein
-none-
D23_1c1525
Neut_1317

fig|6666666.60966.peg.1520
CDS
1430834
1430670
−2
−
165
hypothetical protein
-none-
D23_1c1526
NA

fig|6666666.60966.peg.1521
CDS
1431909
1431424
−3
−
486
hypothetical protein
-none-
D23_1c1527
Neut_1449

fig|6666666.60966.peg.1522
CDS
1432156
1431899
−1
−
258
hypothetical protein
-none-
D23_1c1528
Neut_1450

fig|6666666.60966.peg.1523
CDS
1432650
1432159
−3
−
492
phage-related
-none-
D23_1c1529
Neut_1451








hypothetical protein




fig|6666666.60966.peg.1524
CDS
1432970
1432650
−2
−
321
hypothetical protein
-none-
D23_1c1530
Neut_1452

fig|6666666.60966.peg.1525
CDS
1433143
1432967
−1
−
177
hypothetical protein
-none-
D23_1c1531
Neut_1453

fig|6666666.60966.peg.1526
CDS
1434487
1433552
−1
−
936
hypothetical protein
-none-
D23_1c1533
Neut_1454

fig|6666666.60966.peg.1527
CDS
1437226
1434497
−1
−
2730
hypothetical protein
-none-
D23_1c1534
Neut_1455

fig|6666666.60966.peg.1528
CDS
1437449
1437267
−2
−
183
Phage protein
-none-
D23_1c1535
Neut_1456

fig|6666666.60966.peg.1529
CDS
1437694
1437467
−1
−
228
hypothetical protein
-none-
D23_1c1536
Neut_1457

fig|6666666.60966.peg.1530
CDS
1438472
1437702
−2
−
771
hypothetical protein
-none-
D23_1c1537
Neut_1458

fig|6666666.60966.peg.1531
CDS
1439638
1438469
−1
−
1170
hypothetical protein
-none-
D23_1c1538
Neut_1459

fig|6666666.60966.peg.1532
CDS
1441511
1439631
−2
−
1881
Phage tail length tape-
Phage tail proteins;
D23_1c1539
Neut_1460








measure protein
<br>Phage tail proteins 2



fig|6666666.60966.peg.1533
CDS
1442755
1441508
−1
−
1248
Mobile element protein
-none-
D23_1c1540
Neut_0357

fig|6666666.60966.peg.1534
CDS
1443390
1442854
−3
−
537
Phage protein
-none-
D23_1c1541
Neut_1460

fig|6666666.60966.peg.1535
CDS
1443638
1443390
−2
−
249
hypothetical protein
-none-
D23_1c1542
Neut_1461

fig|6666666.60966.peg.1536
CDS
1444027
1443677
−1
−
351
Phage protein
-none-
D23_1c1543
Neut_1462

fig|6666666.60966.peg.1537
CDS
1444752
1444036
−3
−
717
major tail protein,
-none-
D23_1c1544
Neut_1463








putative




fig|6666666.60966.peg.1538
CDS
1445120
1444758
−2
−
363
hypothetical protein
-none-
D23_1c1545
Neut_1464

fig|6666666.60966.peg.1539
CDS
1445638
1445117
−1
−
522
FIG00959132:
-none-
D23_1c1546
Neut_1465








hypothetical protein




fig|6666666.60966.peg.1540
CDS
1445985
1445650
−3
−
336
Phage protein
-none-
D23_1c1547
Neut_1466

fig|6666666.60966.peg.1541
CDS
1446544
1445987
−1
−
558
Similar to Gene Transfer
-none-
D23_1c1548
Neut_1467








Agent (GTA) ORFG06




fig|6666666.60966.peg.1542
CDS
1446900
1446601
−3
−
300
hypothetical protein
-none-
D23_1c1549
Neut_1468

fig|6666666.60966.peg.1543
CDS
1448136
1446910
−3
−
1227
Phage major capsid
Phage capsid proteins
D23_1c1550
Neut_1469








protein




fig|6666666.60966.peg.1544
CDS
1448949
1448218
−3
−
732
Prophage Clp protease-
cAMP signaling in
D23_1c1551
Neut_1470








like protein
bacteria



fig|6666666.60966.peg.1545
CDS
1450207
1448915
−1
−
1293
Phage portal protein
Phage packaging
D23_1c1552
Neut_1471









machinery



fig|6666666.60966.peg.1546
CDS
1451877
1450204
−3
−
1674
Phage terminase large
Phage packaging
D23_1c1553
Neut_1472








subunit
machinery



fig|6666666.60966.peg.1547
CDS
1452346
1451882
−1
−
465
Phage terminase, small
Phage packaging
D23_1c1554
Neut_1473








subunit
machinery



fig|6666666.60966.peg.1548
CDS
1452801
1452478
−3
−
324
Phage holin
-none-
D23_1c1555
Neut_1474

fig|6666666.60966.peg.1549
CDS
1453267
1452887
−1
−
381
hypothetical protein
-none-
D23_1c1556
Neut_1475

fig|6666666.60966.peg.1550
CDS
1453430
1453269
−2
−
162
hypothetical protein
-none-
D23_1c1557
NA

fig|6666666.60966.peg.1551
CDS
1453630
1453451
−1
−
180
hypothetical protein
-none-
D23_1c1558
NA

fig|6666666.60966.peg.1552
CDS
1453862
1453623
−2
−
240
hypothetical protein
-none-
D23_1c1559
Neut_1477

fig|6666666.60966.peg.1553
CDS
1456504
1454171
−1
−
2334
DNA primase, phage
-none-
D23_1c1560
Neut_1478








associated # P4-type




fig|6666666.60966.peg.1554
CDS
1456740
1456501
−3
−
240
hypothetical protein
-none-
D23_1c1561
NA

fig|6666666.60966.peg.1555
CDS
1456744
1456887
1
+
144
Phage-related protein
-none-
D23_1c1562
Neut_1480

fig|6666666.60966.peg.1556
CDS
1456894
1457172
1
+
279
Helix-turn-helix motif
-none-
D23_1c1563
Neut_1481

fig|6666666.60966.peg.1557
CDS
1457678
1457277
−2
−
402
hypothetical protein
-none-
D23_1c1564
NA

fig|6666666.60966.peg.1558
CDS
1458137
1458478
2
+
342
hypothetical protein
-none-
D23_1c1565
NA

fig|6666666.60966.peg.1559
CDS
1458868
1459158
1
+
291
hypothetical protein
-none-
D23_1c1566
NA

fig|6666666.60966.peg.1561
CDS
1459812
1459672
−3
−
141
hypothetical protein
-none-
D23_1c1567
NA

fig|6666666.60966.peg.1563
CDS
1460270
1460563
2
+
294
Mobile element protein
-none-
D23_1c1568
Neut_1719

fig|6666666.60966.peg.1564
CDS
1460662
1461540
1
+
879
Mobile element protein
-none-
D23_1c1569
Neut_1720

fig|6666666.60966.peg.1565
CDS
1462142
1461954
−2
−
189
hypothetical protein
-none-
D23_1c1570
Neut_1489

fig|6666666.60966.peg.1567
CDS
1462722
1462844
3
+
123
hypothetical protein
-none-
D23_1c1571
NA

fig|6666666.60966.peg.1568
CDS
1463137
1463829
1
+
693
putative nuclease
-none-
D23_1c1572
Neut_1491

fig|6666666.60966.peg.1569
CDS
1464806
1463826
−2
−
981
Abortive infection
-none-
D23_1c1573
NA








bacteriophage











resistance protein




fig|6666666.60966.peg.1570
CDS
1466353
1465106
−1
−
1248
Mobile element protein
-none-
D23_1c1574
Neut_0357

fig|6666666.60966.peg.1573
CDS
1466953
1467108
1
+
156
hypothetical protein
-none-
D23_1c1575
NA

fig|6666666.60966.peg.1574
CDS
1467105
1467389
3
+
285
hypothetical protein
-none-
D23_1c1576
Neut_1493

fig|6666666.60966.peg.1575
CDS
1467386
1467868
2
+
483
hypothetical protein
-none-
D23_1c1577
Neut_1494

fig|6666666.60966.peg.1576
CDS
1467883
1468245
1
+
363
hypothetical protein
-none-
D23_1c1578
Neut_1495

fig|6666666.60966.peg.1577
CDS
1468255
1468638
1
+
384
hypothetical protein
-none-
D23_1c1579
Neut_1496

fig|6666666.60966.peg.1580
CDS
1469337
1470362
3
+
1026
Integrase
-none-
D23_1c1580
Neut_1498

fig|6666666.60966.peg.1581
CDS
1470687
1470989
3
+
303
Exodeoxyribonuclease
DNA repair, bacterial;
D23_1c1582
Neut_1499








VII small subunit (EC
<br>Purine salvage










3.1.11.6)
cluster



fig|6666666.60966.peg.1582
CDS
1470979
1471872
1
+
894
Octaprenyl diphosphate
Isoprenoid Biosynthesis;
D23_1c1583
Neut_1500








synthase (EC 2.5.1.90)/
<br>Isoprenoid










Dimethylallyltransferase
Biosynthesis;










(EC 2.5.1.1)/(2E,6E)-
<br>Isoprenoid










farnesyl diphosphate
Biosynthesis:










synthase (EC 2.5.1.10)/
Interconversions;










Geranylgeranyl
<br>Isoprenoinds for










diphosphate synthase
Quinones;










(EC 2.5.1.29)
<br>Isoprenoinds for











Quinones;











<br>Isoprenoinds for











Quinones;











<br>Isoprenoinds for











Quinones;











<br>Polyprenyl











Diphosphate











Biosynthesis;











<br>Polyprenyl











Diphosphate











Biosynthesis;











<br>Polyprenyl











Diphosphate











Biosynthesis



fig|6666666.60966.peg.1583
CDS
1471935
1473779
3
+
1845
1-deoxy-D-xylulose 5-
Isoprenoid Biosynthesis;
D23_1c1584
Neut_1501








phosphate synthase (EC
<br>Nonmevalonate










2.2.1.7)
Branch of Isoprenoid











Biosynthesis;











<br>Pyridoxin (Vitamin











B6) Biosynthesis;











<br>Thiamin











biosynthesis



fig|6666666.60966.peg.1584
CDS
1473895
1474698
1
+
804
GTP cyclohydrolase I
Folate Biosynthesis;
D23_1c1585
Neut_1502








(EC 3.5.4.16) type 2
<br>Queuosine-











Archaeosine











Biosynthesis; <br>Zinc











regulated enzymes



fig|6666666.60966.peg.1585
CDS
1474865
1475485
2
+
621
InterPro IPR005134
-none-
D23_1c1586
Neut_1503








COGs COG2862




fig|6666666.60966.peg.1586
CDS
1476254
1475514
−2
−
741
FolM Alternative
Folate Biosynthesis
D23_1c1587
Neut_1504








dihydrofolate reductase 1




fig|6666666.60966.peg.1587
CDS
1476327
1477502
3
+
1176
COG1565:
-none-
D23_1c1588
Neut_1505








Uncharacterized











conserved protein




fig|6666666.60966.peg.1588
CDS
1478242
1477499
−1
−
744
5&#39;-
Adenosyl nucleosidases;
D23_1c1589
Neut_1506








methylthioadenosine
<br>Adenosyl










nucleosidase (EC
nucleosidases;










3.2.2.16)/S-
<br>CBSS-










adenosylhomocysteine
320388.3.peg.3759;










nucleosidase (EC
<br>CBSS-










3.2.2.9)
320388.3.peg.3759;











<br>Methionine











Biosynthesis;











<br>Methionine











Degradation;











<br>Polyamine











Metabolism



fig|6666666.60966.peg.1589
CDS
1480269
1478239
−3
−
2031
Squalene--hopene
CBSS-
D23_1c1590
Neut_1507








cyclase (EC 5.4.99.17)
320388.3.peg.3759;











<br>Hopanes



fig|6666666.60966.peg.1590
CDS
1481103
1480384
−3
−
720
Surface lipoprotein
-none-
D23_1c1591
Neut_1508

fig|6666666.60966.peg.1591
CDS
1481997
1481389
−3
−
609
Ferric siderophore
Ton and Tol transport
D23_1c1592
Neut_1509








transport system,
systems










biopolymer transport











protein ExbB




fig|6666666.60966.peg.1592
CDS
1482298
1483644
1
+
1347
Exodeoxyribonuclease
DNA repair, bacterial;
D23_1c1594
Neut_1510








VII large subunit (EC
<br>Purine salvage










3.1.11.6)
cluster



fig|6666666.60966.peg.1593
CDS
1483709
1484089
2
+
381
COG2363
-none-
D23_1c1595
Neut_1511

fig|6666666.60966.peg.1594
CDS
1484150
1485328
2
+
1179
23S rRNA (guanine-N-2-)-
RNA methylation
D23_1c1596
Neut_1512








methyltransferase











rlmL EC 2.1.1.—)




fig|6666666.60966.peg.1595
CDS
1485345
1485833
3
+
489
Periplasmic
Biogenesis of c-type
D23_1c1597
Neut_1513








thiol:disulfide
cytochromes;










oxidoreductase DsbB,
<br>Periplasmic disulfide










required for DsbA
interchange










reoxidation




fig|6666666.60966.peg.1596
CDS
1486114
1486503
1
+
390
Endoribonuclease L-PSP
CBSS-
D23_1c1598
Neut_1514









176299.4.peg.1996A



fig|6666666.60966.peg.1598
CDS
1486998
1486651
−3
−
348
FIG016027: protein of
-none-
D23_1c1599
Neut_1515








unknown function YeaO




fig|6666666.60966.peg.1599
CDS
1487053
1487727
1
+
675
AttE component of
AttEFGH ABC Transport
D23_1c1600
Neut_1516








AttEFGH ABC transport
System










system




fig|6666666.60966.peg.1600
CDS
1487724
1490273
3
+
2550
AttF component of
AttEFGH ABC Transport
D23_1c1601
Neut_1517








AttEFGH ABC transport
System; <br>AttEFGH










system/AttG
ABC Transport System










component of AttEFGH











ABC transport system




fig|6666666.60966.peg.1601
CDS
1490273
1491343
2
+
1071
AttH component of
AttEFGH ABC Transport
D23_1c1602
Neut_1518








AttEFGH ABC transport
System










system




fig|6666666.60966.peg.1602
CDS
1491424
1491666
1
+
243
Molybdopterin
-none-
D23_1c1603
Neut_1519








biosynthesis protein B




fig|6666666.60966.peg.1603
CDS
1491738
1491619
−3
−
120
hypothetical protein
-none-
D23_1c1604
NA

fig|6666666.60966.peg.1605
CDS
1492158
1492982
3
+
825
Particulate methane
Particulate methane
D23_1c1605
Neut_1520








monooxygenase C-
monooxygenase










subunit (EC 1.14.13.25)
(pMMO)



fig|6666666.60966.peg.1607
CDS
1494238
1493309
−1
−
930
Cytochrome c551
Protection from Reactive
D23_1c1607
Neut_1521








peroxidase (EC 1.11.1.5)
Oxygen Species



fig|6666666.60966.peg.1609
CDS
1494804
1495091
3
+
288
Mobile element protein
-none-
D23_1c1608
Neut_2502

fig|6666666.60966.peg.1611
CDS
1495989
1495288
−3
−
702
2-C-methyl-D-erythritol
Isoprenoid Biosynthesis;
D23_1c1609
Neut_1525








4-phosphate
<br>Nonmevalonate










cytidylyltransferase (EC
Branch of Isoprenoid










2.7.7.60)
Biosynthesis;











<br>Possible RNA











degradation cluster;











<br>Stationary phase











repair cluster



fig|6666666.60966.peg.1612
CDS
1496057
1496497
2
+
441
Inosine-5&#39;-
Purine conversions;
D23_1c1610
Neut_1526








monophosphate
<br>Purine salvage










dehydrogenase (EC
cluster










1.1.1.205)




fig|6666666.60966.peg.1613
CDS
1497472
1496552
−1
−
921
Cell division protein
Bacterial Cell Division;
D23_1c1611
Neut_1527








FtsX
<br>Heat shock Cell











division Proteases and a











Methyltransferase



fig|6666666.60966.peg.1614
CDS
1498131
1497469
−3
−
663
Cell division
Bacterial Cell Division;
D23_1c1612
Neut_1528








transporter, ATP-
<br>Heat shock Cell










binding protein FtsE (TC
division Proteases and a










3.A.5.1.1)
Methyltransferase



fig|6666666.60966.peg.1615
CDS
1499195
1498158
−2
−
1038
Signal recognition
Bacterial Cell Division;
D23_1c1613
Neut_1529








particle receptor
<br>Bacterial signal










protein FtsY (=alpha
recognition particle










subunit) (TC 3.A.5.1.1)
(SRP); <br>Heat shock











Cell division Proteases











and a Methyltransferase;











<br>Universal GTPases



fig|6666666.60966.peg.1616
CDS
1499262
1500653
3
+
1392
FIG015547: peptidase,
-none-
D23_1c1614
Neut_1530








M16 family




fig|6666666.60966.peg.1617
CDS
1500780
1501865
3
+
1086
Alanine racemase (EC
Alanine biosynthesis;
D23_1c1615
Neut_1531








5.1.1.1)
<br>Pyruvate Alanine











Serine Interconversions



fig|6666666.60966.peg.1618
CDS
1502688
1501894
−3
−
795
Peptidyl-prolyl cis-trans
Queuosine-Archaeosine
D23_1c1616
Neut_1532








isomerase (EC 5.2.1.8)
Biosynthesis



fig|6666666.60966.peg.1619
CDS
1502854
1502738
−1
−
117
hypothetical protein
-none-
D23_1c1617
NA

fig|6666666.60966.peg.1620
CDS
1503164
1502862
−2
−
303
YciL protein
Broadly distributed
D23_1c1618
Neut_1533









proteins not in











subsystems; <br>CBSS-











211586.9.peg.2729



fig|6666666.60966.peg.1621
CDS
1504431
1503277
−3
−
1155
Rubredoxin-NAD(+)
Rubrerythrin
D23_1c1619
Neut_1534








reductase (EC 1.18.1.1)




fig|6666666.60966.peg.1622
CDS
1504748
1505626
2
+
879
Probable protease htpX
-none-
D23_1c1620
Neut_1535








homolog (EC 3.4.24.—)




fig|6666666.60966.peg.1623
CDS
1505626
1505739
1
+
114
hypothetical protein
-none-
D23_1c1621
NA

fig|6666666.60966.peg.1624
CDS
1506477
1505698
−3
−
780
Surface lipoprotein
-none-
D23_1c1622
Neut_1536

fig|6666666.60966.peg.1625
CDS
1507909
1506626
−1
−
1284
Glutamate-1-
CBSS-196164.1.peg.461;
D23_1c1623
Neut_1537








semialdehyde
<br>Heme and Siroheme










aminotransferase (EC
Biosynthesis










5.4.3.8)




fig|6666666.60966.peg.1626
CDS
1508584
1507946
−1
−
639
Thiamin-phosphate
5-FCL-like protein;
D23_1c1624
Neut_1538








pyrophosphorylase (EC
<br>Thiamin










2.5.1.3)
biosynthesis



fig|6666666.60966.peg.1627
CDS
1509419
1508577
−2
−
843
Phosphomethylpyrimidine
5-FCL-like protein;
D23_1c1625
Neut_1539








kinase (EC 2.7.4.7)
<br>Thiamin











biosynthesis



fig|6666666.60966.peg.1628
CDS
1509508
1509660
1
+
153
Rubredoxin
Rubrerythrin
D23_1c1626
Neut_1540

fig|6666666.60966.peg.1629
CDS
1509660
1510049
3
+
390
Lactoylglutathione lyase
Glutathione: Non-redox
D23_1c1627
Neut_1541








(EC 4.4.1.5)
reactions;











<br>Methylglyoxal











Metabolism



fig|6666666.60966.peg.1630
CDS
1510238
1510603
2
+
366
probable iron binding
-none-
D23_1c1628
Neut_1542








protein from the











HesB_IscA_SufA family




fig|6666666.60966.peg.1631
CDS
1511703
1510612
−3
−
1092
Anhydro-N-
Recycling of
D23_1c1629
Neut_1543








acetylmuramic acid
Peptidoglycan Amino










kinase (EC 2.7.1.—)
Sugars



fig|6666666.60966.peg.1632
CDS
1513070
1511739
−2
−
1332
Peptidase, M23/M37
-none-
D23_1c1630
Neut_1544








family




fig|6666666.60966.peg.1633
CDS
1513163
1514383
2
+
1221
Tyrosyl-tRNA
tRNA aminoacylation,
D23_1c1631
Neut_1545








synthetase (EC 6.1.1.1)
Tyr



fig|6666666.60966.peg.1634
CDS
1514577
1515674
3
+
1098
Myo-inositol 2-
-none-
D23_1c1632
Neut_1547








dehydrogenase (EC











1.1.1.18)




fig|6666666.60966.peg.1635
CDS
1515687
1516748
3
+
1062
N-Acetylneuraminate
CMP-N-
D23_1c1633
Neut_1548








cytidylyltransferase (EC
acetylneuraminate










2.7.7.43)
Biosynthesis; <br>Sialic











Acid Metabolism



fig|6666666.60966.peg.1636
CDS
1516926
1518425
3
+
1500
N-acetylneuraminate
CMP-N-
D23_1c1634
Neut_1549








synthase (EC 2.5.1.56)
acetylneuraminate











Biosynthesis; <br>Sialic











Acid Metabolism



fig|6666666.60966.peg.1637
CDS
1518919
1518437
−1
−
483
Ribonucleotide
Ribonucleotide
D23_1c1635
Neut_1551








reductase
redcution










transcriptional











regulator NrdR




fig|6666666.60966.peg.1638
CDS
1520246
1518996
−2
−
1251
Serine
5-FCL-like protein;
D23_1c1636
Neut_1552








hydroxymethyltransferase
<br>Glycine










(EC 2.1.2.1)
Biosynthesis;











<br>Glycine and Serine











Utilization;











<br>Photorespiration











(oxidative C2 cycle);











<br>Serine Biosynthesis



fig|6666666.60966.peg.1639
CDS
1520440
1521180
1
+
741
PqqC-like protein
Folate Biosynthesis
D23_1c1638
Neut_1553

fig|6666666.60966.peg.1640
CDS
1522218
1521283
−3
−
936
Transcriptional
LysR-family proteins in
D23_1c1639
Neut_1554








activator MetR
Escherichia coli ;











<br>LysR-family proteins











in Salmonella enterica











Typhimurium ;











<br>Methionine











Biosynthesis



fig|6666666.60966.peg.1641
CDS
1522318
1524594
1
+
2277
5-
Methionine Biosynthesis
D23_1c1640
Neut_1555








methyltetrahydropteroyltriglutamate--











homocysteine











methyltransferase (EC











2.1.1.14)




fig|6666666.60966.peg.1643
CDS
1526020
1524767
−1
−
1254
UDP-N-
Peptidoglycan
D23_1c1641
Neut_1556








acetylglucosamine 1-
Biosynthesis; <br>UDP-










carboxyvinyltransferase
N-acetylmuramate from










(EC 2.5.1.7)
Fructose-6-phosphate











Biosynthesis



fig|6666666.60966.peg.1644
CDS
1526108
1526497
2
+
390
Putative translation
-none-
D23_1c1642
Neut_1557








initiation inhibitor, yjgF











family




fig|6666666.60966.peg.1645
CDS
1526528
1528585
2
+
2058
ATP-dependent DNA
-none-
D23_1c1643
Neut_1558








helicase RecG (EC











3.6.1.—)




fig|6666666.60966.peg.1646
CDS
1529436
1528588
−3
−
849
Hypothetical ATP-
-none-
D23_1c1644
Neut_1559








binding protein











UPF0042, contains P-











loop




fig|6666666.60966.peg.1647
CDS
1529521
1530072
1
+
552
Transcription
CBSS-243265.1.peg.198;
D23_1c1645
Neut_1560








elongation factor GreB
<br>Transcription











factors bacterial



fig|6666666.60966.peg.1648
CDS
1532787
1530136
−3
−
2652
Malto-oligosyltrehalose
-none-
D23_1c1646
NA








synthase (EC 5.4.99.15)




fig|6666666.60966.peg.1649
CDS
1533038
1532850
−2
−
189
hypothetical protein
-none-
D23_1c1647
NA

fig|6666666.60966.peg.1650
CDS
1534716
1533031
−3
−
1686
Malto-oligosyltrehalose
-none-
D23_1c1648
Neut_1291








trehalohydrolase (EC











3.2.1.141)




fig|6666666.60966.peg.1651
CDS
1535327
1534896
−2
−
432
Trehalose synthase,
-none-
D23_1c1649
NA








nucleoside diphosphate











glucose dependent




fig|6666666.60966.peg.1652
CDS
1535502
1535386
−3
−
117
hypothetical protein
-none-
D23_1c1650
NA

fig|6666666.60966.peg.1653
CDS
1535501
1536028
2
+
528
Sensory histidine kinase
-none-
D23_1c1651
Neut_1565








QseC




fig|6666666.60966.peg.1654
CDS
1535992
1536651
1
+
660
Sensory histidine kinase
-none-
D23_1c1652
Neut_1565








QseC




fig|6666666.60966.peg.1655
CDS
1537148
1537849
2
+
702
Protein of unknown
-none-
D23_1c1653
Neut_1566








function DUF484




fig|6666666.60966.peg.1656
CDS
1537833
1538798
3
+
966
Tyrosine recombinase
-none-
D23_1c1654
Neut_1567








XerC




fig|6666666.60966.peg.1657
CDS
1539747
1538845
−3
−
903
Arogenate
Chorismate Synthesis;
D23_1c1655
Neut_1568








dehydrogenase (EC
<br>Phenylalanine and










1.3.1.43)
Tyrosine Branches from











Chorismate



fig|6666666.60966.peg.1658
CDS
1540893
1539775
−3
−
1119
Biosynthetic Aromatic
Phenylalanine and
D23_1c1656
Neut_1569








amino acid
Tyrosine Branches from










aminotransferase beta
Chorismate










(EC 2.6.1.57)




fig|6666666.60966.peg.1659
CDS
1541973
1540915
−3
−
1059
Chorismate mutase I
Chorismate Synthesis;
D23_1c1657
Neut_1570








(EC 5.4.99.5)/
<br>Chorismate










Prephenate
Synthesis;










dehydratase (EC
<br>Phenylalanine and










4.2.1.51)
Tyrosine Branches from











Chorismate;











<br>Phenylalanine and











Tyrosine Branches from











Chorismate



fig|6666666.60966.peg.1660
CDS
1543230
1542013
−3
−
1218
D-3-phosphoglycerate
Glycine and Serine
D23_1c1658
Neut_1571








dehydrogenase (EC
Utilization;










1.1.1.95)
<br>Pyridoxin (Vitamin











B6) Biosynthesis;











<br>Serine Biosynthesis



fig|6666666.60966.peg.1661
CDS
1544329
1543223
−1
−
1107
Phosphoserine
Glycine and Serine
D23_1c1659
Neut_1572








aminotransferase (EC
Utilization;










2.6.1.52)
<br>Pyridoxin (Vitamin











B6) Biosynthesis;











<br>Serine Biosynthesis



fig|6666666.60966.peg.1662
CDS
1546893
1544347
−3
−
2547
DNA gyrase subunit A
Cell Division Subsystem
D23_1c1660
Neut_1573








(EC 5.99.1.3)
including YidCD;











<br>DNA gyrase











subunits; <br>DNA











replication cluster 1;











<br>DNA











topoisomerases, Type II,











ATP-dependent;











<br>Resistance to











fluoroquinolones



fig|6666666.60966.peg.1663
CDS
1547556
1546963
−3
−
594
COGs COG2854
-none-
D23_1c1661
Neut_1574

fig|6666666.60966.peg.1664
CDS
1548691
1547573
−1
−
1119
Glycosyl transferase,
-none-
D23_1c1662
Neut_1575








family 2




fig|6666666.60966.peg.1665
CDS
1549918
1548755
−1
−
1164
Possible Fe—S
-none-
D23_1c1663
Neut_1576








oxidoreductase




fig|6666666.60966.peg.1666
CDS
1550134
1550247
1
+
114
hypothetical protein
-none-
D23_1c1664
NA

fig|6666666.60966.peg.1668
CDS
1550439
1552481
3
+
2043
Transketolase (EC
Calvin-Benson cycle;
D23_1c1666
Neut_1577








2.2.1.1)
<br>Pentose phosphate











pathway



fig|6666666.60966.peg.1669
CDS
1552544
1553551
2
+
1008
NADPH-dependent
Calvin-Benson cycle;
D23_1c1667
Neut_1578








glyceraldehyde-3-
<br>Calvin-Benson cycle;










phosphate
<br>Glycolysis and










dehydrogenase (EC
Gluconeogenesis;










1.2.1.13)/NAD-
<br>Glycolysis and










dependent
Gluconeogenesis;










glyceraldehyde-3-
<br>Pyridoxin (Vitamin










phosphate
B6) Biosynthesis










dehydrogenase (EC











1.2.1.12)




fig|6666666.60966.peg.1670
CDS
1553775
1553659
−3
−
117
hypothetical protein
-none-
D23_1c1668
NA

fig|6666666.60966.peg.1671
CDS
1553870
1555048
2
+
1179
Phosphoglycerate
Calvin-Benson cycle;
D23_1c1669
Neut_1579








kinase (EC 2.7.2.3)
<br>Glycolysis and











Gluconeogenesis



fig|6666666.60966.peg.1672
CDS
1555083
1556573
3
+
1491
Pyruvate kinase (EC
Glycerate metabolism;
D23_1c1670
Neut_1580








2.7.1.40)
<br>Glycolysis and











Gluconeogenesis;











<br>Pyruvate











metabolism I:











anaplerotic reactions,











PEP



fig|6666666.60966.peg.1673
CDS
1556682
1557746
3
+
1065
Fructose-bisphosphate
Calvin-Benson cycle;
D23_1c1671
Neut_1581








aldolase class II (EC
<br>Glycolysis and










4.1.2.13)
Gluconeogenesis



fig|6666666.60966.peg.1674
CDS
1558432
1560090
1
+
1659
Cytochrome c oxidases
Terminal cytochrome C
D23_1c1672
Neut_1582








subunit CcoN (EC
oxidases










1.9.3.1)




fig|6666666.60966.peg.1675
CDS
1560080
1560688
2
+
609
Cytochrome c oxidase
Terminal cytochrome C
D23_1c1673
Neut_1583








subunit CcoO (EC
oxidases










1.9.3.1)




fig|6666666.60966.peg.1676
CDS
1560753
1561364
3
+
612
Copper-containing
Denitrification;
D23_1c1674
Neut_1584








nitrite reductase (EC
<br>Denitrifying










1.7.2.1)
reductase gene clusters



fig|6666666.60966.peg.1677
CDS
1561404
1562054
3
+
651
Cytochrome oxidase
Biogenesis of
D23_1c1675
Neut_1585








biogenesis protein
cytochrome c oxidases










Sco1/SenC/PrrC,











putative copper











metallochaperone




fig|6666666.60966.peg.1678
CDS
1562150
1562635
2
+
486
hypothetical
-none-
D23_1c1676
Neut_1586








cytochrome oxidase











associated membrane











protein




fig|6666666.60966.peg.1679
CDS
1563699
1562746
−3
−
954
Rare lipoprotein A
Peptidoglycan
D23_1c1677
Neut_1587








precursor
Biosynthesis



fig|6666666.60966.peg.1680
CDS
1564813
1563704
−1
−
1110
Rod shape-determining
Bacterial Cytoskeleton;
D23_1c1678
Neut_1588








protein RodA
<br>Bacterial cell











division cluster;











<br>Peptidoglycan











Biosynthesis



fig|6666666.60966.peg.1681
CDS
1566713
1564836
−2
−
1878
Penicillin-binding
16S rRNA modification
D23_1c1679
Neut_1589








protein 2 (PBP-2)
within P site of











ribosome; <br>Bacterial











cell division cluster;











<br>CBSS-











83331.1.peg.3039;











<br>Peptidoglycan











Biosynthesis



fig|6666666.60966.peg.1682
CDS
1567261
1566710
−1
−
552
Rod shape-determining
Bacterial Cell Division;
D23_1c1680
Neut_1590








protein MreD
<br>Bacterial











Cytoskeleton;











<br>Bacterial cell











division cluster;











<br>CBSS-











354.1.peg.2917



fig|6666666.60966.peg.1683
CDS
1568123
1567233
−2
−
891
Rod shape-determining
Bacterial Cell Division;
D23_1c1681
Neut_1591








protein MreC
<br>Bacterial











Cytoskeleton;











<br>Bacterial cell











division cluster;











<br>CBSS-











354.1.peg.2917



fig|6666666.60966.peg.1684
CDS
1569547
1568486
−1
−
1062
Rod shape-determining
Bacterial Cell Division;
D23_1c1682
Neut_1592








protein MreB
<br>Bacterial











Cytoskeleton;











<br>Bacterial cell











division cluster



fig|6666666.60966.peg.1685
CDS
1569665
1569997
2
+
333
Aspartyl-tRNA(Asn)
tRNA aminoacylation,
D23_1c1683
Neut_1593








amidotransferase
Asp and Asn; <br>tRNA










subunit C (EC 6.3.5.6) @
aminoacylation, Glu and










Glutamyl-tRNA(Gln)
Gln










amidotransferase











subunit C (EC 6.3.5.7)




fig|6666666.60966.peg.1686
CDS
1570062
1571522
3
+
1461
Aspartyl-tRNA(Asn)
tRNA aminoacylation,
D23_1c1684
Neut_1594








amidotransferase
Asp and Asn; <br>tRNA










subunit A (EC 6.3.5.6) @
aminoacylation, Glu and










Glutamyl-tRNA(Gln)
Gln










amidotransferase











subunit A (EC 6.3.5.7)




fig|6666666.60966.peg.1687
CDS
1571587
1573023
1
+
1437
Aspartyl-tRNA(Asn)
tRNA aminoacylation,
D23_1c1685
Neut_1595








amidotransferase
Asp and Asn; <br>tRNA










subunit B (EC 6.3.5.6) @
aminoacylation, Glu and










Glutamyl-tRNA(Gln)
Gln










amidotransferase











subunit B (EC 6.3.5.7)




fig|6666666.60966.peg.1688
CDS
1573150
1573001
−1
−
150
hypothetical protein
-none-
D23_1c1686
NA

fig|6666666.60966.peg.1689
CDS
1573320
1573129
−3
−
192
FIG00859257:
-none-
D23_1c1687
NA








hypothetical protein




fig|6666666.60966.peg.1691
CDS
1574140
1573703
−1
−
438
heat shock protein,
-none-
D23_1c1688
Neut_1596








Hsp20 family




fig|6666666.60966.peg.1692
CDS
1574662
1574802
1
+
141
Integrase
-none-
D23_1c1690
Neut_1498

fig|6666666.60966.peg.1693
CDS
1575055
1574942
−1
−
114
hypothetical protein
-none-
D23_1c1692
NA

fig|6666666.60966.peg.1694
CDS
1575572
1575369
−2
−
204
hypothetical protein
-none-
D23_1c1693
NA

fig|6666666.60966.peg.1696
CDS
1575911
1575753
−2
−
159
Mobile element protein
-none-
D23_1c1694
Neut_1094

fig|6666666.60966.peg.1697
CDS
1576265
1578433
2
+
2169
GTP pyrophosphokinase
Stringent Response,
D23_1c1695
Neut_1601








(EC 2.7.6.5), (p)ppGpp
(p)ppGpp metabolism;










synthetase II/
<br>Stringent Response,










Guanosine-
(p)ppGpp metabolism










3&#39;,5&#39;-











bis(diphosphate)











3&#39;-











pyrophosphohydrolase











(EC 3.1.7.2)




fig|6666666.60966.peg.1698
CDS
1578452
1579135
2
+
684
FIG00858669:
-none-
D23_1c1696
Neut_1602








hypothetical protein




fig|6666666.60966.peg.1699
CDS
1579798
1579145
−1
−
654
Periplasmic
Biogenesis of c-type
D23_1c1697
Neut_1603








thiol:disulfide
cytochromes;










interchange protein
<br>Periplasmic disulfide










DsbA
interchange



fig|6666666.60966.peg.1700
CDS
1580580
1579915
−3
−
666
Cell division protein
-none-
D23_1c1698
Neut_1604

fig|6666666.60966.peg.1701
CDS
1582304
1580604
−2
−
1701
Arginyl-tRNA synthetase
tRNA aminoacylation,
D23_1c1699
Neut_1605








(EC 6.1.1.19)
Arg



fig|6666666.60966.peg.1702
CDS
1582613
1583272
2
+
660
FIG00859197:
-none-
D23_1c1700
Neut_1606








hypothetical protein




fig|6666666.60966.peg.1703
CDS
1583410
1584297
1
+
888
Methylenetetrahydrofolate
5-FCL-like protein;
D23_1c1701
Neut_1607








dehydrogenase
<br>One-carbon










(NADP+) (EC 1.5.1.5)/
metabolism by










Methenyltetrahydrofolate
tetrahydropterines;










cyclohydrolase (EC
<br>One-carbon










3.5.4.9)
metabolism by











tetrahydropterines



fig|6666666.60966.peg.1704
CDS
1584339
1586999
3
+
2661
Pyruvate
5-FCL-like protein;
D23_1c1702
Neut_1608








dehydrogenase E1
<br>Dehydrogenase










component (EC 1.2.4.1)
complexes;











<br>Methionine











Degradation;











<br>Pyruvate











metabolism II: acetyl-











CoA, acetogenesis from











pyruvate



fig|6666666.60966.peg.1705
CDS
1587072
1588421
3
+
1350
Dihydrolipoamide
5-FCL-like protein;
D23_1c1703
Neut_1609








acetyltransferase
<br>Dehydrogenase










component of pyruvate
complexes;










dehydrogenase
<br>Pyruvate










complex (EC 2.3.1.12)
metabolism II: acetyl-











CoA, acetogenesis from











pyruvate



fig|6666666.60966.peg.1706
CDS
1588457
1589170
2
+
714
Nicotinate-nucleotide
NAD and NADP cofactor
D23_1c1704
Neut_1610








adenylyltransferase (EC
biosynthesis global










2.7.7.18)




fig|6666666.60966.peg.1707
CDS
1589167
1589532
1
+
366
Iojap protein
-none-
D23_1c1705
Neut_1611

fig|6666666.60966.peg.1708
CDS
1589624
1590091
2
+
468
LSU m3Psi1915
RNA methylation;
D23_1c1706
Neut_1612








methyltransferase RlmH
<br>Ribosome











biogenesis bacterial;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.1709
CDS
1590169
1590792
1
+
624
Septum formation
Bacterial Cell Division;
D23_1c1707
Neut_1613








protein Maf
<br>Bacterial











Cytoskeleton;











<br>Bacterial cell











division cluster;











<br>CBSS-











354.1.peg.2917



fig|6666666.60966.peg.1710
CDS
1590825
1592276
3
+
1452
Cytoplasmic axial
Bacterial Cell Division;
D23_1c1708
Neut_1614








filament protein CafA
<br>CBSS-










and Ribonuclease G (EC
354.1.peg.2917;










3.1.4.—)
<br>RNA processing and











degradation, bacterial



fig|6666666.60966.peg.1711
CDS
1592500
1593222
1
+
723
Ferric siderophore
Ton and Tol transport
D23_1c1709
Neut_1615








transport system,
systems










periplasmic binding











protein TonB




fig|6666666.60966.peg.1712
CDS
1593226
1594023
1
+
798
MotA/TolQ/ExbB
Ton and Tol transport
D23_1c1710
Neut_1616








proton channel family
systems










protein




fig|6666666.60966.peg.1713
CDS
1594023
1594448
3
+
426
Biopolymer transport
Ton and Tol transport
D23_1c1711
Neut_1617








protein ExbD/TolR
systems



fig|6666666.60966.peg.1714
CDS
1595300
1594518
−2
−
783
23S rRNA (guanosine-
RNA methylation
D23_1c1712
Neut_1618








2&#39;-O-)-











methyltransferase rlmB











(EC 2.1.1.—)




fig|6666666.60966.peg.1715
CDS
1597532
1595328
−2
−
2205
3&#39;-to-5&#39;
RNA processing and
D23_1c1713
Neut_1619








exoribonuclease RNase R
degradation, bacterial



fig|6666666.60966.peg.1717
CDS
1598152
1599303
1
+
1152
DNA polymerase IV (EC
DNA repair, bacterial
D23_1c1715
Neut_1620








2.7.7.7)




fig|6666666.60966.peg.1718
CDS
1599507
1599391
−3
−
117
hypothetical protein
-none-
D23_1c1716
NA

fig|6666666.60966.peg.1719
CDS
1599639
1601015
3
+
1377
Flagellar regulatory
Flagellum
D23_1c1717
Neut_1621








protein FleQ




fig|6666666.60966.peg.1720
CDS
1601809
1601045
−1
−
765
hypothetical protein
-none-
D23_1c1718
Neut_1622

fig|6666666.60966.peg.1721
CDS
1604085
1601893
−3
−
2193
hypothetical protein
-none-
D23_1c1719
Neut_1623

fig|6666666.60966.peg.1722
CDS
1605035
1604157
−2
−
879
Mobile element protein
-none-
D23_1c1720
Neut_1720

fig|6666666.60966.peg.1723
CDS
1605427
1605134
−1
−
294
Mobile element protein
-none-
D23_1c1721
Neut_1719

fig|6666666.60966.peg.1724
CDS
1606591
1605455
−1
−
1137
8-amino-7-
Biotin biosynthesis;
D23_1c1722
Neut_2137








oxononanoate synthase
<br>Biotin biosynthesis










(EC 2.3.1.47)
Experimental; <br>Biotin











synthesis cluster



fig|6666666.60966.peg.1725
CDS
1608741
1606597
−3
−
2145
hypothetical protein
-none-
D23_1c1723
NA

fig|6666666.60966.peg.1726
CDS
1610072
1608738
−2
−
1335
hypothetical protein
-none-
D23_1c1724
NA

fig|6666666.60966.peg.1727
CDS
1610798
1610106
−2
−
693
hypothetical protein
-none-
D23_1c1725
Neut_1626

fig|6666666.60966.peg.1728
CDS
1611531
1610833
−3
−
699
hypothetical protein
-none-
D23_1c1726
Neut_1626

fig|6666666.60966.peg.1729
CDS
1611922
1612056
1
+
135
hypothetical protein
-none-
D23_1c1727
NA

fig|6666666.60966.peg.1731
CDS
1612368
1612991
3
+
624
InterPro IPR000379
-none-
D23_1c1729
Neut_1627








COGs COG2945




fig|6666666.60966.peg.1732
CDS
1614001
1613204
−1
−
798
Carbonic anhydrase (EC
Zinc regulated enzymes
D23_1c1730
Neut_1628








4.2.1.1)




fig|6666666.60966.peg.1734
CDS
1614522
1614355
−3
−
168
hypothetical protein
-none-
D23_1c1731
NA

fig|6666666.60966.peg.1735
CDS
1614827
1614699
−2
−
129
hypothetical protein
-none-
D23_1c1732
NA

fig|6666666.60966.peg.1736
CDS
1614794
1616134
2
+
1341
Probable
-none-
D23_1c1733
Neut_1630








transmembrane protein




fig|6666666.60966.peg.1737
CDS
1617043
1616225
−1
−
819
rRNA methylases
-none-
D23_1c1734
Neut_1631

fig|6666666.60966.peg.1738
CDS
1617516
1617061
−3
−
456
Mobile element protein
-none-
D23_1c1735
Neut_2502

fig|6666666.60966.peg.1739
CDS
1617913
1617479
−1
−
435
Mobile element protein
-none-
D23_1c1736
Neut_0884

fig|6666666.60966.peg.1740
CDS
1618427
1618293
−2
−
135
hypothetical protein
-none-
D23_1c1738
NA

fig|6666666.60966.peg.1741
CDS
1619838
1618420
−3
−
1419
Dihydrolipoamide
5-FCL-like protein;
D23_1c1739
Neut_1632








dehydrogenase (EC
<br>Glycine cleavage










1.8.1.4)
system;











<br>Photorespiration











(oxidative C2 cycle);











<br>TCA Cycle



fig|6666666.60966.peg.1742
CDS
1620067
1621053
1
+
987
Malate dehydrogenase
TCA Cycle
D23_1c1740
Neut_1633








(EC 1.1.1.37)




fig|6666666.60966.peg.1743
CDS
1621562
1621107
−2
−
456
Thiol peroxidase, Bcp-
CBSS-
D23_1c1741
Neut_1634








type (EC 1.11.1.15)
316057.3.peg.3521;











<br>Thioredoxin-











disulfide reductase



fig|6666666.60966.peg.1744
CDS
1622938
1621595
−1
−
1344
Cytochrome c heme
Biogenesis of c-type
D23_1c1742
Neut_1635








lyase subunit CcmH
cytochromes;











<br>Copper homeostasis



fig|6666666.60966.peg.1745
CDS
1623399
1622935
−3
−
465
Cytochrome c heme
Biogenesis of c-type
D23_1c1743
Neut_1636








lyase subunit CcmL
cytochromes



fig|6666666.60966.peg.1746
CDS
1623982
1623458
−1
−
525
Cytochrome c-type
Biogenesis of c-type
D23_1c1744
Neut_1637








biogenesis protein
cytochromes;










CcmG/DsbE,
<br>Periplasmic disulfide










thiol:disulfide
interchange










oxidoreductase




fig|6666666.60966.peg.1747
CDS
1626024
1623979
−3
−
2046
Cytochrome c heme
Biogenesis of c-type
D23_1c1745
Neut_1638








lyase subunit CcmF
cytochromes;











<br>Copper homeostasis



fig|6666666.60966.peg.1748
CDS
1626514
1626065
−1
−
450
Cytochrome c-type
Biogenesis of c-type
D23_1c1746
Neut_1639








biogenesis protein
cytochromes










CcmE, heme chaperone




fig|6666666.60966.peg.1749
CDS
1627373
1626690
−2
−
684
Cytochrome c-type
Biogenesis of c-type
D23_1c1747
Neut_1641








biogenesis protein
cytochromes










CcmC, putative heme











lyase for CcmE




fig|6666666.60966.peg.1750
CDS
1628195
1627536
−2
−
660
ABC transporter
Biogenesis of c-type
D23_1c1748
Neut_1642








involved in cytochrome
cytochromes










c biogenesis, CcmB











subunit




fig|6666666.60966.peg.1751
CDS
1628729
1628202
−2
−
528
ABC transporter
Biogenesis of c-type
D23_1c1749
Neut_1643








involved in cytochrome
cytochromes










c biogenesis, ATPase











component CcmA




fig|6666666.60966.peg.1752
CDS
1629793
1628927
−1
−
867
tRNA pseudouridine
CBSS-
D23_1c1750
Neut_1644








synthase B (EC 4.2.1.70)
138119.3.peg.2719;











<br>RNA pseudouridine











syntheses;











<br>Riboflavin, FMN and











FAD metabolism in











plants; <br>tRNA











modification Bacteria;











<br>tRNA processing



fig|6666666.60966.peg.1753
CDS
1630354
1630001
−1
−
354
Ribosome-binding
CBSS-
D23_1c1751
Neut_1645








factor A
138119.3.peg.2719;











<br>NusA-TFII Cluster;











<br>Translation











initiation factors











bacterial



fig|6666666.60966.peg.1754
CDS
1633073
1630407
−2
−
2667
Translation initiation
CBSS-
D23_1c1752
Neut_1646








factor 2
138119.3.peg.2719;











<br>NusA-TFII Cluster;











<br>Translation











initiation factors











bacterial; <br>Universal











GTPases



fig|6666666.60966.peg.1756
CDS
1634664
1633192
−3
−
1473
Transcription
NusA-TFII Cluster;
D23_1c1753
Neut_1647








termination protein
<br>Transcription










NusA
factors bacterial



fig|6666666.60966.peg.1757
CDS
1635199
1634717
−1
−
483
COG0779: clustered
-none-
D23_1c1754
Neut_1648








with transcription











termination protein











NusA




fig|6666666.60966.peg.1760
CDS
1636174
1636611
1
+
438
FIG00859331:
-none-
D23_1c1755
Neut_1650








hypothetical protein




fig|6666666.60966.peg.1761
CDS
1637012
1636686
−2
−
327
Cytochrome c4
Soluble cytochromes
D23_1c1756
Neut_1651









and functionally related











electron carriers



fig|6666666.60966.peg.1762
CDS
1637371
1637045
−1
−
327
Putative periplasmic
-none-
D23_1c1757
Neut_1652








cytochrome type-C











oxidoreductase signal











peptide protein (EC 1.—.—.—)




fig|6666666.60966.peg.1763
CDS
1639430
1637484
−2
−
1947
COG0488: ATPase
-none-
D23_1c1758
Neut_1653








components of ABC











transporters with











duplicated ATPase











domains




fig|6666666.60966.peg.1765
CDS
1639660
1640709
1
+
1050
Selenide, water dikinase
Selenocysteine
D23_1c1759
Neut_1654








(EC 2.7.9.3)
metabolism; <br>tRNA











modification Bacteria



fig|6666666.60966.peg.1766
CDS
1640702
1641868
2
+
1167
Selenophosphate-
Selenocysteine
D23_1c1760
Neut_1655








dependent tRNA 2-
metabolism; <br>tRNA










selenouridine synthase
modification Bacteria



fig|6666666.60966.peg.1767
CDS
1642217
1642050
−2
−
168
hypothetical protein
-none-
D23_1c1761
NA

fig|6666666.60966.peg.1768
CDS
1643785
1642217
−1
−
1569
4-cresol dehydrogenase
Cresol degradation
D23_1c1762
Neut_1656








[hydroxylating]











flavoprotein subunit (EC











1.17.99.1)




fig|6666666.60966.peg.1769
CDS
1644507
1643782
−3
−
726
PchX protein
-none-
D23_1c1763
Neut_1657

fig|6666666.60966.peg.1770
CDS
1644874
1644518
−1
−
357
4-cresol dehydrogenase
Cresol degradation
D23_1c1764
Neut_1658








[hydroxylating]











cytochrome c subunit











precursor




fig|6666666.60966.peg.1771
CDS
1646175
1645138
−3
−
1038
Dihydroorotase (EC
De Novo Pyrimidine
D23_1c1766
Neut_1659








3.5.2.3)
Synthesis; <br>Zinc











regulated enzymes



fig|6666666.60966.peg.1772
CDS
1647130
1646273
−1
−
858
rRNA small subunit
16S rRNA modification
D23_1c1767
Neut_1660








methyltransferase I
within P site of











ribosome; <br>CBSS-











160492.1.peg.550;











<br>Heat shock dnaK











gene cluster extended



fig|6666666.60966.peg.1773
CDS
1647311
1649101
2
+
1791
ABC transporter,
-none-
D23_1c1769
Neut_1661








multidrug efflux family




fig|6666666.60966.peg.1774
CDS
1649206
1649556
1
+
351
Predicted endonuclease
CBSS-160492.1.peg.550
D23_1c1770
Neut_1662








distantly related to











archaeal Holliday











junction resolvase




fig|6666666.60966.peg.1776
CDS
1651143
1649929
−3
−
1215
hypothetical protein
-none-
D23_1c1771
Neut_1663

fig|6666666.60966.peg.1777
CDS
1651568
1651446
−2
−
123
hypothetical protein
-none-
D23_1c1772
NA

fig|6666666.60966.peg.1778
CDS
1651714
1652223
1
+
510
Putative lipoprotein
-none-
D23_1c1773
Neut_1664

fig|6666666.60966.peg.1779
CDS
1652740
1661706
1
+
8967
Cyclic beta-1,2-glucan
Synthesis of
D23_1c1774
Neut_1665








synthase (EC 2.4.1.—)
osmoregulated











periplasmic glucans



fig|6666666.60966.peg.1780
CDS
1662138
1661821
−3
−
318
Mobile element protein
-none-
D23_1c1775
Neut_1666

fig|6666666.60966.peg.1781
CDS
1662168
1662344
3
+
177
hypothetical protein
-none-
D23_1c1776
NA

fig|6666666.60966.peg.1782
CDS
1662546
1662406
−3
−
141
Mobile element protein
-none-
D23_1c1777
Neut_2190

fig|6666666.60966.peg.1783
CDS
1663286
1663158
−2
−
129
hypothetical protein
-none-
D23_1c1778
NA

fig|6666666.60966.peg.1784
CDS
1663556
1664518
2
+
963
Mobile element protein
-none-
D23_1c1779
Neut_1746

fig|6666666.60966.peg.1785
CDS
1666051
1664585
−1
−
1467
ATP-dependent RNA
ATP-dependent RNA
D23_1c1780
Neut_1668








helicase
helicases, bacterial










Bcep18194_A5658




fig|6666666.60966.peg.1786
CDS
1666377
1666147
−3
−
231
Mobile element protein
-none-
D23_1c1781
Neut_2088

fig|6666666.60966.peg.1787
CDS
1666620
1666441
−3
−
180
Mobile element protein
-none-
D23_1c1782
Neut_0332

fig|6666666.60966.peg.1788
CDS
1667117
1666644
−2
−
474
Mobile element protein
-none-
D23_1c1783
NA

fig|6666666.60966.peg.1789
CDS
1668091
1667294
−1
−
798
FIG00861229:
-none-
D23_1c1784
Neut_1669








hypothetical protein




fig|6666666.60966.peg.1790
CDS
1668254
1668093
−2
−
162
hypothetical protein
-none-
D23_1c1785
NA

fig|6666666.60966.peg.1791
CDS
1669037
1668330
−2
−
708
Cytochrome c family
-none-
D23_1c1786
Neut_2333








protein




fig|6666666.60966.peg.1792
CDS
1670220
1669099
−3
−
1122
FIG00859557:
-none-
D23_1c1787
Neut_1792








hypothetical protein




fig|6666666.60966.peg.1793
CDS
1671929
1670217
−2
−
1713
Hydroxylamine
-none-
D23_1c1788
Neut_2335








oxidoreductase











precursor (EC 1.7.3.4)




fig|6666666.60966.peg.1794
CDS
1672280
1672017
−2
−
264
SSU ribosomal protein
-none-
D23_1c1789
NA








S20p




fig|6666666.60966.peg.1795
CDS
1672473
1672634
3
+
162
hypothetical protein
-none-
D23_1c1790
NA

fig|6666666.60966.peg.1796
CDS
1672870
1672601
−1
−
270
Mobile element protein
-none-
D23_1c1791
Neut_2450

fig|6666666.60966.peg.1797
CDS
1673187
1672894
−3
−
294
hypothetical protein
-none-
D23_1c1792
Neut_2449

fig|6666666.60966.peg.1798
CDS
1673875
1673648
−1
−
228
hypothetical protein
-none-
D23_1c1795
Neut_1676

fig|6666666.60966.peg.1799
CDS
1674438
1674052
−3
−
387
FIG002082: Protein
A Gammaproteobacteria
D23_1c1796
Neut_1677








SirB2
Cluster Relating to











Translation



fig|6666666.60966.peg.1800
CDS
1674844
1674500
−1
−
345
FIG00858740:
-none-
D23_1c1797
Neut_1678








hypothetical protein




fig|6666666.60966.peg.1801
CDS
1675595
1674939
−2
−
657
Probable membrane
-none-
D23_1c1798
Neut_1679








protein




fig|6666666.60966.peg.1802
CDS
1675804
1675601
−1
−
204
Probable membrane
-none-
D23_1c1800
Neut_1679








protein




fig|6666666.60966.peg.1803
CDS
1676931
1675825
−3
−
1107
GbcA Glycine betaine
-none-
D23_1c1801
Neut_1680








demethylase subunit A




fig|6666666.60966.peg.1804
CDS
1677301
1678686
1
+
1386
FIG00858667:
-none-
D23_1c1802
Neut_1681








hypothetical protein




fig|6666666.60966.peg.1805
CDS
1678742
1680964
2
+
2223
Helicase PriA essential
-none-
D23_1c1803
Neut_1682








for oriC/DnaA-











independent DNA











replication




fig|6666666.60966.peg.1806
CDS
1681478
1681032
−2
−
447
Universal stress protein
-none-
D23_1c1804
Neut_1683

fig|6666666.60966.peg.1807
CDS
1683246
1681597
−3
−
1650
Folate transporter 3
-none-
D23_1c1805
Neut_1684

fig|6666666.60966.peg.1808
CDS
1684397
1683258
−2
−
1140
Outer membrane stress
Periplasmic Stress
D23_1c1806
Neut_1685








sensor protease DegS
Response;











<br>Proteolysis in











bacteria, ATP-dependent



fig|6666666.60966.peg.1809
CDS
1684396
1685181
1
+
786
FIG137478:
-none-
D23_1c1807
Neut_1686








Hypothetical protein











YbgI




fig|6666666.60966.peg.1810
CDS
1685374
1685249
−1
−
126
hypothetical protein
-none-
D23_1c1808
NA

fig|6666666.60966.peg.1811
CDS
1685328
1686644
3
+
1317
Membrane-bound lytic
Murein Hydrolases
D23_1c1809
Neut_1687








murein transglycosylase











A precursor (EC 3.2.1.—)




fig|6666666.60966.peg.1812
CDS
1687397
1686684
−2
−
714
Thiol:disulfide
Periplasmic disulfide
D23_1c1810
Neut_1688








interchange protein
interchange










DsbC




fig|6666666.60966.peg.1813
CDS
1688609
1687443
−2
−
1167
2-octaprenyl-3-methyl-
CBSS-87626.3.peg.3639;
D23_1c1811
Neut_1689








6-methoxy-1,4-
<br>Ubiquinone










benzoquinol
Biosynthesis;










hydroxylase (EC
<br>Ubiquinone










1.14.13.—)
Biosynthesis-gjo



fig|6666666.60966.peg.1814
CDS
1688840
1690807
2
+
1968
Acetyl-coenzyme A
Pyruvate metabolism II:
D23_1c1812
Neut_1690








synthetase (EC 6.2.1.1)
acetyl-CoA, acetogenesis











from pyruvate



fig|6666666.60966.peg.1815
CDS
1690825
1691799
1
+
975
Beta-lactamase related
-none-
D23_1c1813
Neut_1691








protein




fig|6666666.60966.peg.1816
CDS
1693183
1691903
−1
−
1281
amidohydrolase
-none-
D23_1c1814
Neut_1692

fig|6666666.60966.peg.1817
CDS
1693463
1693633
2
+
171
Mobile element protein
-none-
D23_1c1816
Neut_1693

fig|6666666.60966.peg.1818
CDS
1694024
1695034
2
+
1011
Fatty acid desaturase
-none-
D23_1c1817
Neut_1694

fig|6666666.60966.peg.1819
CDS
1696649
1695402
−2
−
1248
Mobile element protein
-none-
D23_1c1818
Neut_0357

fig|6666666.60966.peg.1820
CDS
1697303
1696830
−2
−
474
Mobile element protein
-none-
D23_1c1820
Neut_1256

fig|6666666.60966.peg.1821
CDS
1697769
1697377
−3
−
393
hypothetical protein
-none-
D23_1c1821
Neut_2449

fig|6666666.60966.peg.1822
CDS
1698235
1698032
−1
−
204
hypothetical protein
-none-
D23_1c1822
Neut_0363

fig|6666666.60966.peg.1823
CDS
1698639
1698322
−3
−
318
hypothetical protein
-none-
D23_1c1823
Neut_1695

fig|6666666.60966.peg.1824
CDS
1698977
1698639
−2
−
339
Mobile element protein
-none-
D23_1c1824
Neut_1696

fig|6666666.60966.peg.1825
CDS
1699393
1702311
1
+
2919
Na(+) H(+) antiporter
Multi-subunit cation
D23_1c1825
Neut_1697








subunit A/Na(+) H(+)
antiporter; <br>Multi-










antiporter subunit B
subunit cation antiporter



fig|6666666.60966.peg.1826
CDS
1702311
1702655
3
+
345
Na(+) H(+) antiporter
Multi-subunit cation
D23_1c1826
Neut_1698








subunit C
antiporter



fig|6666666.60966.peg.1827
CDS
1702652
1704298
2
+
1647
Na(+) H(+) antiporter
Multi-subunit cation
D23_1c1827
Neut_1699








subunit D
antiporter



fig|6666666.60966.peg.1828
CDS
1704295
1704780
1
+
486
Na(+) H(+) antiporter
Multi-subunit cation
D23_1c1828
Neut_1700








subunit E
antiporter



fig|6666666.60966.peg.1829
CDS
1704777
1705058
3
+
282
Na(+) H(+) antiporter
Multi-subunit cation
D23_1c1829
Neut_1701








subunit F
antiporter



fig|6666666.60966.peg.1830
CDS
1705055
1705480
2
+
426
Na(+) H(+) antiporter
Multi-subunit cation
D23_1c1830
Neut_1702








subunit G
antiporter



fig|6666666.60966.peg.1831
CDS
1708136
1705638
−2
−
2499
FIG00809136:
-none-
D23_1c1831
Neut_1703








hypothetical protein




fig|6666666.60966.peg.1832
CDS
1709066
1708266
−2
−
801
ABC transporter ATP-
-none-
D23_1c1832
Neut_1704








binding protein YvcR




fig|6666666.60966.peg.1833
CDS
1709065
1709676
1
+
612
Arylesterase precursor
-none-
D23_1c1833
Neut_1705








(EC 3.1.1.2)




fig|6666666.60966.peg.1834
CDS
1710780
1709716
−3
−
1065
Ribosomal large subunit
RNA pseudouridine
D23_1c1834
Neut_1706








pseudouridine synthase
syntheses;










C (EC 4.2.1.70)
<br>Ribosome











biogenesis bacterial



fig|6666666.60966.peg.1835
CDS
1711189
1713738
1
+
2550
Ribonuclease E (EC
RNA processing and
D23_1c1835
Neut_1707








3.1.26.12)
degradation, bacterial;











<br>Ribosome











biogenesis bacterial



fig|6666666.60966.peg.1836
CDS
1714787
1713870
−2
−
918
Tyrosine recombinase
-none-
D23_1c1836
Neut_1708








XerD




fig|6666666.60966.peg.1837
CDS
1715754
1714909
−3
−
846
CcsA-related protein
-none-
D23_1c1837
Neut_1709

fig|6666666.60966.peg.1838
CDS
1715897
1717246
2
+
1350
Signal recognition
Bacterial signal
D23_1c1838
Neut_1710








particle, subunit Ffh
recognition particle










SRP54 (TC 3.A.5.1.1)
(SRP); <br>Universal











GTPases



fig|6666666.60966.peg.1839
CDS
1717562
1718059
2
+
498
Cytosine/adenosine
-none-
D23_1c1840
Neut_1711








deaminases




fig|6666666.60966.peg.1840
CDS
1719089
1718079
−2
−
1011
collagen triple helix
-none-
D23_1c1841
Neut_1712








repeat domain protein




fig|6666666.60966.peg.1841
CDS
1719941
1719435
−2
−
507
Mobile element protein
-none-
D23_1c1843
Neut_1353

fig|6666666.60966.peg.1843
CDS
1720927
1720256
−1
−
672
Putative TEGT family
CBSS-326442.4.peg.1852
D23_1c1844
Neut_1715








carrier/transport











protein




fig|6666666.60966.peg.1844
CDS
1721245
1721081
−1
−
165
hypothetical protein
-none-
D23_1c1845
Neut_1716

fig|6666666.60966.peg.1845
CDS
1721933
1721268
−2
−
666
Mobile element protein
-none-
D23_1c1846
Neut_1717

fig|6666666.60966.peg.1846
CDS
1722745
1722137
−1
−
609
Aldehyde
Glycerolipid and
D23_1c1847
Neut_0700








dehydrogenase (EC
Glycerophospholipid










1.2.1.3)
Metabolism in Bacteria;











<br>Methylglyoxal











Metabolism;











<br>Methylglyoxal











Metabolism;











<br>Pyruvate











metabolism II: acetyl-











CoA, acetogenesis from











pyruvate



fig|6666666.60966.peg.1847
CDS
1722896
1723189
2
+
294
Mobile element protein
-none-
D23_1c1848
Neut_1719

fig|6666666.60966.peg.1848
CDS
1723288
1724166
1
+
879
Mobile element protein
-none-
D23_1c1849
Neut_1720

fig|6666666.60966.peg.1849
CDS
1724724
1724179
−3
−
546
Aldehyde
Glycerolipid and
D23_1c1850
Neut_0700








dehydrogenase (EC
Glycerophospholipid










1.2.1.3)
Metabolism in Bacteria;











<br>Methylglyoxal











Metabolism;











<br>Methylglyoxal











Metabolism;











<br>Pyruvate











metabolism II: acetyl-











CoA, acetogenesis from











pyruvate



fig|6666666.60966.peg.1850
CDS
1726242
1724995
−3
−
1248
Mobile element protein
-none-
D23_1c1851
Neut_0357

fig|6666666.60966.peg.1851
CDS
1727368
1727126
−1
−
243
Mobile element protein
-none-
D23_1c1854
Neut_2190

fig|6666666.60966.peg.1852
CDS
1727480
1727641
2
+
162
hypothetical protein
-none-
D23_1c1855
NA

fig|6666666.60966.peg.1853
CDS
1727757
1727873
3
+
117
hypothetical protein
-none-
D23_1c1856
NA

fig|6666666.60966.peg.1854
CDS
1727880
1728818
3
+
939
Major facilitator family
-none-
D23_1c1857
NA








transporter




fig|6666666.60966.peg.1855
CDS
1728936
1730123
3
+
1188
Cytosine deaminase (EC
CBSS-
D23_1c1858
Neut_1722








3.5.4.1)
326442.4.peg.1852;











<br>Creatine and











Creatinine Degradation;











<br>pyrimidine











conversions



fig|6666666.60966.peg.1857
CDS
1730427
1730624
3
+
198
Mobile element protein
-none-
D23_1c1859
Neut_1748

fig|6666666.60966.peg.1858
CDS
1730716
1730937
1
+
222
Mobile element protein
-none-
D23_1c1860
Neut_1747

fig|6666666.60966.peg.1859
CDS
1731165
1733414
3
+
2250
Lead, cadmium, zinc
Copper Transport
D23_1c1862
Neut_1724








and mercury
System; <br>Copper










transporting ATPase (EC
homeostasis










3.6.3.3) (EC 3.6.3.5);











Copper-translocating P-











type ATPase (EC 3.6.3.4)




fig|6666666.60966.peg.1860
CDS
1733755
1733946
1
+
192
hypothetical protein
-none-
D23_1c1863
Neut_1734

fig|6666666.60966.peg.1861
CDS
1734020
1735762
2
+
1743
Asparagine synthetase
Cyanophycin
D23_1c1864
Neut_1735








[glutamine-hydrolyzing]
Metabolism;










(EC 6.3.5.4)
<br>Glutamate and











Aspartate uptake in











Bacteria; <br>Glutamine,











Glutamate, Aspartate











and Asparagine











Biosynthesis



fig|6666666.60966.peg.1862
CDS
1735929
1737425
3
+
1497
major facilitator
-none-
D23_1c1865
Neut_1736








superfamily MFS_1




fig|6666666.60966.peg.1863
CDS
1737575
1737841
2
+
267
Mobile element protein
-none-
D23_1c1866
NA

fig|6666666.60966.peg.1864
CDS
1737835
1737975
1
+
141
Mobile element protein
-none-
D23_1c1867
NA

fig|6666666.60966.peg.1865
CDS
1738803
1738006
−3
−
798
Mobile element protein
-none-
D23_1c1868
Neut_1888

fig|6666666.60966.peg.1866
CDS
1739186
1738917
−2
−
270
Mobile element protein
-none-
D23_1c1869
Neut_2500

fig|6666666.60966.peg.1868
CDS
1740582
1739374
−3
−
1209
hypothetical protein
-none-
D23_1c1870
Neut_1740

fig|6666666.60966.peg.1869
CDS
1742717
1740588
−2
−
2130
Ferrichrome-iron
-none-
D23_1c1871
Neut_1741








receptor




fig|6666666.60966.peg.1870
CDS
1744008
1742806
−3
−
1203
Vibrioferrin
-none-
D23_1c1872
Neut_1742








decarboxylase protein











PvsE




fig|6666666.60966.peg.1871
CDS
1745819
1744005
−2
−
1815
Vibrioferrin amide bond
-none-
D23_1c1873
Neut_1743








forming protein PvsD @











Siderophore synthetase











superfamily, group A




fig|6666666.60966.peg.1872
CDS
1747001
1745829
−2
−
1173
Vibrioferrin membrane-
-none-
D23_1c1874
Neut_1744








spanning transport











protein PvsC




fig|6666666.60966.peg.1873
CDS
1748855
1747044
−2
−
1812
Anthrachelin
-none-
D23_1c1875
Neut_1745








biosynthesis protein











AsbB @ Siderophore











synthetase superfamily,











group C @ Siderophore











synthetase component,











ligase




fig|6666666.60966.peg.1874
CDS
1749327
1749151
−3
−
177
Mobile element protein
-none-
D23_1c1876
Neut_1747

fig|6666666.60966.peg.1876
CDS
1750647
1749685
−3
−
963
Mobile element protein
-none-
D23_1c1878
Neut_1278

fig|6666666.60966.peg.1877
CDS
1751012
1752274
2
+
1263
hypothetical protein
-none-
D23_1c1879
Neut_1749

fig|6666666.60966.peg.1878
CDS
1752303
1753133
3
+
831
Potassium efflux system
Potassium homeostasis
D23_1c1880
NA








KefA protein/Small-











conductance











mechanosensitive











channel




fig|6666666.60966.peg.1879
CDS
1753722
1753153
−3
−
570
hypothetical protein
-none-
D23_1c1881
NA

fig|6666666.60966.peg.1880
CDS
1753823
1754629
2
+
807
Glutamate racemase
Glutamine, Glutamate,
D23_1c1882
Neut_1752








(EC 5.1.1.3)
Aspartate and











Asparagine Biosynthesis;











<br>Peptidoglycan











Biosynthesis



fig|6666666.60966.peg.1881
CDS
1754733
1755689
3
+
957
Universal stress protein
-none-
D23_1c1883
Neut_1753

fig|6666666.60966.peg.1882
CDS
1756978
1755725
−1
−
1254
DNA repair protein
DNA repair, bacterial;
D23_1c1884
Neut_1754








RadA
<br>Proteolysis in











bacteria, ATP-dependent



fig|6666666.60966.peg.1883
CDS
1757073
1757201
3
+
129
hypothetical protein
-none-
D23_1c1885
NA

fig|6666666.60966.peg.1884
CDS
1758757
1757372
−1
−
1386
L-serine dehydratase
Glycine and Serine
D23_1c1887
Neut_1760








(EC 4.3.1.17)
Utilization; <br>Pyruvate











Alanine Serine











Interconversions



fig|6666666.60966.peg.1886
CDS
1759312
1760013
1
+
702
Serine protease
Transcription initiation,
D23_1c1890
Neut_1761








precursor MucD/AlgY
bacterial sigma factors










associated with sigma











factor RpoE




fig|6666666.60966.peg.1887
CDS
1760622
1761584
3
+
963
Mobile element protein
-none-
D23_1c1892
Neut_1278

fig|6666666.60966.peg.1888
CDS
1761643
1762524
1
+
882
FIG071646: Sugar
Cell wall related cluster
D23_1c1893
Neut_1762








transferase




fig|6666666.60966.peg.1889
CDS
1762574
1764655
2
+
2082
Sensory transduction
-none-
D23_1c1894
Neut_1763








histidine kinases




fig|6666666.60966.peg.1890
CDS
1764739
1766601
1
+
1863
Lipid A export ATP-
-none-
D23_1c1895
Neut_1764








binding/permease











protein MsbA




fig|6666666.60966.peg.1891
CDS
1769731
1766636
−1
−
3096
Cobalt-zinc-cadmium
Cobalt-zinc-cadmium
D23_1c1896
Neut_1765








resistance protein CzcA;
resistance; <br>Cobalt-










Cation efflux system
zinc-cadmium resistance










protein CusA




fig|6666666.60966.peg.1892
CDS
1770897
1769734
−3
−
1164
Cobalt/zinc/cadmium
Cobalt-zinc-cadmium
D23_1c1897
Neut_1766








efflux RND transporter,
resistance










membrane fusion











protein, CzcB family




fig|6666666.60966.peg.1893
CDS
1772112
1770907
−3
−
1206
Heavy metal RND efflux
Cobalt-zinc-cadmium
D23_1c1898
Neut_1767








outer membrane
resistance










protein, CzcC family




fig|6666666.60966.peg.1894
CDS
1773163
1772504
−1
−
660
FIG00859115:
-none-
D23_1c1899
Neut_1768








hypothetical protein




fig|6666666.60966.peg.1895
CDS
1773250
1773996
1
+
747
Glycerophosphoryl
CBSS-
D23_1c1900
Neut_1769








diester
176299.4.peg.1996A;










phosphodiesterase (EC
<br>Glycerol and










3.1.4.46)
Glycerol-3-phosphate











Uptake and Utilization



fig|6666666.60966.peg.1896
CDS
1774006
1775181
1
+
1176
Aerobic glycerol-3-
Glycerol and Glycerol-3-
D23_1c1901
Neut_1770








phosphate
phosphate Uptake and










dehydrogenase (EC
Utilization;










1.1.5.3)
<br>Glycerolipid and











Glycerophospholipid











Metabolism in Bacteria;











<br>Respiratory











dehydrogenases 1



fig|6666666.60966.peg.1897
CDS
1775543
1775211
−2
−
333
FIG00859262:
-none-
D23_1c1902
Neut_1771








hypothetical protein




fig|6666666.60966.peg.1898
CDS
1776076
1775636
−1
−
441
FIG00859309:
-none-
D23_1c1903
Neut_1772








hypothetical protein




fig|6666666.60966.peg.1899
CDS
1777538
1776078
−2
−
1461
Dihydrolipoamide
Dehydrogenase
D23_1c1904
Neut_1773








dehydrogenase of 2-
complexes; <br>TCA










oxoglutarate
Cycle










dehydrogenase (EC











1.8.1.4)




fig|6666666.60966.peg.1900
CDS
1778658
1777612
−3
−
1047
Beta N-acetyl-
Murein Hydrolases;
D23_1c1905
Neut_1774








glucosaminidase (EC
<br>Recycling of










3.2.1.52)
Peptidoglycan Amino











Sugars



fig|6666666.60966.peg.1901
CDS
1779038
1778661
−2
−
378
Holo-[acyl-carrier
Fatty Acid Biosynthesis
D23_1c1906
Neut_1775








protein] synthase (EC
FASII










2.7.8.7)




fig|6666666.60966.peg.1902
CDS
1779760
1779035
−1
−
726
Pyridoxine 5&#39;-
Pyridoxin (Vitamin B6)
D23_1c1907
Neut_1776








phosphate synthase (EC
Biosynthesis










2.6.99.2)




fig|6666666.60966.peg.1903
CDS
1780768
1779878
−1
−
891
GTP-binding protein Era
Bacterial Cell Division;
D23_1c1908
Neut_1777









<br>Glycyl-tRNA











synthetase containing











cluster; <br>Universal











GTPases



fig|6666666.60966.peg.1904
CDS
1781583
1780846
−3
−
738
Ribonuclease III (EC
RNA processing and
D23_1c1909
Neut_1778








3.1.26.3)
degradation, bacterial



fig|6666666.60966.peg.1905
CDS
1781963
1781580
−2
−
384
possible
-none-
D23_1c1910
Neut_1779








transmembrane protein




fig|6666666.60966.peg.1906
CDS
1782802
1781999
−1
−
804
Signal peptidase I (EC
Signal peptidase
D23_1c1911
Neut_1780








3.4.21.89)




fig|6666666.60966.peg.1907
CDS
1784670
1782874
−3
−
1797
Translation elongation
Heat shock dnaK gene
D23_1c1912
Neut_1781








factor LepA
cluster extended;











<br>Translation











elongation factors











bacterial; <br>Universal











GTPases



fig|6666666.60966.peg.1908
CDS
1784806
1784651
−1
−
156
hypothetical protein
-none-
D23_1c1913
NA

fig|6666666.60966.peg.1909
CDS
1785160
1784972
−1
−
189
COGs COG0526
-none-
D23_1c1914
Neut_1782

fig|6666666.60966.peg.1910
CDS
1786580
1785222
−2
−
1359
Serine protease
Transcription initiation,
D23_1c1915
Neut_1783








precursor MucD/AlgY
bacterial sigma factors










associated with sigma











factor RpoE




fig|6666666.60966.peg.1911
CDS
1787446
1786871
−1
−
576
InterPro IPR001687
-none-
D23_1c1916
Neut_1784








COGs COG3073




fig|6666666.60966.peg.1912
CDS
1788062
1787460
−2
−
603
RNA polymerase sigma
Transcription initiation,
D23_1c1917
Neut_1785








factor RpoE
bacterial sigma factors



fig|6666666.60966.peg.1913
CDS
1789111
1788260
−1
−
852
Magnesium and cobalt
CBSS-
D23_1c1919
Neut_1786








efflux protein CorC
56780.10.peg.1536;











<br>Copper











homeostasis: copper











tolerance; <br>Glycyl-











tRNA synthetase











containing cluster;











<br>Magnesium











transport; <br>tRNA-











methylthiotransferase











containing cluster



fig|6666666.60966.peg.1914
CDS
1789590
1789165
−3
−
426
Metal-dependent
CBSS-
D23_1c1920
Neut_1787








hydrolase YbeY,
56780.10.peg.1536;










involved in rRNA and/or
<br>Glycyl-tRNA










ribosome maturation
synthetase containing










and assembly
cluster; <br>tRNA-











methylthiotransferase











containing cluster



fig|6666666.60966.peg.1915
CDS
1790629
1789619
−1
−
1011
Phosphate starvation-
-none-
D23_1c1921
Neut_1788








inducible ATPase PhoH











with RNA binding motif




fig|6666666.60966.peg.1916
CDS
1792022
1790691
−2
−
1332
tRNA-i(6)A37
Methylthiotransferases;
D23_1c1922
Neut_1789








methylthiotransferase
<br>tRNA-











methylthiotransferase











containing cluster;











<br>tRNA modification











Bacteria; <br>tRNA











processing



fig|6666666.60966.peg.1917
CDS
1793040
1792321
−3
−
720
Cytochrome c-type
-none-
D23_1c1923
Neut_1790








protein TorY




fig|6666666.60966.peg.1918
CDS
1793750
1793043
−2
−
708
Cytochrome c family
-none-
D23_1c1924
Neut_2333








protein




fig|6666666.60966.peg.1919
CDS
1794933
1793812
−3
−
1122
FIG00859557:
-none-
D23_1c1925
Neut_1792








hypothetical protein




fig|6666666.60966.peg.1920
CDS
1796642
1794930
−2
−
1713
Hydroxylamine
-none-
D23_1c1926
Neut_2335








oxidoreductase











precursor (EC 1.7.3.4)




fig|6666666.60966.peg.1921
CDS
1801076
1796862
−2
−
4215
DNA-directed RNA

Mycobacterium

D23_1c1927
Neut_1794








polymerase beta&#39;
virulence operon










subunit (EC 2.7.7.6)
involved in DNA











transcription; <br>RNA











polymerase bacterial



fig|6666666.60966.peg.1922
CDS
1805314
1801235
−1
−
4080
DNA-directed RNA

Mycobacterium

D23_1c1928
Neut_1795








polymerase beta
virulence operon










subunit (EC 2.7.7.6)
involved in DNA











transcription; <br>RNA











polymerase bacterial



fig|6666666.60966.peg.1923
CDS
1806051
1805680
−3
−
372
LSU ribosomal protein
LSU ribosomal proteins
D23_1c1929
Neut_1796








L7/L12 (P1/P2)
cluster



fig|6666666.60966.peg.1924
CDS
1806648
1806133
−3
−
516
LSU ribosomal protein
LSU ribosomal proteins
D23_1c1930
Neut_1797








L10p (P0)
cluster



fig|6666666.60966.peg.1925
CDS
1807793
1807098
−2
−
696
LSU ribosomal protein
LSU ribosomal proteins
D23_1c1931
Neut_1798








Lip (L10Ae)
cluster



fig|6666666.60966.peg.1926
CDS
1808121
1807795
−3
−
327
LSU ribosomal protein
LSU ribosomal proteins
D23_1c1932
Neut_1799








L11p (L12e)
cluster



fig|6666666.60966.peg.1927
CDS
1808877
1808344
−3
−
534
Transcription
LSU ribosomal proteins
D23_1c1934
Neut_1800








antitermination protein
cluster;










NusG
<br>Transcription











factors bacterial



fig|6666666.60966.peg.1928
CDS
1809240
1808896
−3
−
345
Preprotein translocase
LSU ribosomal proteins
D23_1c1935
Neut_1801








subunit SecE (TC
cluster










3.A.5.1.1)




fig|6666666.60966.peg.1929
CDS
1810674
1809484
−3
−
1191
Translation elongation

Mycobacterium

D23_1c1937
Neut_1802








factor Tu
virulence operon











involved in protein











synthesis (SSU ribosomal











proteins);











<br>Translation











elongation factors











bacterial; <br>Universal











GTPases



fig|6666666.60966.peg.1930
CDS
1813382
1811220
−2
−
2163
Type IV pilus biogenesis
-none-
D23_1c1941
Neut_1803

fig|6666666.60966.peg.1931
CDS
1813906
1813379
−1
−
528
Type IV pilus biogenesis
-none-
D23_1c1942
Neut_1804








protein PilP




fig|6666666.60966.peg.1932
CDS
1814553
1813903
−3
−
651
Type IV pilus biogenesis
-none-
D23_1c1943
Neut_1805








protein PilO




fig|6666666.60966.peg.1933
CDS
1815161
1814550
−2
−
612
Type IV pilus biogenesis
-none-
D23_1c1944
Neut_1806








protein PilN




fig|6666666.60966.peg.1934
CDS
1816207
1815158
−1
−
1050
Type IV pilus biogenesis
-none-
D23_1c1945
Neut_1807








protein PilM




fig|6666666.60966.peg.1936
CDS
1816441
1818753
1
+
2313
Multimodular
Peptidoglycan
D23_1c1947
Neut_1808








transpeptidase-
Biosynthesis










transglycosylase (EC











2.4.1.129) (EC 3.4.—.—)




fig|6666666.60966.peg.1937
CDS
1819961
1819041
−2
−
921
Deacetylases, including
-none-
D23_1c1948
Neut_1809








yeast histone











deacetylase and acetoin











utilization protein




fig|6666666.60966.peg.1939
CDS
1820319
1820170
−3
−
150
hypothetical protein
-none-
D23_1c1949
Neut_1810

fig|6666666.60966.peg.1941
CDS
1820799
1820638
−3
−
162
Addiction module
-none-
D23_1c1950
Neut_1811








antidote protein




fig|6666666.60966.peg.1942
CDS
1821096
1820914
−3
−
183
hypothetical protein
-none-
D23_1c1951
Neut_1812

fig|6666666.60966.peg.1943
CDS
1821848
1821985
2
+
138
Prevent host death
Phd-Doc, YdcE-YdcD
D23_1c1953
NA








protein, Phd antitoxin
toxin-antitoxin











(programmed cell death)











systems



fig|6666666.60966.peg.1944
CDS
1821982
1822278
1
+
297
Death on curing
Phd-Doc, YdcE-YdcD
D23_1c1954
NA








protein, Doc toxin
toxin-antitoxin











(programmed cell death)











systems



fig|6666666.60966.peg.1945
CDS
1822608
1822423
−3
−
186
hypothetical protein
-none-
D23_1c1955
Neut_1816

fig|6666666.60966.peg.1946
CDS
1822933
1822688
−1
−
246
hypothetical protein
-none-
D23_1c1956
Neut_1817

fig|6666666.60966.peg.1947
CDS
1823491
1823150
−1
−
342
Predicted
-none-
D23_1c1957
NA








transcriptional











regulator




fig|6666666.60966.peg.1948
CDS
1823708
1823484
−2
−
225
Phage-related protein
-none-
D23_1c1958
NA

fig|6666666.60966.peg.1952
CDS
1824892
1824704
−1
−
189
hypothetical protein
-none-
D23_1c1959
NA

fig|6666666.60966.peg.1953
CDS
1825371
1825036
−3
−
336
Mobile element protein
-none-
D23_1c1960
Neut_1624

fig|6666666.60966.peg.1954
CDS
1825828
1825352
−1
−
477
Mobile element protein
-none-
D23_1c1961
Neut_1888

fig|6666666.60966.peg.1955
CDS
1826127
1825942
−3
−
186
Mobile element protein
-none-
D23_1c1962
Neut_2500

fig|6666666.60966.peg.1956
CDS
1826660
1826472
−2
−
189
Mobile element protein
-none-
D23_1c1963
Neut_1821

fig|6666666.60966.peg.1958
CDS
1827279
1826920
−3
−
360
Flagellin protein FlaG
Flagellum
D23_1c1964
Neut_1822

fig|6666666.60966.peg.1959
CDS
1827931
1827644
−1
−
288
Excinuclease ABC, C
-none-
D23_1c1965
Neut_1823








subunit-like




fig|6666666.60966.peg.1960
CDS
1829557
1828115
−1
−
1443
Flagellin protein FlaB
Flagellum; <br>Flagellum
D23_1c1967
Neut_1824









in Campylobacter



fig|6666666.60966.peg.1961
CDS
1830108
1830230
3
+
123
hypothetical protein
-none-
D23_1c1968
NA

fig|6666666.60966.peg.1962
CDS
1831067
1830276
−2
−
792
Mobile element protein
-none-
D23_1c1969
Neut_1888

fig|6666666.60966.peg.1963
CDS
1831366
1831181
−1
−
186
Mobile element protein
-none-
D23_1c1970
Neut_2500

fig|6666666.60966.peg.1964
CDS
1831759
1831616
−1
−
144
hypothetical protein
-none-
D23_1c1971
NA

fig|6666666.60966.peg.1965
CDS
1832465
1831749
−2
−
717
hypothetical protein
-none-
D23_1c1972
Neut_1827

fig|6666666.60966.peg.1967
CDS
1835117
1833291
−2
−
1827
DNA mismatch repair
DNA repair, bacterial
D23_1c1973
Neut_1828








protein MutL
MutL-MutS system



fig|6666666.60966.peg.1968
CDS
1835287
1835946
1
+
660
Ribose 5-phosphate
Calvin-Benson cycle;
D23_1c1974
Neut_1829








isomerase A (EC 5.3.1.6)
<br>D-ribose utilization;











<br>Pentose phosphate











pathway



fig|6666666.60966.peg.1969
CDS
1836022
1836150
1
+
129
hypothetical protein
-none-
D23_1c1975
NA

fig|6666666.60966.peg.1970
CDS
1836140
1836859
2
+
720
Phosphate transport
High affinity phosphate
D23_1c1976
Neut_1830








system regulatory
transporter and control










protein PhoU
of PHO regulon;











<br>Phosphate











metabolism



fig|6666666.60966.peg.1971
CDS
1836819
1838420
3
+
1602
Exopolyphosphatase
Phosphate metabolism;
D23_1c1977
Neut_1831








(EC 3.6.1.11)
<br>Polyphosphate



fig|6666666.60966.peg.1972
CDS
1838878
1838429
−1
−
450
Type IV pilus biogenesis
-none-
D23_1c1978
Neut_1832








protein PilE




fig|6666666.60966.peg.1973
CDS
1842290
1838922
−2
−
3369
Type IV fimbrial
-none-
D23_1c1979
Neut_1833








biogenesis protein PilY1




fig|6666666.60966.peg.1974
CDS
1843213
1842362
−1
−
852
Type IV fimbrial
-none-
D23_1c1980
Neut_1834








biogenesis protein PilX




fig|6666666.60966.peg.1975
CDS
1844303
1843239
−2
−
1065
Type IV fimbrial
-none-
D23_1c1981
Neut_1835








biogenesis protein PilW




fig|6666666.60966.peg.1976
CDS
1844806
1844321
−1
−
486
Type IV fimbrial
-none-
D23_1c1982
Neut_1836








biogenesis protein PilV




fig|6666666.60966.peg.1977
CDS
1845339
1844830
−3
−
510
Type IV fimbrial
-none-
D23_1c1983
Neut_1837








biogenesis protein FimT




fig|6666666.60966.peg.1978
CDS
1845616
1845783
1
+
168
hypothetical protein
-none-
D23_1c1984
NA

fig|6666666.60966.peg.1979
CDS
1846400
1845768
−2
−
633
DNA-binding response
-none-
D23_1c1985
Neut_1839








regulator, LuxR family




fig|6666666.60966.peg.1980
CDS
1847948
1846452
−2
−
1497
Sensory box histidine
-none-
D23_1c1986
Neut_1840








kinase/response











regulator




fig|6666666.60966.peg.1981
CDS
1848084
1848206
3
+
123
hypothetical protein
-none-
D23_1c1987
NA

fig|6666666.60966.peg.1982
CDS
1850161
1848614
−1
−
1548
pilin glycosylation
-none-
D23_1c1988
Neut_1841








enzyme, putative




fig|6666666.60966.peg.1985
CDS
1852587
1850815
−3
−
1773
Gamma-
Glutathione:
D23_1c1989
Neut_1843








glutamyltranspeptidase
Biosynthesis and










(EC 2.3.2.2)
gamma-glutamyl cycle



fig|6666666.60966.peg.1986
CDS
1853865
1852903
−3
−
963
Mobile element protein
-none-
D23_1c1990
Neut_1746

fig|6666666.60966.peg.1987
CDS
1854432
1853923
−3
−
510
putative
-none-
D23_1c1991
Neut_1845








transmembrane protein




fig|6666666.60966.peg.1988
CDS
1855175
1854606
−2
−
570
hypothetical protein
-none-
D23_1c1992
Neut_1849

fig|6666666.60966.peg.1989
CDS
1855822
1855421
−1
−
402
Glyoxalase family protein
-none-
D23_1c1993
Neut_1850

fig|6666666.60966.peg.1990
CDS
1855948
1855835
−1
−
114
hypothetical protein
-none-
D23_1c1994
NA

fig|6666666.60966.peg.1991
CDS
1856595
1856026
−3
−
570
hypothetical protein
-none-
D23_1c1995
Neut_1851

fig|6666666.60966.peg.1992
CDS
1856572
1856703
1
+
132
hypothetical protein
-none-
D23_1c1996
NA

fig|6666666.60966.peg.1993
CDS
1858627
1856756
−1
−
1872
hypothetical protein
-none-
D23_1c1997
Neut_1853

fig|6666666.60966.peg.1994
CDS
1860549
1858642
−3
−
1908
hypothetical protein
-none-
D23_1c1998
Neut_1854

fig|6666666.60966.peg.1995
CDS
1860536
1860667
2
+
132
hypothetical protein
-none-
D23_1c1999
NA

fig|6666666.60966.peg.1996
CDS
1861687
1860761
−1
−
927
Expressed protein
-none-
D23_1c2000
Neut_1857








precursor




fig|6666666.60966.peg.1997
CDS
1862145
1861684
−3
−
462
hypothetical protein
-none-
D23_1c2001
Neut_1858

fig|6666666.60966.peg.1998
CDS
1865471
1862334
−2
−
3138
Proline dehydrogenase
Proline, 4-
D23_1c2002
Neut_1859








(EC 1.5.99.8) (Proline
hydroxyproline uptake










oxidase)/Delta-1-
and utilization;










pyrroline-5-carboxylate
<br>Respiratory










dehydrogenase (EC
dehydrogenases 1










1.5.1.12)




fig|6666666.60966.peg.2000
CDS
1865859
1865701
−3
−
159
hypothetical protein
-none-
D23_1c2003
Neut_1860

fig|6666666.60966.peg.2001
CDS
1866618
1866328
−3
−
291
hypothetical protein
-none-
D23_1c2004
NA

fig|6666666.60966.peg.2002
CDS
1866574
1866861
1
+
288
Probable
-none-
D23_1c2005
Neut_1861








transmembrane protein




fig|6666666.60966.peg.2004
CDS
1867176
1867955
3
+
780
hypothetical protein
-none-
D23_1c2006
Neut_1863

fig|6666666.60966.peg.2005
CDS
1870128
1868077
−3
−
2052
Serine peptidase
-none-
D23_1c2007
Neut_1864

fig|6666666.60966.peg.2006
CDS
1870373
1870546
2
+
174
hypothetical protein
-none-
D23_1c2008
NA

fig|6666666.60966.peg.2007
CDS
1871555
1870827
−2
−
729
1-acyl-sn-glycerol-3-
Glycerolipid and
D23_1c2009
Neut_1866








phosphate
Glycerophospholipid










acyltransferase (EC
Metabolism in Bacteria










2.3.1.51)




fig|6666666.60966.peg.2008
CDS
1872097
1871555
−1
−
543
Histidinol-phosphatase
Histidine Biosynthesis
D23_1c2010
Neut_1867








(EC 3.1.3.15)




fig|6666666.60966.peg.2009
CDS
1874271
1872124
−3
−
2148
Glycyl-tRNA synthetase
Glycyl-tRNA synthetase;
D23_1c2011
Neut_1868








beta chain (EC 6.1.1.14)
<br>Glycyl-tRNA











synthetase containing











cluster; <br>tRNA











aminoacylation, Gly



fig|6666666.60966.peg.2010
CDS
1875191
1874268
−2
−
924
Glycyl-tRNA synthetase
Glycyl-tRNA synthetase;
D23_1c2012
Neut_1869








alpha chain (EC
<br>Glycyl-tRNA










6.1.1.14)
synthetase containing











cluster; <br>tRNA











aminoacylation, Gly



fig|6666666.60966.peg.2011
CDS
1876717
1875224
−1
−
1494
Apolipoprotein N-
Copper homeostasis:
D23_1c2013
Neut_1870








acyltransferase (EC
copper tolerance;










2.3.1.—)/Copper
<br>Lipoprotein










homeostasis protein
Biosynthesis; <br>tRNA-










CutE
methylthiotransferase











containing cluster;











<br>tRNA-











methylthiotransferase











containing cluster



fig|6666666.60966.peg.2012
CDS
1877111
1876773
−2
−
339
FIG00859587:
-none-
D23_1c2014
Neut_1871








hypothetical protein




fig|6666666.60966.peg.2013
CDS
1877265
1877122
−3
−
144
hypothetical protein
-none-
D23_1c2015
NA

fig|6666666.60966.peg.2014
CDS
1877596
1879305
1
+
1710
Multicopper oxidase
Copper homeostasis
D23_1c2016
Neut_1872

fig|6666666.60966.peg.2015
CDS
1879305
1880399
3
+
1095
Zinc ABC transporter,
-none-
D23_1c2017
Neut_1873








periplasmic-binding











protein ZnuA




fig|6666666.60966.peg.2016
CDS
1881044
1880847
−2
−
198
hypothetical protein
-none-
D23_1c2018
NA

fig|6666666.60966.peg.2017
CDS
1881486
1881962
3
+
477
Cytochrome c oxidase
Terminal cytochrome C
D23_1c2020
Neut_1874








(B(O/a)3-type) chain II
oxidases










(EC 1.9.3.1)




fig|6666666.60966.peg.2018
CDS
1882000
1883478
1
+
1479
Cytochrome c oxidase
Terminal cytochrome C
D23_1c2021
Neut_1875








(B(O/a)3-type) chain I
oxidases










(EC 1.9.3.1)




fig|6666666.60966.peg.2019
CDS
1883574
1884203
3
+
630
Cytochrome oxidase
Biogenesis of
D23_1c2022
Neut_1876








biogenesis protein
cytochrome c oxidases










Sco1/SenC/PrrC,











putative copper











metallochaperone




fig|6666666.60966.peg.2020
CDS
1884187
1884756
1
+
570
hypothetical
-none-
D23_1c2023
Neut_1877








cytochrome oxidase











associated membrane











protein




fig|6666666.60966.peg.2021
CDS
1885726
1884809
−1
−
918
Nitrite transporter from
-none-
D23_1c2024
Neut_1878








formate/nitrite family




fig|6666666.60966.peg.2022
CDS
1887084
1886077
−3
−
1008
UDP-glucose 4-
CBSS-
D23_1c2026
Neut_1879








epimerase (EC 5.1.3.2)
296591.1.peg.2330;











<br>N-linked











Glycosylation in











Bacteria; <br>Rhamnose











containing glycans



fig|6666666.60966.peg.2023
CDS
1888047
1887160
−3
−
888
Glucose-1-phosphate
Rhamnose containing
D23_1c2027
Neut_1880








thymidylyltransferase
glycans; <br>dTDP-










(EC 2.7.7.24)
rhamnose synthesis



fig|6666666.60966.peg.2024
CDS
1888279
1888148
−1
−
132
hypothetical protein
-none-
D23_1c2028
NA

fig|6666666.60966.peg.2025
CDS
1888278
1889198
3
+
921
2-hydroxy-3-
Glycerate metabolism;
D23_1c2029
Neut_1881








oxopropionate
<br>Photorespiration










reductase (EC 1.1.1.60)
(oxidative C2 cycle)



fig|6666666.60966.peg.2026
CDS
1889188
1890642
1
+
1455
Glycolate
Glycolate, glyoxylate
D23_1c2030
Neut_1882








dehydrogenase (EC
interconversions;










1.1.99.14), subunit GlcD
<br>Photorespiration











(oxidative C2 cycle)



fig|6666666.60966.peg.2027
CDS
1890667
1891767
1
+
1101
Glycolate
Glycolate, glyoxylate
D23_1c2031
Neut_1883








dehydrogenase (EC
interconversions;










1.1.99.14), FAD-binding
<br>Photorespiration










subunit GlcE
(oxidative C2 cycle)



fig|6666666.60966.peg.2028
CDS
1891771
1893039
1
+
1269
Glycolate
Glycolate, glyoxylate
D23_1c2032
Neut_1884








dehydrogenase (EC
interconversions;










1.1.99.14), iron-sulfur
<br>Photorespiration










subunit GlcF
(oxidative C2 cycle)



fig|6666666.60966.peg.2029
CDS
1893781
1893065
−1
−
717
Putative predicted
Restriction-Modification
D23_1c2033
Neut_1885








metal-dependent
System










hydrolase




fig|6666666.60966.peg.2030
CDS
1894582
1893806
−1
−
777
5&#39;-
Adenosyl nucleosidases;
D23_1c2034
Neut_1886








methylthioadenosine
<br>Adenosyl










nucleosidase (EC
nucleosidases;










3.2.2.16)/S-
<br>CBSS-










adenosylhomocysteine
320388.3.peg.3759;










nucleosidase (EC
<br>CBSS-










3.2.2.9)
320388.3.peg.3759;











<br>Methionine











Biosynthesis;











<br>Methionine











Degradation;











<br>Polyamine











Metabolism



fig|6666666.60966.peg.2031
CDS
1896116
1894656
−2
−
1461
Exodeoxyribonuclease I
DNA Repair Base
D23_1c2035
Neut_1887








(EC 3.1.11.1)
Excision



fig|6666666.60966.peg.2032
CDS
1896438
1897133
3
+
696
FIG00657740:
-none-
D23_1c2036
Neut_1890








hypothetical protein




fig|6666666.60966.peg.2033
CDS
1898282
1897428
−2
−
855
5,10-
5-FCL-like protein;
D23_1c2038
Neut_1891








methylenetetrahydrofolate
<br>Methionine










reductase (EC
Biosynthesis; <br>One-










1.5.1.20)
carbon metabolism by











tetrahydropterines



fig|6666666.60966.peg.2034
CDS
1898327
1898494
2
+
168
hypothetical protein
-none-
D23_1c2039
NA

fig|6666666.60966.peg.2035
CDS
1899999
1898563
−3
−
1437
Adenosylhomocysteinase
Methionine
D23_1c2041
Neut_1892








(EC 3.3.1.1)
Biosynthesis;











<br>Methionine











Degradation



fig|6666666.60966.peg.2036
CDS
1901244
1900135
−3
−
1110
S-adenosylmethionine
Methionine
D23_1c2042
Neut_1893








synthetase (EC 2.5.1.6)
Biosynthesis;











<br>Methionine











Degradation



fig|6666666.60966.peg.2037
CDS
1901543
1902289
2
+
747
Short chain
-none-
D23_1c2043
Neut_1894








dehydrogenase




fig|6666666.60966.peg.2038
CDS
1902336
1902812
3
+
477
ATPase YjeE, predicted
-none-
D23_1c2044
Neut_1895








to have essential role in











cell wall biosynthesis




fig|6666666.60966.peg.2039
CDS
1903046
1904116
2
+
1071
N-acetylmuramoyl-L-
Murein Hydrolases;
D23_1c2045
Neut_1896








alanine amidase (EC
<br>Recycling of










3.5.1.28)
Peptidoglycan Amino











Acids; <br>Zinc











regulated enzymes



fig|6666666.60966.peg.2040
CDS
1904922
1904170
−3
−
753
FIG00859340:
-none-
D23_1c2046
Neut_1897








hypothetical protein




fig|6666666.60966.peg.2041
CDS
1905860
1904919
−2
−
942
Ribosomal protein L11
Heat shock dnaK gene
D23_1c2047
Neut_1898








methyltransferase (EC
cluster extended;










2.1.1.—)
<br>Ribosome











biogenesis bacterial



fig|6666666.60966.peg.2042
CDS
1907254
1905896
−1
−
1359
Biotin carboxylase of
Fatty Acid Biosynthesis
D23_1c2048
Neut_1899








acetyl-CoA carboxylase
FASII










(EC 6.3.4.14)




fig|6666666.60966.peg.2043
CDS
1907784
1907326
−3
−
459
Biotin carboxyl carrier
Fatty Acid Biosynthesis
D23_1c2049
Neut_1900








protein of acetyl-CoA
FASII










carboxylase




fig|6666666.60966.peg.2045
CDS
1908294
1907989
−3
−
306
3-dehydroquinate
Chorismate Synthesis;
D23_1c2050
Neut_1901








dehydratase II (EC
<br>Common Pathway










4.2.1.10)
For Synthesis of











Aromatic Compounds











(DAHP synthase to











chorismate);











<br>Quinate











degradation



fig|6666666.60966.peg.2047
CDS
1908606
1909715
3
+
1110
Glycine oxidase ThiO
Thiamin biosynthesis
D23_1c2051
Neut_1902








(EC 1.4.3.19)




fig|6666666.60966.peg.2048
CDS
1910693
1909722
−2
−
972
4-hydroxy-3-methylbut-
Isoprenoid Biosynthesis;
D23_1c2052
Neut_1903








2-enyl diphosphate
<br>Nonmevalonate










reductase (EC 1.17.1.2)
Branch of Isoprenoid











Biosynthesis



fig|6666666.60966.peg.2049
CDS
1910983
1911267
1
+
285
FIG00858797:
-none-
D23_1c2053
Neut_1904








hypothetical protein




fig|6666666.60966.peg.2050
CDS
1911307
1912386
1
+
1080
Histidinol-phosphate
Histidine Biosynthesis
D23_1c2054
Neut_1905








aminotransferase (EC











2.6.1.9)




fig|6666666.60966.peg.2051
CDS
1912429
1913016
1
+
588
Imidazoleglycerol-
Histidine Biosynthesis
D23_1c2055
Neut_1906








phosphate dehydratase











(EC 4.2.1.19)




fig|6666666.60966.peg.2052
CDS
1913079
1913687
3
+
609
Imidazole glycerol
Histidine Biosynthesis
D23_1c2056
Neut_1907








phosphate synthase











amidotransferase











subunit (EC 2.4.2.—)




fig|6666666.60966.peg.2053
CDS
1913772
1914518
3
+
747
Phosphoribosylformimino-
Chorismate:
D23_1c2057
Neut_1908








5-aminoimidazole
Intermediate for










carboxamide ribotide
synthesis of Tryptophan,










isomerase (EC 5.3.1.16)
PAPA antibiotics, PABA,











3-hydroxyanthranilate











and more.; <br>Histidine











Biosynthesis



fig|6666666.60966.peg.2054
CDS
1914604
1915380
1
+
777
Imidazole glycerol
Histidine Biosynthesis
D23_1c2058
Neut_1909








phosphate synthase











cyclase subunit (EC











4.1.3.—)




fig|6666666.60966.peg.2055
CDS
1915424
1915909
2
+
486
Phosphoribosyl-AMP
Histidine Biosynthesis;
D23_1c2059
Neut_1910








cyclohydrolase (EC
<br>Zinc regulated










3.5.4.19)
enzymes



fig|6666666.60966.peg.2056
CDS
1915906
1916259
1
+
354
Phosphoribosyl-ATP
Histidine Biosynthesis;
D23_1c2060
Neut_1911








pyrophosphatase (EC
<br>Riboflavin synthesis










3.6.1.31)
cluster



fig|6666666.60966.peg.2057
CDS
1916261
1916611
2
+
351
FIG146285:
-none-
D23_1c2061
Neut_1912








Diadenosine











tetraphosphate (Ap4A)











hydrolase and other HIT











family hydrolases




fig|6666666.60966.peg.2058
CDS
1916631
1916864
3
+
234
Twin-arginine
Cluster-based Subsystem
D23_1c2062
Neut_1913








translocation protein
Grouping Hypotheticals-










TatA
perhaps Proteosome











Related; <br>Twin-











arginine translocation











system



fig|6666666.60966.peg.2060
CDS
1916950
1917342
1
+
393
Twin-arginine
Twin-arginine
D23_1c2063
Neut_1914








translocation protein
translocation system










TatB




fig|6666666.60966.peg.2061
CDS
1917433
1918209
1
+
777
Twin-arginine
Cluster-based Subsystem
D23_1c2064
Neut_1915








translocation protein
Grouping Hypotheticals-










TatC
perhaps Proteosome











Related; <br>Twin-











arginine translocation











system



fig|6666666.60966.peg.2062
CDS
1918395
1920518
3
+
2124
Outer membrane
-none-
D23_1c2065
Neut_1916








vitamin B12 receptor











BtuB




fig|6666666.60966.peg.2063
CDS
1920528
1921118
3
+
591
Optional hypothetical
-none-
D23_1c2066
Neut_1917








component of the B12











transporter BtuM




fig|6666666.60966.peg.2064
CDS
1921118
1921726
2
+
609
Cob(I)alamin
-none-
D23_1c2067
Neut_1918








adenosyltransferase (EC











2.5.1.17)




fig|6666666.60966.peg.2065
CDS
1922713
1922826
1
+
114
hypothetical protein
-none-
D23_1c2069
NA

fig|6666666.60966.peg.2067
CDS
1923447
1924253
3
+
807
Cytochrome bd-type
-none-
D23_1c2070
Neut_1920








quinol oxidase, subunit 1




fig|6666666.60966.peg.2068
CDS
1926393
1924288
−3
−
2106
Methionyl-tRNA
Scaffold proteins for
D23_1c2071
Neut_1921








synthetase (EC 6.1.1.10)
[4Fe—4S] cluster











assembly (MRP family);











<br>tRNA











aminoacylation, Met



fig|6666666.60966.peg.2069
CDS
1926506
1926390
−2
−
117
hypothetical protein
-none-
D23_1c2072
NA

fig|6666666.60966.peg.2070
CDS
1926499
1927584
1
+
1086
Scaffold protein for
Scaffold proteins for
D23_1c2073
Neut_1922








[4Fe—4S] cluster
[4Fe—4S] cluster










assembly ApbC, MRP-
assembly (MRP family)










like




fig|6666666.60966.peg.2071
CDS
1927630
1928163
1
+
534
Deoxycytidine
pyrimidine conversions
D23_1c2074
Neut_1923








triphosphate deaminase











(EC 3.5.4.13)




fig|6666666.60966.peg.2072
CDS
1928619
1928251
−3
−
369
COGs COG1917
-none-
D23_1c2075
Neut_1924

fig|6666666.60966.peg.2073
CDS
1929401
1928631
−2
−
771
Inner membrane
-none-
D23_1c2076
Neut_1925








protein




fig|6666666.60966.peg.2074
CDS
1929596
1929889
2
+
294
Mobile element protein
-none-
D23_1c2077
Neut_1719

fig|6666666.60966.peg.2075
CDS
1929988
1930866
1
+
879
Mobile element protein
-none-
D23_1c2078
Neut_1720

fig|6666666.60966.peg.2076
CDS
1930961
1933699
2
+
2739
Ca ion P-type ATPase
-none-
D23_1c2079
Neut_1926

fig|6666666.60966.peg.2078
CDS
1934003
1934323
2
+
321
hypothetical protein
-none-
D23_1c2080
Neut_1927

fig|6666666.60966.peg.2079
CDS
1935608
1934517
−2
−
1092
Prophage Lp2 protein 6
-none-
D23_1c2081
Neut_1928

fig|6666666.60966.peg.2081
CDS
1935893
1936396
2
+
504
ABC transporter ATP-
-none-
D23_1c2083
Neut_1936








binding protein YvcR




fig|6666666.60966.peg.2083
CDS
1936587
1936880
3
+
294
Mobile element protein
-none-
D23_1c2085
Neut_1719

fig|6666666.60966.peg.2084
CDS
1936979
1937857
2
+
879
Mobile element protein
-none-
D23_1c2086
Neut_1720

fig|6666666.60966.peg.2085
CDS
1938082
1937936
−1
−
147
hypothetical protein
-none-
D23_1c2087
Neut_1937

fig|6666666.60966.peg.2086
CDS
1938637
1938188
−1
−
450
Ferric uptake regulation
Bacterial RNA-
D23_1c2088
Neut_1938








protein FUR
metabolizing Zn-











dependent hydrolases;











<br>Oxidative stress



fig|6666666.60966.peg.2087
CDS
1938848
1939330
2
+
483
Outer membrane
Lipopolysaccharide
D23_1c2089
Neut_1939








lipoprotein SmpA, a
assembly










component of the











essential YaeT outer-











membrane protein











assembly complex




fig|6666666.60966.peg.2088
CDS
1939327
1940133
1
+
807
Dihydrodipicolinate
-none-
D23_1c2090
Neut_1940








reductase (EC 1.3.1.26)




fig|6666666.60966.peg.2089
CDS
1941855
1940347
−3
−
1509
ATPase
-none-
D23_1c2091
Neut_1941

fig|6666666.60966.peg.2090
CDS
1942209
1942087
−3
−
123
hypothetical protein
-none-
D23_1c2092
NA

fig|6666666.60966.peg.2091
CDS
1942220
1942459
2
+
240
Type I restriction-
Restriction-Modification
D23_1c2093
Neut_1942








modification system,
System; <br>Type I










DNA-methyltransferase
Restriction-Modification










subunit M (EC 2.1.1.72)




fig|6666666.60966.peg.2092
CDS
1942456
1942860
1
+
405
Cell filamentation
-none-
D23_1c2094
Neut_1943








protein fic




fig|6666666.60966.peg.2093
CDS
1942823
1943278
2
+
456
Mobile element protein
-none-
D23_1c2095
Neut_2502

fig|6666666.60966.peg.2094
CDS
1943305
1944786
1
+
1482
Outer membrane
-none-
D23_1c2096
Neut_1945








component of tripartite











multidrug resistance











system




fig|6666666.60966.peg.2095
CDS
1944830
1946014
2
+
1185
Membrane fusion
Multidrug Resistance
D23_1c2097
Neut_1946








protein of RND family
Efflux Pumps










multidrug efflux pump




fig|6666666.60966.peg.2096
CDS
1946018
1949131
2
+
3114
RND efflux system,
Multidrug Resistance
D23_1c2098
Neut_1947








inner membrane
Efflux Pumps










transporter CmeB




fig|6666666.60966.peg.2097
CDS
1949252
1949386
2
+
135
Type I restriction-
Restriction-Modification
D23_1c2099
NA








modification system,
System; <br>Type I










restriction subunit R (EC
Restriction-Modification










3.1.21.3)




fig|6666666.60966.peg.2098
CDS
1949446
1950246
1
+
801
Bis(5&#39;-nucleosyl)-
EC49-61
D23_1c2100
Neut_1949








tetraphosphatase,











symmetrical (EC











3.6.1.41)




fig|6666666.60966.peg.2099
CDS
1951009
1950200
−1
−
810
1-acyl-sn-glycerol-3-
Glycerolipid and
D23_1c2101
Neut_1950








phosphate
Glycerophospholipid










acyltransferase (EC
Metabolism in Bacteria










2.3.1.51)




fig|6666666.60966.peg.2100
CDS
1952008
1951073
−1
−
936
InterPro IPR002173
-none-
D23_1c2103
Neut_1951








COGs COG0524




fig|6666666.60966.peg.2101
CDS
1953491
1952040
−2
−
1452
Glycine dehydrogenase
Glycine and Serine
D23_1c2104
Neut_1952








[decarboxylating]
Utilization; <br>Glycine










(glycine cleavage
cleavage system;










system P2 protein) (EC
<br>Photorespiration










1.4.4.2)
(oxidative C2 cycle)



fig|6666666.60966.peg.2102
CDS
1954921
1953566
−1
−
1356
Glycine dehydrogenase
Glycine and Serine
D23_1c2105
Neut_1953








[decarboxylating]
Utilization; <br>Glycine










(glycine cleavage
cleavage system;










system P1 protein) (EC
<br>Photorespiration










1.4.4.2)
(oxidative C2 cycle)



fig|6666666.60966.peg.2103
CDS
1955520
1955131
−3
−
390
Glycine cleavage system
Glycine and Serine
D23_1c2106
Neut_1954








H protein
Utilization; <br>Glycine











cleavage system;











<br>Photorespiration











(oxidative C2 cycle)



fig|6666666.60966.peg.2104
CDS
1956682
1955591
−1
−
1092
Aminomethyltransferase
CBSS-87626.3.peg.3639;
D23_1c2107
Neut_1955








(glycine cleavage
<br>Glycine and Serine










system T protein) (EC
Utilization; <br>Glycine










2.1.2.10)
cleavage system;











<br>Photorespiration











(oxidative C2 cycle)



fig|6666666.60966.peg.2106
CDS
1957270
1957133
−1
−
138
hypothetical protein
-none-
D23_1c2108
NA

fig|6666666.60966.peg.2107
CDS
1958337
1957420
−3
−
918
Coproporphyrinogen III
Heme and Siroheme
D23_1c2109
Neut_1956








oxidase, aerobic (EC
Biosynthesis










1.3.3.3)




fig|6666666.60966.peg.2108
CDS
1958499
1959671
3
+
1173
Chorismate synthase
Chorismate Synthesis;
D23_1c2110
Neut_1957








(EC 4.2.3.5)
<br>Common Pathway











For Synthesis of











Aromatic Compounds











(DAHP synthase to











chorismate)



fig|6666666.60966.peg.2110
CDS
1960360
1961133
1
+
774
IncF plasmid
-none-
D23_1c2111
Neut_1959








conjugative transfer











surface exclusion











protein TraT




fig|6666666.60966.peg.2111
CDS
1961191
1961517
1
+
327
hypothetical protein
-none-
D23_1c2112
NA

fig|6666666.60966.peg.2112
CDS
1961582
1962544
2
+
963
Mobile element protein
-none-
D23_1c2114
Neut_1862

fig|6666666.60966.peg.2113
CDS
1962848
1962729
−2
−
120
hypothetical protein
-none-
D23_1c2115
NA

fig|6666666.60966.peg.2115
CDS
1965546
1963441
−3
−
2106
Ferrichrome-iron
-none-
D23_1c2116
Neut_1962








receptor




fig|6666666.60966.peg.2118
CDS
1967221
1966565
−1
−
657
Protein of unknown
-none-
D23_1c2119
Neut_1964








function DUF208




fig|6666666.60966.peg.2119
CDS
1967389
1968672
1
+
1284
FIG00858634:
-none-
D23_1c2120
Neut_1965








hypothetical protein




fig|6666666.60966.peg.2120
CDS
1968691
1969206
1
+
516
FIG00859317:
-none-
D23_1c2121
Neut_1966








hypothetical protein




fig|6666666.60966.peg.2121
CDS
1969209
1969910
3
+
702
InterPro IPR000179
-none-
D23_1c2122
Neut_1967








COGs COG1423




fig|6666666.60966.peg.2122
CDS
1969960
1970334
1
+
375
InterPro IPR003807
-none-
D23_1c2123
Neut_1968








COGs COG2149




fig|6666666.60966.peg.2123
CDS
1971838
1970381
−1
−
1458
Catalase (EC 1.11.1.6)
Oxidative stress;
D23_1c2124
Neut_1969









<br>Photorespiration











(oxidative C2 cycle);











<br>Protection from











Reactive Oxygen Species



fig|6666666.60966.peg.2124
CDS
1973211
1971865
−3
−
1347
FIG00858984:
-none-
D23_1c2125
Neut_1970








hypothetical protein




fig|6666666.60966.peg.2125
CDS
1974046
1973246
−1
−
801
Protein of unknown
-none-
D23_1c2126
Neut_1971








function DUF81




fig|6666666.60966.peg.2126
CDS
1974579
1974124
−3
−
456
Protein of unknown
-none-
D23_1c2127
Neut_1972








function DUF55




fig|6666666.60966.peg.2127
CDS
1976514
1974985
−3
−
1530
Capsular polysaccharide
Capsular Polysaccharides
D23_1c2128
NA








biosynthesis protein
Biosynthesis and










WcbQ
Assembly



fig|6666666.60966.peg.2128
CDS
1977322
1976504
−1
−
819
Oxidoreductase, short-
Capsular Polysaccharides
D23_1c2129
Neut_1974








chain
Biosynthesis and










dehydrogenase/reductase
Assembly










family (EC 1.1.1.—)




fig|6666666.60966.peg.2129
CDS
1978801
1977323
−1
−
1479
Glycosyltransferase
-none-
D23_1c2130
Neut_1975

fig|6666666.60966.peg.2130
CDS
1979888
1978803
−2
−
1086
possible spore protein
-none-
D23_1c2131
Neut_1976








[UI:20467420]




fig|6666666.60966.peg.2131
CDS
1981090
1979921
−1
−
1170
FIG00858788:
-none-
D23_1c2132
Neut_1977








hypothetical protein




fig|6666666.60966.peg.2132
CDS
1982214
1981231
−3
−
984
hypothetical protein
-none-
D23_1c2133
NA

fig|6666666.60966.peg.2133
CDS
1982778
1982218
−3
−
561
hypothetical protein
-none-
D23_1c2134
NA

fig|6666666.60966.peg.2134
CDS
1983862
1982783
−1
−
1080
Glycosyltransferase (EC
-none-
D23_1c2135
Neut_1982








2.4.1.—)




fig|6666666.60966.peg.2135
CDS
1984198
1983896
−1
−
303
hypothetical protein
-none-
D23_1c2136
Neut_1983

fig|6666666.60966.peg.2136
CDS
1984883
1984704
−2
−
180
Mobile element protein
-none-
D23_1c2137
Neut_1984

fig|6666666.60966.peg.2137
CDS
1985076
1984852
−3
−
225
hypothetical protein
-none-
D23_1c2138
NA

fig|6666666.60966.peg.2139
CDS
1985629
1986384
1
+
756
hypothetical protein
-none-
D23_1c2139
Neut_1985

fig|6666666.60966.peg.2140
CDS
1987287
1988645
3
+
1359
FIG00860556:
-none-
D23_1c2140
Neut_1986








hypothetical protein




fig|6666666.60966.peg.2141
CDS
1988761
1989375
1
+
615
Cytochrome oxidase
Biogenesis of
D23_1c2141
Neut_1987








biogenesis protein
cytochrome c oxidases










Sco1/SenC/PrrC,











putative copper











metallochaperone




fig|6666666.60966.peg.2142
CDS
1989381
1990007
3
+
627
FIG00859788:
-none-
D23_1c2142
Neut_1988








hypothetical protein




fig|6666666.60966.peg.2145
CDS
1990866
1990588
−3
−
279
hypothetical membrane
-none-
D23_1c2144
Neut_1990








protein




fig|6666666.60966.peg.2146
CDS
1991501
1991046
−2
−
456
InterPro IPR000485
-none-
D23_1c2145
Neut_1991

fig|6666666.60966.peg.2147
CDS
1993914
1991785
−3
−
2130
Phosphate
Fermentations: Lactate;
D23_1c2146
Neut_1995








acetyltransferase (EC
<br>Pyruvate










2.3.1.8)
metabolism II: acetyl-











CoA, acetogenesis from











pyruvate



fig|6666666.60966.peg.2148
CDS
1995278
1994253
−2
−
1026
Fructose-bisphosphate
Calvin-Benson cycle;
D23_1c2147
Neut_1996








aldolase class I (EC
<br>Glycolysis and










4.1.2.13)
Gluconeogenesis



fig|6666666.60966.peg.2150
CDS
1995705
1995851
3
+
147
hypothetical protein
-none-
D23_1c2148
NA

fig|6666666.60966.peg.2152
CDS
1995966
1996298
3
+
333
DNA-binding protein
-none-
D23_1c2150
Neut_1998

fig|6666666.60966.peg.2154
CDS
1996639
1996932
1
+
294
protein of unknown
-none-
D23_1c2151
Neut_1999








function DUF497




fig|6666666.60966.peg.2155
CDS
1996922
1997203
2
+
282
hypothetical protein
-none-
D23_1c2152
Neut_2000

fig|6666666.60966.peg.2156
CDS
1997890
1998093
1
+
204
Mobile element protein
-none-
D23_1c2154
NA

fig|6666666.60966.peg.2157
CDS
1998565
1998266
−1
−
300
VapC toxin protein
Toxin-antitoxin replicon
D23_1c2155
NA









stabilization systems



fig|6666666.60966.peg.2158
CDS
1998899
1998666
−2
−
234
VapB protein (antitoxin
Toxin-antitoxin replicon
D23_1c2156
NA








to VapC)
stabilization systems



fig|6666666.60966.peg.2159
CDS
1999186
1999344
1
+
159
hypothetical protein
-none-
D23_1c2157
NA

fig|6666666.60966.peg.2160
CDS
1999629
1999339
−3
−
291
transcriptional
-none-
D23_1c2158
NA








regulator, XRE family




fig|6666666.60966.peg.2161
CDS
1999997
1999692
−2
−
306
Phage-related protein
-none-
D23_1c2159
NA

fig|6666666.60966.peg.2162
CDS
2000147
2000022
−2
−
126
hypothetical protein
-none-
D23_1c2160
NA

fig|6666666.60966.peg.2163
CDS
2000220
2000486
3
+
267
Mobile element protein
-none-
D23_1c2161
NA

fig|6666666.60966.peg.2164
CDS
2000507
2000995
2
+
489
Mobile element protein
-none-
D23_1c2162
NA

fig|6666666.60966.peg.2165
CDS
2001470
2000997
−2
−
474
Mobile element protein
-none-
D23_1c2163
Neut_1256

fig|6666666.60966.peg.2166
CDS
2001936
2001544
−3
−
393
hypothetical protein
-none-
D23_1c2164
Neut_2449

fig|6666666.60966.peg.2167
CDS
2002011
2002328
3
+
318
Mobile element protein
-none-
D23_1c2165
NA

fig|6666666.60966.peg.2168
CDS
2003529
2002369
−3
−
1161
CDP-4-dehydro-6-
-none-
D23_1c2166
NA








deoxy-D-glucose 3-











dehydratase (EC 4.2.1.—)




fig|6666666.60966.peg.2169
CDS
2004426
2003539
−3
−
888
NAD-dependent
CBSS-296591.1.peg.2330
D23_1c2167
NA








epimerase/dehydratase











family protein




fig|6666666.60966.peg.2170
CDS
2005586
2004468
−2
−
1119
GDP-mannose 4,6-
-none-
D23_1c2168
Neut_0156








dehydratase (EC











4.2.1.47)




fig|6666666.60966.peg.2171
CDS
2007467
2005632
−2
−
1836
hypothetical protein
-none-
D23_1c2169
NA

fig|6666666.60966.peg.2172
CDS
2010568
2007473
−1
−
3096
Minor teichoic acid
-none-
D23_1c2170
NA








biosynthesis protein











GgaB




fig|6666666.60966.peg.2173
CDS
2012163
2010694
−3
−
1470
InterPro IPR001173
-none-
D23_1c2171
NA








COGs COG0463




fig|6666666.60966.peg.2174
CDS
2015828
2012172
−2
−
3657
Beta-1,3-
-none-
D23_1c2172
NA








glucosyltransferase




fig|6666666.60966.peg.2175
CDS
2017307
2016147
−2
−
1161
Capsular polysaccharide
Capsular Polysaccharides
D23_1c2173
NA








export system inner
Biosynthesis and










membrane protein KpsE
Assembly



fig|6666666.60966.peg.2176
CDS
2017966
2017304
−1
−
663
Capsular polysaccharide
Capsular Polysaccharides
D23_1c2174
Neut_0152








ABC transporter, ATP-
Biosynthesis and










binding protein KpsT
Assembly



fig|6666666.60966.peg.2177
CDS
2018757
2017963
−3
−
795
Capsular polysaccharide
Capsular Polysaccharides
D23_1c2175
NA








ABC transporter,
Biosynthesis and










permease protein KpsM
Assembly;











<br>Rhamnose











containing glycans



fig|6666666.60966.peg.2178
CDS
2019947
2018757
−2
−
1191
Capsular polysaccharide
Capsular Polysaccharides
D23_1c2176
Neut_2119








biosynthesis/export
Biosynthesis and










periplasmic protein
Assembly










WcbC




fig|6666666.60966.peg.2179
CDS
2021279
2019957
−2
−
1323
8-amino-7-
Biotin biosynthesis;
D23_1c2177
Neut_0461








oxononanoate synthase
<br>Biotin biosynthesis










(EC 2.3.1.47)
Experimental; <br>Biotin











synthesis cluster



fig|6666666.60966.peg.2180
CDS
2025121
2021276
−1
−
3846
Capsular polysaccharide
-none-
D23_1c2178
NA








biosynthesis fatty acid











synthase WcbR




fig|6666666.60966.peg.2181
CDS
2028811
2025266
−1
−
3546
Capsular polysaccharide
-none-
D23_1c2179
Neut_2003








biosynthesis fatty acid











synthase WcbR




fig|6666666.60966.peg.2182
CDS
2029053
2029166
3
+
114
hypothetical protein
-none-
D23_1c2180
NA

fig|6666666.60966.peg.2183
CDS
2029212
2029352
3
+
141
hypothetical protein
-none-
D23_1c2181
NA

fig|6666666.60966.peg.2184
CDS
2031017
2029434
−2
−
1584
L-aspartate oxidase (EC

Mycobacterium

D23_1c2182
Neut_2004








1.4.3.16)
virulence operon











possibly involved in











quinolinate biosynthesis;











<br>NAD and NADP











cofactor biosynthesis











global



fig|6666666.60966.peg.2185
CDS
2031267
2032187
3
+
921
Branched-chain amino
Alanine biosynthesis;
D23_1c2184
Neut_2005








acid aminotransferase
<br>Branched-Chain










(EC 2.6.1.42)
Amino Acid Biosynthesis;











<br>Leucine











Biosynthesis;











<br>Pyruvate Alanine











Serine Interconversions



fig|6666666.60966.peg.2186
CDS
2032212
2032421
3
+
210
FIG00858455:
-none-
D23_1c2185
Neut_2006








hypothetical protein




fig|6666666.60966.peg.2187
CDS
2032485
2033864
3
+
1380
Phosphomannomutase
Mannose Metabolism
D23_1c2186
Neut_2007








(EC 5.4.2.8)/











Phosphoglucomutase











(EC 5.4.2.2)




fig|6666666.60966.peg.2188
CDS
2033901
2035508
3
+
1608
NAD synthetase (EC
NAD and NADP cofactor
D23_1c2187
Neut_2008








6.3.1.5)/Glutamine
biosynthesis global;










amidotransferase chain
<br>NAD and NADP










of NAD synthetase
cofactor biosynthesis











global



fig|6666666.60966.peg.2189
CDS
2035472
2037178
2
+
1707
Exported zinc
-none-
D23_1c2188
Neut_2009








metalloprotease YfgC











precursor




fig|6666666.60966.peg.2190
CDS
2037257
2038402
2
+
1146
Macrolide-specific
Multidrug Resistance
D23_1c2189
Neut_2010








efflux protein MacA
Efflux Pumps



fig|6666666.60966.peg.2191
CDS
2038413
2039180
3
+
768
Macrolide export ATP-
Multidrug Resistance
D23_1c2190
Neut_2011








binding/permease
Efflux Pumps










protein MacB (EC 3.6.3.—)




fig|6666666.60966.peg.2192
CDS
2039177
2040400
2
+
1224
Macrolide export ATP-
Multidrug Resistance
D23_1c2191
Neut_2012








binding/permease
Efflux Pumps










protein MacB (EC 3.6.3.—)




fig|6666666.60966.peg.2193
CDS
2040442
2040612
1
+
171
hypothetical protein
-none-
D23_1c2192
NA

fig|6666666.60966.peg.2195
CDS
2040690
2040875
3
+
186
hypothetical protein
-none-
D23_1c2193
NA

fig|6666666.60966.peg.2196
CDS
2040926
2042374
2
+
1449
ATP synthase beta chain
-none-
D23_1c2194
Neut_2013








(EC 3.6.3.14)




fig|6666666.60966.peg.2197
CDS
2042371
2042781
1
+
411
ATP synthase epsilon
-none-
D23_1c2195
Neut_2014








chain (EC 3.6.3.14)




fig|6666666.60966.peg.2198
CDS
2042778
2043059
3
+
282
ATP synthase protein I
-none-
D23_1c2196
Neut_2015

fig|6666666.60966.peg.2199
CDS
2043105
2043398
3
+
294
FIG048548: ATP
-none-
D23_1c2197
Neut_2016








synthase protein I2




fig|6666666.60966.peg.2200
CDS
2043420
2044112
3
+
693
ATP synthase A chain
-none-
D23_1c2198
Neut_2017








(EC 3.6.3.14)




fig|6666666.60966.peg.2201
CDS
2044115
2044393
2
+
279
ATP synthase C chain
-none-
D23_1c2199
Neut_2018








(EC 3.6.3.14)




fig|6666666.60966.peg.2202
CDS
2044400
2045170
2
+
771
ATP synthase B chain
-none-
D23_1c2200
Neut_2019








(EC 3.6.3.14)




fig|6666666.60966.peg.2203
CDS
2045183
2046733
2
+
1551
ATP synthase alpha
-none-
D23_1c2201
Neut_2020








chain (EC 3.6.3.14)




fig|6666666.60966.peg.2204
CDS
2046810
2047607
3
+
798
ATP synthase gamma
-none-
D23_1c2202
Neut_2021








chain (EC 3.6.3.14)




fig|6666666.60966.peg.2206
CDS
2048344
2050986
1
+
2643
DNA mismatch repair
DNA repair, bacterial
D23_1c2204
Neut_2022








protein MutS
MutL-MutS system;











<br>DNA repair system











including RecA, MutS











and a hypothetical











protein



fig|6666666.60966.peg.2207
CDS
2051500
2051021
−1
−
480
FKBP-type peptidyl-
G3E family of P-loop
D23_1c2205
Neut_2023








prolyl cis-trans
GTPases (metallocenter










isomerase SlyD (EC
biosynthesis);










5.2.1.8)
<br>Peptidyl-prolyl cis-











trans isomerase;











<br>Potassium











homeostasis



fig|6666666.60966.peg.2208
CDS
2052207
2051656
−3
−
552
Ribonuclease HII (EC
Ribonuclease H;
D23_1c2206
Neut_2024








3.1.26.4)
<br>Ribonucleases in











Bacillus



fig|6666666.60966.peg.2209
CDS
2052737
2052294
−2
−
444
(3R)-hydroxymyristoyl-
-none-
D23_1c2207
Neut_2025








[acyl carrier protein]











dehydratase (EC 4.2.1.—)




fig|6666666.60966.peg.2210
CDS
2053333
2052770
−1
−
564
Outer membrane
Lipopolysaccharide
D23_1c2208
Neut_2026








protein H precursor
assembly;











<br>Periplasmic Stress











Response



fig|6666666.60966.peg.2211
CDS
2055635
2053359
−2
−
2277
Outer membrane
Lipopolysaccharide
D23_1c2209
Neut_2027








protein assembly factor
assembly










YaeT precursor




fig|6666666.60966.peg.2212
CDS
2057020
2055638
−1
−
1383
Membrane-associated
-none-
D23_1c2210
Neut_2028








zinc metalloprotease




fig|6666666.60966.peg.2213
CDS
2058265
2057024
−1
−
1242
1-deoxy-D-xylulose 5-
CBSS-83331.1.peg.3039;
D23_1c2211
Neut_2029








phosphate
<br>Isoprenoid










reductoisomerase (EC
Biosynthesis;










1.1.1.267)
<br>Nonmevalonate











Branch of Isoprenoid











Biosynthesis



fig|6666666.60966.peg.2214
CDS
2059089
2058262
−3
−
828
Phosphatidate
Glycerolipid and
D23_1c2212
Neut_2030








cytidylyltransferase (EC
Glycerophospholipid










2.7.7.41)
Metabolism in Bacteria



fig|6666666.60966.peg.2215
CDS
2059870
2059124
−1
−
747
Undecaprenyl
CBSS-83331.1.peg.3039;
D23_1c2213
Neut_2031








diphosphate synthase
<br>Isoprenoid










(EC 2.5.1.31)
Biosynthesis;











<br>Isoprenoinds for











Quinones;











<br>Polyprenyl











Diphosphate











Biosynthesis



fig|6666666.60966.peg.2216
CDS
2060476
2059919
−1
−
558
Ribosome recycling
Ribosome recycling
D23_1c2214
Neut_2032








factor
related cluster;











<br>Translation











termination factors











bacterial



fig|6666666.60966.peg.2217
CDS
2061239
2060577
−2
−
663
Uridylate kinase (EC
-none-
D23_1c2215
Neut_2033








2.7.4.—)




fig|6666666.60966.peg.2218
CDS
2061489
2061361
−3
−
129
hypothetical protein
-none-
D23_1c2216
NA

fig|6666666.60966.peg.2219
CDS
2062729
2061845
−1
−
885
Translation elongation
CBSS-
D23_1c2217
Neut_2034








factor Ts
312309.3.peg.1965;











<br>Ribosome recycling











related cluster;











<br>Translation











elongation factors











bacterial



fig|6666666.60966.peg.2220
CDS
2063557
2062802
−1
−
756
SSU ribosomal protein
CBSS-
D23_1c2218
Neut_2035








S2p (SAe)
312309.3.peg.1965;











<br>Ribosome recycling











related cluster



fig|6666666.60966.peg.2221
CDS
2064515
2063772
−2
−
744
transcriptional
Oxidative stress
D23_1c2219
Neut_2036








regulator, Crp/Fnr











family




fig|6666666.60966.peg.2222
CDS
2064873
2064562
−3
−
312
Cytochrome c, class I
-none-
D23_1c2220
Neut_2037

fig|6666666.60966.peg.2223
CDS
2067162
2065111
−3
−
2052
Zinc-regulated outer
-none-
D23_1c2221
Neut_2038








membrane receptor




fig|6666666.60966.peg.2225
CDS
2067907
2068395
1
+
489
Zinc uptake regulation
Glycyl-tRNA synthetase
D23_1c2222
NA








protein ZUR
containing cluster;











<br>Oxidative stress;











<br>Zinc regulated











enzymes



fig|6666666.60966.peg.2226
CDS
2068438
2068560
1
+
123
Mobile element protein
-none-
D23_1c2223
Neut_0884

fig|6666666.60966.peg.2228
CDS
2068811
2069020
2
+
210
hypothetical protein
-none-
D23_1c2224
NA

fig|6666666.60966.peg.2231
CDS
2069466
2069332
−3
−
135
hypothetical protein
-none-
D23_1c2225
NA

fig|6666666.60966.peg.2232
CDS
2069455
2070327
1
+
873
COG0613, Predicted
A cluster relating to
D23_1c2226
Neut_2039








metal-dependent
Tryptophanyl-tRNA










phosphoesterases (PHP
synthetase; <br>tRNA










family)
modification Bacteria



fig|6666666.60966.peg.2233
CDS
2070450
2071082
3
+
633
YciO family
-none-
D23_1c2227
Neut_2040

fig|6666666.60966.peg.2234
CDS
2071075
2071740
1
+
666
FIG004556: membrane
A cluster relating to
D23_1c2228
Neut_2041








metalloprotease
Tryptophanyl-tRNA











synthetase



fig|6666666.60966.peg.2235
CDS
2071817
2073019
2
+
1203
Tryptophanyl-tRNA
A cluster relating to
D23_1c2229
Neut_2042








synthetase (EC 6.1.1.2)
Tryptophanyl-tRNA











synthetase; <br>tRNA











aminoacylation, Trp



fig|6666666.60966.peg.2236
CDS
2073064
2073864
1
+
801
Segregation and
-none-
D23_1c2230
Neut_2043








condensation protein A




fig|6666666.60966.peg.2237
CDS
2073830
2074480
2
+
651
Segregation and
-none-
D23_1c2231
Neut_2044








condensation protein B




fig|6666666.60966.peg.2238
CDS
2074504
2075751
1
+
1248
Isocitrate
5-FCL-like protein;
D23_1c2232
Neut_2045








dehydrogenase [NADP]
<br>TCA Cycle










(EC 1.1.1.42)




fig|6666666.60966.peg.2239
CDS
2076095
2075892
−2
−
204
Cold shock protein CspD
Cold shock, CspA family
D23_1c2233
Neut_2046









of proteins



fig|6666666.60966.peg.2240
CDS
2076577
2076407
−1
−
171
hypothetical protein
-none-
D23_1c2234
NA

fig|6666666.60966.peg.2241
CDS
2076576
2076779
3
+
204
ATP-dependent Clp
ClpAS cluster;
D23_1c2235
Neut_2047








protease adaptor
<br>Proteolysis in










protein ClpS
bacteria, ATP-dependent



fig|6666666.60966.peg.2242
CDS
2076781
2079051
1
+
2271
ATP-dependent Clp
ClpAS cluster;
D23_1c2236
Neut_2048








protease ATP-binding
<br>Proteolysis in










subunit ClpA
bacteria, ATP-











dependent;











<br>Ribosome recycling











related cluster



fig|6666666.60966.peg.2243
CDS
2079170
2080129
2
+
960
TRAP transporter solute
TRAP Transporter
D23_1c2237
Neut_2049








receptor, unknown
unknown substrate 6










substrate 6




fig|6666666.60966.peg.2244
CDS
2080157
2080885
2
+
729
Orotate
De Novo Pyrimidine
D23_1c2238
Neut_2050








phosphoribosyltransferase
Synthesis










(EC 2.4.2.10)




fig|6666666.60966.peg.2245
CDS
2081203
2082156
1
+
954
COGs COG0715
-none-
D23_1c2239
Neut_2051

fig|6666666.60966.peg.2246
CDS
2082161
2082997
2
+
837
Alkanesulfonates
Alkanesulfonate
D23_1c2240
Neut_2052








transport system
assimilation










permease protein




fig|6666666.60966.peg.2247
CDS
2083232
2083038
−2
−
195
hypothetical protein
-none-
D23_1c2241
NA

fig|6666666.60966.peg.2248
CDS
2083287
2083823
3
+
537
ABC-type
Alkanesulfonate
D23_1c2242
Neut_2053








nitrate/sulfonate/bicarbonate
assimilation










transport system,











ATPase component




fig|6666666.60966.peg.2249
CDS
2083938
2086493
3
+
2556
Glycogen
Glycogen metabolism
D23_1c2243
Neut_2054








phosphorylase (EC











2.4.1.1)




fig|6666666.60966.peg.2251
CDS
2086807
2086661
−1
−
147
hypothetical protein
-none-
D23_1c2244
NA

fig|6666666.60966.peg.2252
CDS
2086806
2087288
3
+
483
Flagellar biosynthesis
Flagellum
D23_1c2245
Neut_2055








protein FliL




fig|6666666.60966.peg.2253
CDS
2087301
2088293
3
+
993
Flagellar motor switch
Flagellar motility;
D23_1c2246
Neut_2056








protein FliM
<br>Flagellum



fig|6666666.60966.peg.2254
CDS
2088322
2088795
1
+
474
Flagellar motor switch
Flagellar motility;
D23_1c2247
Neut_2057








protein FliN
<br>Flagellum



fig|6666666.60966.peg.2255
CDS
2088822
2089265
3
+
444
Flagellar biosynthesis
Flagellum
D23_1c2248
Neut_2058








protein FliQ




fig|6666666.60966.peg.2256
CDS
2089255
2090040
1
+
786
Flagellar biosynthesis
Flagellum
D23_1c2249
Neut_2059








protein FliP




fig|6666666.60966.peg.2257
CDS
2090056
2090331
1
+
276
Flagellar biosynthesis
Flagellum
D23_1c2250
Neut_2060








protein FliQ




fig|6666666.60966.peg.2258
CDS
2090429
2091229
2
+
801
Flagellar biosynthesis
Flagellar motility;
D23_1c2251
Neut_2061








protein FliR
<br>Flagellum



fig|6666666.60966.peg.2259
CDS
2091389
2093485
2
+
2097
FIG00858519:
-none-
D23_1c2252
Neut_2062








hypothetical protein




fig|6666666.60966.peg.2260
CDS
2093591
2095027
2
+
1437
FIG00858578:
-none-
D23_1c2253
Neut_2063








hypothetical protein




fig|6666666.60966.peg.2261
CDS
2096049
2095090
−3
−
960
alpha/beta hydrolase
-none-
D23_1c2254
Neut_2064








fold




fig|6666666.60966.peg.2262
CDS
2096035
2096187
1
+
153
hypothetical protein
-none-
D23_1c2255
NA

fig|6666666.60966.peg.2263
CDS
2097510
2096296
−3
−
1215
Argininosuccinate
Arginine Biosynthesis--
D23_1c2256
Neut_2065








synthase (EC 6.3.4.5)
gjo; <br>Arginine











Biosynthesis extended



fig|6666666.60966.peg.2264
CDS
2098473
2097550
−3
−
924
Ornithine
Arginine Biosynthesis--
D23_1c2257
Neut_2066








carbamoyltransferase
gjo; <br>Arginine










(EC 2.1.3.3)
Biosynthesis extended;











<br>Arginine and











Ornithine Degradation



fig|6666666.60966.peg.2266
CDS
2099808
2099680
−3
−
129
hypothetical protein
-none-
D23_1c2259
Neut_2067

fig|6666666.60966.peg.2265
CDS
2099605
2098649
−1
−
957
Acetylornithine
Arginine Biosynthesis--
D23_1c2259
Neut_2067








aminotransferase (EC
gjo; <br>Arginine










2.6.1.11)
Biosynthesis extended



fig|6666666.60966.peg.2267
CDS
2100416
2100066
−2
−
351
FIG00858925:
-none-
D23_1c2260
Neut_2068








hypothetical protein




fig|6666666.60966.peg.2268
CDS
2100762
2100517
−3
−
246
FIG00859242:
-none-
D23_1c2261
Neut_2069








hypothetical protein




fig|6666666.60966.peg.2269
CDS
2102838
2100763
−3
−
2076
FIG00858999:
-none-
D23_1c2262
Neut_2070








hypothetical protein




fig|6666666.60966.peg.2270
CDS
2103683
2102844
−2
−
840
Cysteine synthase B (EC
Cysteine Biosynthesis
D23_1c2263
Neut_2071








2.5.1.47)




fig|6666666.60966.peg.2272
CDS
2106646
2103854
−1
−
2793
FIG00860005:
-none-
D23_1c2264
Neut_2072








hypothetical protein




fig|6666666.60966.peg.2274
CDS
2109519
2108932
−3
−
588
hypothetical protein
-none-
D23_1c2268
Neut_2074

fig|6666666.60966.peg.2275
CDS
2110331
2109591
−2
−
741
putative (U92432) ORF4
-none-
D23_1c2269
Neut_2316








(Nitrosospira sp. NpAV)




fig|6666666.60966.peg.2276
CDS
2111663
2110398
−2
−
1266
Particulate methane
Particulate methane
D23_1c2270
Neut_2317








monooxygenase B-
monooxygenase










subunit (EC 1.14.13.25)
(pMMO)



fig|6666666.60966.peg.2277
CDS
2112493
2111663
−1
−
831
Particulate methane
Particulate methane
D23_1c2271
Neut_2318








monooxygenase A-
monooxygenase










subunit (EC 1.14.13.25)
(pMMO)



fig|6666666.60966.peg.2278
CDS
2113482
2112667
−3
−
816
Particulate methane
Particulate methane
D23_1c2272
Neut_2319








monooxygenase C-
monooxygenase










subunit (EC 1.14.13.25)
(pMMO)



fig|6666666.60966.peg.2279
CDS
2114624
2114052
−2
−
573
CDP-diacylglycerol--
Glycerolipid and
D23_1c2273
Neut_2079








glycerol-3-phosphate 3-
Glycerophospholipid










phosphatidyltransferase
Metabolism in Bacteria










(EC 2.7.8.5)




fig|6666666.60966.peg.2280
CDS
2116254
2114755
−3
−
1500
Glycerol kinase (EC
Glycerol and Glycerol-3-
D23_1c2274
Neut_2080








2.7.1.30)
phosphate Uptake and











Utilization;











<br>Glycerolipid and











Glycerophospholipid











Metabolism in Bacteria



fig|6666666.60966.peg.2281
CDS
2116718
2116305
−2
−
414
Regulator of nucleoside
Transcription factors
D23_1c2275
Neut_2081








diphosphate kinase
bacterial



fig|6666666.60966.peg.2282
CDS
2116748
2116897
2
+
150
hypothetical protein
-none-
D23_1c2276
NA

fig|6666666.60966.peg.2283
CDS
2117727
2117005
−3
−
723
Phosphate regulon
High affinity phosphate
D23_1c2277
Neut_2082








transcriptional
transporter and control










regulatory protein PhoB
of PHO regulon;










(SphR)
<br>PhoR-PhoB two-











component regulatory











system; <br>Phosphate











metabolism



fig|6666666.60966.peg.2284
CDS
2119187
2118225
−2
−
963
Mobile element protein
-none-
D23_1c2278
Neut_1746

fig|6666666.60966.peg.2287
CDS
2121603
2120356
−3
−
1248
Aspartokinase (EC
CBSS-216591.1.peg.168;
D23_1c2282
Neut_2084








2.7.2.4)
<br>Lysine Biosynthesis











DAP Pathway, GJO











scratch; <br>Threonine











and Homoserine











Biosynthesis



fig|6666666.60966.peg.2288
CDS
2122439
2121855
−2
−
585
Putative peptidoglycan
-none-
D23_1c2283
Neut_2085








binding domain 1




fig|6666666.60966.peg.2289
CDS
2122914
2124089
3
+
1176
Acetate kinase (EC
Fermentations: Lactate;
D23_1c2284
Neut_2086








2.7.2.1)
<br>Pyruvate











metabolism II: acetyl-











CoA, acetogenesis from











pyruvate



fig|6666666.60966.peg.2290
CDS
2124134
2126509
2
+
2376
Xylulose-5-phosphate
Fermentations: Lactate;
D23_1c2285
Neut_2087








phosphoketolase (EC
<br>Fermentations:










4.1.2.9); Fructose-6-
Lactate; <br>Pentose










phosphate
phosphate pathway;










phosphoketolase (EC
<br>Pentose phosphate










4.1.2.22)
pathway



fig|6666666.60966.peg.2291
CDS
2126813
2126977
2
+
165
hypothetical protein
-none-
D23_1c2287
NA

fig|6666666.60966.peg.2292
CDS
2128152
2127058
−3
−
1095
Transaldolase (EC
Pentose phosphate
D23_1c2288
Neut_2089








2.2.1.2)
pathway



fig|6666666.60966.peg.2293
CDS
2128367
2128218
−2
−
150
hypothetical protein
-none-
D23_1c2289
NA

fig|6666666.60966.peg.2294
CDS
2128351
2128908
1
+
558
FIG006045: Sigma
Iron siderophore sensor
D23_1c2290
Neut_2090








factor, ECF subfamily
& receptor system



fig|6666666.60966.peg.2295
CDS
2128915
2129877
1
+
963
Iron siderophore sensor
Iron siderophore sensor
D23_1c2291
Neut_2091








protein
& receptor system



fig|6666666.60966.peg.2296
CDS
2129956
2132253
1
+
2298
TonB-dependent
Ton and Tol transport
D23_1c2292
Neut_2092








receptor
systems



fig|6666666.60966.peg.2297
CDS
2132801
2132271
−2
−
531
FIG00858714:
-none-
D23_1c2293
Neut_2093








hypothetical protein




fig|6666666.60966.peg.2298
CDS
2133157
2132813
−1
−
345
FIG00858447:
-none-
D23_1c2294
Neut_2094








hypothetical protein




fig|6666666.60966.peg.2299
CDS
2134515
2133133
−3
−
1383
Xaa-Pro
Aminopeptidases (EC
D23_1c2295
Neut_2095








aminopeptidase (EC
3.4.11.—); <br>CBSS-










3.4.11.9)
87626.3.peg.3639



fig|6666666.60966.peg.2301
CDS
2134633
2135313
1
+
681
Ribulose-phosphate 3-
Calvin-Benson cycle;
D23_1c2296
Neut_2096








epimerase (EC 5.1.3.1)
<br>Pentose phosphate











pathway; <br>Riboflavin











synthesis cluster



fig|6666666.60966.peg.2302
CDS
2135328
2136050
3
+
723
Phosphoglycolate
2-phosphoglycolate
D23_1c2297
Neut_2097








phosphatase (EC
salvage; <br>Glycolate,










3.1.3.18)
glyoxylate











interconversions;











<br>Photorespiration











(oxidative C2 cycle)



fig|6666666.60966.peg.2303
CDS
2136160
2137647
1
+
1488
Anthranilate synthase,
Chorismate:
D23_1c2298
Neut_2098








aminase component (EC
Intermediate for










4.1.3.27)
synthesis of Tryptophan,











PAPA antibiotics, PABA,











3-hydroxyanthranilate











and more.;











<br>Tryptophan











synthesis



fig|6666666.60966.peg.2304
CDS
2138110
2137682
−1
−
429
Ferredoxin reductase
Anaerobic respiratory
D23_1c2299
Neut_2099









reductases



fig|6666666.60966.peg.2305
CDS
2138482
2138138
−1
−
345
FIG00858997:
-none-
D23_1c2300
Neut_2100








hypothetical protein




fig|6666666.60966.peg.2306
CDS
2138586
2139236
3
+
651
Iron-sulfur cluster
CBSS-196164.1.peg.1690
D23_1c2301
Neut_2101








regulator SufR




fig|6666666.60966.peg.2307
CDS
2139353
2140534
2
+
1182
FIG00859085:
-none-
D23_1c2302
Neut_2102








hypothetical protein




fig|6666666.60966.peg.2308
CDS
2142375
2140606
−3
−
1770
Dihydrolipoamide
Pyruvate metabolism II:
D23_1c2304
Neut_2103








dehydrogenase of
acetyl-CoA, acetogenesis










pyruvate
from pyruvate; <br>TCA










dehydrogenase
Cycle










complex (EC 1.8.1.4)




fig|6666666.60966.peg.2309
CDS
2143648
2142380
−1
−
1269
Gamma-glutamyl
Proline Synthesis
D23_1c2305
Neut_2104








phosphate reductase











(EC 1.2.1.41)




fig|6666666.60966.peg.2310
CDS
2144399
2143713
−2
−
687
InterPro IPR001440
-none-
D23_1c2306
Neut_2105








COGs COG0457




fig|6666666.60966.peg.2311
CDS
2145656
2144412
−2
−
1245
TPR/glycosyl
-none-
D23_1c2307
Neut_2106








transferase domain











protein




fig|6666666.60966.peg.2312
CDS
2146522
2145650
−1
−
873
Esterase/lipase/thioesterase
-none-
D23_1c2308
Neut_2107








family active site




fig|6666666.60966.peg.2313
CDS
2147373
2146519
−3
−
855
Esterase/lipase/thioesterase
-none-
D23_1c2309
Neut_2108








family active site




fig|6666666.60966.peg.2314
CDS
2147631
2147380
−3
−
252
FIG00858580:
-none-
D23_1c2310
Neut_2109








hypothetical protein




fig|6666666.60966.peg.2315
CDS
2147817
2149007
3
+
1191
Tetraacyldisaccharide
Broadly distributed
D23_1c2311
Neut_2110








4&#39;-kinase (EC
proteins not in










2.7.1.130)/FIG002473:
subsystems; <br>KDO2-










Protein YcaR in KDO2-
Lipid A biosynthesis










Lipid A biosynthesis
cluster 2; <br>KDO2-










cluster
Lipid A biosynthesis











cluster 2



fig|6666666.60966.peg.2316
CDS
2149225
2149353
1
+
129
hypothetical protein
-none-
D23_1c2312
NA

fig|6666666.60966.peg.2318
CDS
2150705
2149527
−2
−
1179
Lipid carrier: UDP-N-
CBSS-
D23_1c2313
Neut_2112








acetylgalactosaminyltransferase
296591.1.peg.2330;










(EC 2.4.1.—)/
<br>CBSS-










Alpha-1,3-N-
296591.1.peg.2330;










acetylgalactosamine
<br>CBSS-










transferase PglA (EC
296591.1.peg.2330;










2.4.1.—); Putative
<br>N-linked










glycosyltransferase
Glycosylation in











Bacteria; <br>N-linked











Glycosylation in Bacteria



fig|6666666.60966.peg.2319
CDS
2151819
2150689
−3
−
1131
Glycosyl transferase,
-none-
D23_1c2314
Neut_2113








group 1 family protein




fig|6666666.60966.peg.2320
CDS
2153132
2151816
−2
−
1317
hypothetical protein
-none-
D23_1c2315
NA

fig|6666666.60966.peg.2321
CDS
2154290
2153199
−2
−
1092
Alpha-1,4-N-
N-linked Glycosylation in
D23_1c2316
Neut_2115








acetylgalactosamine
Bacteria










transferase PglJ (EC











2.4.1.—)




fig|6666666.60966.peg.2322
CDS
2155270
2154290
−1
−
981
COGs COG0439
-none-
D23_1c2317
Neut_2116

fig|6666666.60966.peg.2323
CDS
2156578
2155337
−1
−
1242
Membrane protein
-none-
D23_1c2318
Neut_2117








involved in the export











of O-antigen, teichoic











acid lipoteichoic acids




fig|6666666.60966.peg.2324
CDS
2156818
2157207
1
+
390
Low molecular weight
Capsular Polysaccharides
D23_1c2319
Neut_2118








protein-tyrosine-
Biosynthesis and










phosphatase Wzb (EC
Assembly










3.1.3.48)




fig|6666666.60966.peg.2325
CDS
2157230
2158477
2
+
1248
Capsule polysaccharide
-none-
D23_1c2320
Neut_2119








export protein




fig|6666666.60966.peg.2326
CDS
2158531
2160774
1
+
2244
Tyrosine-protein kinase
Capsular Polysaccharides
D23_1c2321
Neut_2120








Wzc (EC 2.7.10.2)
Biosynthesis and











Assembly



fig|6666666.60966.peg.2327
CDS
2160771
2162330
3
+
1560
Undecaprenyl-
-none-
D23_1c2322
Neut_2121








phosphate N-











acetylglucosaminyl 1-











phosphate transferase











(EC 2.7.8.—)




fig|6666666.60966.peg.2329
CDS
2165972
2162400
−2
−
3573
Chromosome partition
DNA structural proteins,
D23_1c2323
Neut_2122








protein smc
bacterial



fig|6666666.60966.peg.2330
CDS
2166059
2166478
2
+
420
NADPH-dependent 7-
-none-
D23_1c2324
Neut_2123








cyano-7-deazaguanine











reductase (EC 1.7.1.13)




fig|6666666.60966.peg.2331
CDS
2166527
2167927
2
+
1401
Fumarate hydratase
TCA Cycle
D23_1c2325
Neut_2124








class II (EC 4.2.1.2)




fig|6666666.60966.peg.2332
CDS
2168192
2168052
−2
−
141
hypothetical protein
-none-
D23_1c2326
NA

fig|6666666.60966.peg.2333
CDS
2168473
2168640
1
+
168
hypothetical protein
-none-
D23_1c2327
NA

fig|6666666.60966.peg.2334
CDS
2168888
2169181
2
+
294
Mobile element protein
-none-
D23_1c2328
Neut_1719

fig|6666666.60966.peg.2335
CDS
2169280
2170158
1
+
879
Mobile element protein
-none-
D23_1c2329
Neut_1720

fig|6666666.60966.peg.2337
CDS
2171884
2170655
−1
−
1230
diguanylate
-none-
D23_1c2332
Neut_2126








phosphodiesterase




fig|6666666.60966.peg.2338
CDS
2172707
2171898
−2
−
810
Putative diheme
Soluble cytochromes
D23_1c2333
Neut_2127








cytochrome c-553
and functionally related











electron carriers



fig|6666666.60966.peg.2339
CDS
2172852
2172977
3
+
126
hypothetical protein
-none-
D23_1c2334
NA

fig|6666666.60966.peg.2340
CDS
2175331
2172950
−1
−
2382
Type II secretory
-none-
D23_1c2335
Neut_2128








pathway, ATPase











PulE/Tfp pilus assembly











pathway, ATPase PilB




fig|6666666.60966.peg.2341
CDS
2176108
2175344
−1
−
765
CAMP
cAMP signaling in
D23_1c2336
Neut_2129








phosphodiesterases
bacteria










class-II:Metallo-beta-











lactamase superfamily




fig|6666666.60966.peg.2342
CDS
2176622
2176197
−2
−
426
Universal stress protein
-none-
D23_1c2337
Neut_2130








(Usp)




fig|6666666.60966.peg.2343
CDS
2177459
2176734
−2
−
726
Membrane protein
-none-
D23_1c2338
Neut_2131








TerC, possibly involved











in tellurium resistance




fig|6666666.60966.peg.2344
CDS
2178586
2177462
−1
−
1125
Patatin
-none-
D23_1c2339
Neut_2132

fig|6666666.60966.peg.2345
CDS
2178900
2179850
3
+
951
Proline iminopeptidase
Proline, 4-
D23_1c2340
Neut_2133








(EC 3.4.11.5)
hydroxyproline uptake











and utilization



fig|6666666.60966.peg.2346
CDS
2180553
2179870
−3
−
684
Dethiobiotin synthetase
Biotin biosynthesis;
D23_1c2341
Neut_2134








(EC 6.3.3.3)
<br>Biotin biosynthesis











Experimental; <br>Biotin











synthesis cluster



fig|6666666.60966.peg.2347
CDS
2181452
2180556
−2
−
897
Biotin synthesis protein
Biotin biosynthesis;
D23_1c2342
Neut_2135








BioC
<br>Biotin biosynthesis











Experimental; <br>Biotin











synthesis cluster



fig|6666666.60966.peg.2348
CDS
2182200
2181442
−3
−
759
Biotin synthesis protein
Biotin biosynthesis;
D23_1c2343
Neut_2136








BioH
<br>Biotin biosynthesis











Experimental; <br>Biotin











synthesis cluster



fig|6666666.60966.peg.2349
CDS
2183365
2182202
−1
−
1164
8-amino-7-
Biotin biosynthesis;
D23_1c2344
Neut_2137








oxononanoate synthase
<br>Biotin biosynthesis










(EC 2.3.1.47)
Experimental; <br>Biotin











synthesis cluster



fig|6666666.60966.peg.2350
CDS
2184393
2183371
−3
−
1023
Biotin synthase (EC
Biotin biosynthesis;
D23_1c2345
Neut_2138








2.8.1.6)
<br>Biotin biosynthesis











Experimental; <br>Biotin











synthesis cluster



fig|6666666.60966.peg.2351
CDS
2184641
2184453
−2
−
189
hypothetical protein
-none-
D23_1c2346
NA

fig|6666666.60966.peg.2352
CDS
2184698
2185168
2
+
471
Competence protein F
Biotin biosynthesis
D23_1c2347
Neut_2139








homolog,
Experimental; <br>Biotin










phosphoribosyltransferase
synthesis cluster;










domain; protein
<br>CBSS-










YhgH required for
216591.1.peg.168










utilization of DNA as











sole source of carbon











and energy




fig|6666666.60966.peg.2353
CDS
2185222
2185686
1
+
465
tRNA (cytidine(34)-
Biotin synthesis cluster;
D23_1c2348
Neut_2140








2&#39;-O)-
<br>RNA methylation










methyltransferase (EC











2.1.1.207) ## TrmL




fig|6666666.60966.peg.2354
CDS
2185773
2186303
3
+
531
protein of unknown
-none-
D23_1c2349
Neut_2141








function DUF1130




fig|6666666.60966.peg.2355
CDS
2186489
2187325
2
+
837
SAM-dependent
-none-
D23_1c2350
Neut_2142








methyltransferase (EC











2.1.1.—)




fig|6666666.60966.peg.2356
CDS
2189013
2187523
−3
−
1491
Glucose-6-phosphate 1-
Pentose phosphate
D23_1c2351
Neut_2143








dehydrogenase (EC
pathway










1.1.1.49)




fig|6666666.60966.peg.2357
CDS
2189925
2189017
−3
−
909
6-phosphogluconate
D-gluconate and
D23_1c2352
Neut_2144








dehydrogenase,
ketogluconates










decarboxylating (EC
metabolism;










1.1.1.44)
<br>Pentose phosphate











pathway



fig|6666666.60966.peg.2358
CDS
2191152
2189995
−3
−
1158
COGs COG1397
-none-
D23_1c2353
Neut_2145

fig|6666666.60966.peg.2359
CDS
2191494
2191195
−3
−
300
UPF0235 protein
CBSS-630.2.peg.3360
D23_1c2354
Neut_2146








VC0458




fig|6666666.60966.peg.2360
CDS
2192054
2191494
−2
−
561
Integral membrane
CBSS-630.2.peg.3360
D23_1c2355
Neut_2147








protein YggT, involved











in response to











extracytoplasmic stress











(osmotic shock)




fig|6666666.60966.peg.2361
CDS
2192939
2192127
−2
−
813
Pyrroline-5-carboxylate
A Hypothetical Protein
D23_1c2356
Neut_2148








reductase (EC 1.5.1.2)
Related to Proline











Metabolism; <br>CBSS-











630.2.peg.3360;











<br>Proline Synthesis



fig|6666666.60966.peg.2362
CDS
2193210
2193019
−3
−
192
FIG00859708:
-none-
D23_1c2357
Neut_2149








hypothetical protein




fig|6666666.60966.peg.2364
CDS
2194302
2194580
3
+
279
Ribonuclease P protein
Cell Division Subsystem
D23_1c2359
Neut_2152








component (EC
including YidCD;










3.1.26.5)
<br>RNA modification











cluster; <br>tRNA











processing



fig|6666666.60966.peg.2365
CDS
2194877
2196745
2
+
1869
Inner membrane
CTP synthase (EC
D23_1c2360
Neut_2154








protein translocase
6.3.4.2) cluster; <br>Cell










component YidC, long
Division Subsystem










form
including YidCD;











<br>RNA modification











cluster



fig|6666666.60966.peg.2366
CDS
2196792
2198171
3
+
1380
GTPase and tRNA-U34
Cell Division Subsystem
D23_1c2361
Neut_2155








5-formylation enzyme
including YidCD;










TrmE
<br>RNA modification











and chromosome











partitioning cluster;











<br>RNA modification











cluster; <br>Universal











GTPases; <br>mnm5U34











biosynthesis bacteria;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.2367
CDS
2198398
2198667
1
+
270
SSU ribosomal protein
-none-
D23_1c2363
Neut_2156








S15p (S13e)




fig|6666666.60966.peg.2368
CDS
2198846
2200963
2
+
2118
Polyribonucleotide
Bacterial RNA-
D23_1c2364
Neut_2157








nucleotidyltransferase
metabolizing Zn-










(EC 2.7.7.8)
dependent hydrolases;











<br>Polyadenylation











bacterial



fig|6666666.60966.peg.2369
CDS
2201167
2201039
−1
−
129
hypothetical protein
-none-
D23_1c2365
NA

fig|6666666.60966.peg.2371
CDS
2201553
2202926
3
+
1374
RND efflux system,
Multidrug Resistance
D23_1c2367
Neut_2158








outer membrane
Efflux Pumps










lipoprotein CmeC




fig|6666666.60966.peg.2372
CDS
2203015
2204220
1
+
1206
Membrane fusion
Multidrug Resistance
D23_1c2368
Neut_2159








protein of RND family
Efflux Pumps










multidrug efflux pump




fig|6666666.60966.peg.2373
CDS
2204238
2207432
3
+
3195
RND efflux system,
Multidrug Resistance
D23_1c2369
Neut_2160








inner membrane
Efflux Pumps










transporter CmeB




fig|6666666.60966.peg.2375
CDS
2208043
2207702
−1
−
342
hypothetical protein
-none-
D23_1c2370
Neut_2161

fig|6666666.60966.peg.2376
CDS
2208812
2208072
−2
−
741
conserved hypothetical
-none-
D23_1c2371
Neut_2162








protein [ Pyrococcus











horikoshii ]; COG2102:











Predicted ATPases of











PP-loop superfamily;











IPR002761: Domain of











unknown function











DUF71




fig|6666666.60966.peg.2377
CDS
2209043
2208924
−2
−
120
FIG00859479:
-none-
D23_1c2372
Neut_2163








hypothetical protein




fig|6666666.60966.peg.2379
CDS
2210878
2209472
−1
−
1407
GTP-binding protein
CBSS-
D23_1c2374
Neut_2164








EngA
290633.1.peg.1906;











<br>CBSS-











498211.3.peg.1415;











<br>Universal GTPases



fig|6666666.60966.peg.2380
CDS
2212159
2210930
−1
−
1230
Outer membrane
CBSS-
D23_1c2375
Neut_2165








protein YfgL, lipoprotein
290633.1.peg.1906;










component of the
<br>CBSS-










protein assembly
498211.3.peg.1415;










complex (forms a
<br>Lipopolysaccharide










complex with YaeT,
assembly










YfiO, and NlpB)




fig|6666666.60966.peg.2381
CDS
2212800
2212162
−3
−
639
Mlr7403 protein
CBSS-
D23_1c2376
Neut_2166









290633.1.peg.1906;











<br>CBSS-











498211.3.peg.1415



fig|6666666.60966.peg.2382
CDS
2214088
2212823
−1
−
1266
Histidyl-tRNA
CBSS-
D23_1c2377
Neut_2167








synthetase (EC 6.1.1.21)
498211.3.peg.1415;











<br>tRNA











aminoacylation, His



fig|6666666.60966.peg.2383
CDS
2215286
2214081
−2
−
1206
1-hydroxy-2-methyl-2-
CBSS-
D23_1c2378
Neut_2168








(E)-butenyl 4-
498211.3.peg.1415;










diphosphate synthase
<br>CBSS-










(EC 1.17.7.1)
83331.1.peg.3039;











<br>Isoprenoid











Biosynthesis;











<br>Nonmevalonate











Branch of Isoprenoid











Biosynthesis



fig|6666666.60966.peg.2384
CDS
2216438
2215359
−2
−
1080
FIG021952: putative
CBSS-498211.3.peg.1415
D23_1c2379
Neut_2169








membrane protein




fig|6666666.60966.peg.2385
CDS
2217306
2216428
−3
−
879
Type IV pilus biogenesis
CBSS-498211.3.peg.1415
D23_1c2380
Neut_2170








protein PilF




fig|6666666.60966.peg.2386
CDS
2218414
2217275
−1
−
1140
Ribosomal RNA large
CBSS-
D23_1c2381
Neut_2171








subunit
498211.3.peg.1415;










methyltransferase N (EC
<br>RNA methylation










2.1.1.—)




fig|6666666.60966.peg.2387
CDS
2218877
2218452
−2
−
426
Nucleoside diphosphate
CBSS-
D23_1c2382
Neut_2172








kinase (EC 2.7.4.6)
498211.3.peg.1415;











<br>Purine conversions;











<br>pyrimidine











conversions



fig|6666666.60966.peg.2389
CDS
2219591
2219175
−2
−
417
Chain A, Red Copper
-none-
D23_1c2383
Neut_2173








Protein Nitrosocyanin




fig|6666666.60966.peg.2390
CDS
2220042
2221430
3
+
1389
Aminotransferase
Hopanes
D23_1c2384
Neut_2174








HpnO, required for











aminobacteriohopanetriol




fig|6666666.60966.peg.2391
CDS
2222146
2221442
−1
−
705
DNA polymerase III
CBSS-228410.1.peg.134;
D23_1c2385
Neut_2175








epsilon subunit (EC
<br>CBSS-










2.7.7.7)
342610.3.peg.1536



fig|6666666.60966.peg.2392
CDS
2222646
2222158
−3
−
489
Ribonuclease HI (EC
CBSS-228410.1.peg.134;
D23_1c2386
Neut_2176








3.1.26.4)
<br>CBSS-











342610.3.peg.1536;











<br>Ribonuclease H



fig|6666666.60966.peg.2393
CDS
2223440
2222706
−2
−
735
FIG005121: SAM-
CBSS-228410.1.peg.134;
D23_1c2387
Neut_2177








dependent
<br>CBSS-










methyltransferase (EC
342610.3.peg.1536;










2.1.1.—)
<br>Glutathione: Non-











redox reactions



fig|6666666.60966.peg.2394
CDS
2223500
2224267
2
+
768
Hydroxyacylglutathione
CBSS-228410.1.peg.134;
D23_1c2388
Neut_2178








hydrolase (EC 3.1.2.6)
<br>CBSS-











342610.3.peg.1536;











<br>Glutathione: Non-











redox reactions;











<br>Methylglyoxal











Metabolism



fig|6666666.60966.peg.2396
CDS
2225143
2224571
−1
−
573
hypothetical protein
-none-
D23_1c2389
Neut_2179

fig|6666666.60966.peg.2397
CDS
2225287
2225162
−1
−
126
hypothetical protein
-none-
D23_1c2390
NA

fig|6666666.60966.peg.2398
CDS
2226167
2225250
−2
−
918
hypothetical protein
-none-
D23_1c2391
Neut_2180

fig|6666666.60966.peg.2399
CDS
2228864
2226171
−2
−
2694
Helicase, SNF2/RAD54
-none-
D23_1c2392
Neut_2181








family




fig|6666666.60966.peg.2401
CDS
2229650
2229480
−2
−
171
hypothetical protein
-none-
D23_1c2393
NA

fig|6666666.60966.peg.2402
CDS
2229693
2230814
3
+
1122
Oxidoreductase, FMN-
-none-
D23_1c2394
Neut_2182








binding




fig|6666666.60966.peg.2403
CDS
2230925
2231368
2
+
444
Ornithine
Arginine and Ornithine
D23_1c2395
Neut_2183








cyclodeaminase (EC
Degradation










4.3.1.12)




fig|6666666.60966.peg.2404
CDS
2231434
2233005
1
+
1572
Phosphoglucomutase
-none-
D23_1c2396
Neut_2184








(EC 5.4.2.2)




fig|6666666.60966.peg.2405
CDS
2233192
2233344
1
+
153
hypothetical protein
-none-
D23_1c2397
NA

fig|6666666.60966.peg.2406
CDS
2234195
2233347
−2
−
849
Mobile element protein
-none-
D23_1c2398
Neut_1888

fig|6666666.60966.peg.2407
CDS
2234437
2234252
−1
−
186
Mobile element protein
-none-
D23_1c2399
Neut_2500

fig|6666666.60966.peg.2408
CDS
2234636
2235049
2
+
414
Cobalt-zinc-cadmium
Cobalt-zinc-cadmium
D23_1c2400
Neut_2185








resistance protein
resistance



fig|6666666.60966.peg.2409
CDS
2235949
2235359
−1
−
591
Hydroxyacylglutathione
CBSS-228410.1.peg.134;
D23_1c2401
Neut_2178








hydrolase (EC 3.1.2.6)
<br>CBSS-











342610.3.peg.1536;











<br>Glutathione: Non-











redox reactions;











<br>Methylglyoxal











Metabolism



fig|6666666.60966.peg.2410
CDS
2236135
2236287
1
+
153
hypothetical protein
-none-
D23_1c2403
Neut_1255

fig|6666666.60966.peg.2411
CDS
2236295
2236462
2
+
168
hypothetical protein
-none-
D23_1c2404
Neut_2449

fig|6666666.60966.peg.2412
CDS
2236616
2236419
−2
−
198
Mobile element protein
-none-
D23_1c2405
Neut_2268

fig|6666666.60966.peg.2414
CDS
2236758
2237006
3
+
249
Mobile element protein
-none-
D23_1c2406
Neut_1756

fig|6666666.60966.peg.2417
CDS
2240037
2237515
−3
−
2523
Aconitate hydratase (EC
TCA Cycle
D23_1c2409
Neut_2457








4.2.1.3)




fig|6666666.60966.peg.2418
CDS
2240239
2240093
−1
−
147
Aconitate hydratase (EC
TCA Cycle
D23_1c2410
NA








4.2.1.3)




fig|6666666.60966.peg.2419
CDS
2240661
2241623
3
+
963
Mobile element protein
-none-
D23_1c2411
Neut_1278

fig|6666666.60966.peg.2421
CDS
2241835
2241987
1
+
153
Mobile element protein
-none-
D23_1c2413
NA

fig|6666666.60966.peg.2422
CDS
2242232
2242522
2
+
291
hypothetical protein
-none-
D23_1c2414
NA

fig|6666666.60966.peg.2423
CDS
2242506
2243450
3
+
945
Agmatinase (EC
Arginine and Ornithine
D23_1c2415
Neut_2187








3.5.3.11)
Degradation;











<br>Polyamine











Metabolism



fig|6666666.60966.peg.2424
CDS
2243462
2245420
2
+
1959
Biosynthetic arginine
Arginine and Ornithine
D23_1c2416
Neut_2188








decarboxylase (EC
Degradation;










4.1.1.19)
<br>Polyamine











Metabolism



fig|6666666.60966.peg.2425
CDS
2246086
2245436
−1
−
651
Mobile element protein
-none-
D23_1c2417
Neut_2189

fig|6666666.60966.peg.2426
CDS
2247251
2246148
−2
−
1104
hypothetical protein
-none-
D23_1c2418
Neut_2191

fig|6666666.60966.peg.2427
CDS
2247251
2247436
2
+
186
Mobile element protein
-none-
D23_1c2419
Neut_2500

fig|6666666.60966.peg.2428
CDS
2247493
2248341
1
+
849
Mobile element protein
-none-
D23_1c2420
Neut_1375

fig|6666666.60966.peg.2430
CDS
2249188
2249352
1
+
165
Mobile element protein
-none-
D23_1c2422
Neut_2186

fig|6666666.60966.peg.2431
CDS
2249749
2251734
1
+
1986
Protein-L-isoaspartate
Protein-L-isoaspartate O-
D23_1c2423
Neut_2323








O-methyltransferase
methyltransferase;










(EC 2.1.1.77)
<br>Stationary phase











repair cluster; <br>Ton











and Tol transport











systems



fig|6666666.60966.peg.2432
CDS
2252354
2253127
2
+
774
hypothetical protein
-none-
D23_1c2424
Neut_2196

fig|6666666.60966.peg.2433
CDS
2253955
2253515
−1
−
441
tRNA pseudouridine
Colicin V and Bacteriocin
D23_1c2425
Neut_2203








synthase A (EC 4.2.1.70)
Production Cluster;











<br>RNA pseudouridine











syntheses; <br>tRNA











modification Bacteria;











<br>tRNA processing



fig|6666666.60966.peg.2434
CDS
2254408
2254247
−1
−
162
hypothetical protein
-none-
D23_1c2426
NA

fig|6666666.60966.peg.2435
CDS
2256251
2254536
−2
−
1716
Selenoprotein O and
Selenoprotein O
D23_1c2427
Neut_2204








cysteine-containing











homologs




fig|6666666.60966.peg.2436
CDS
2256898
2257503
1
+
606
GCN5-related N-
-none-
D23_1c2429
Neut_2208








acetyltransferase




fig|6666666.60966.peg.2437
CDS
2258004
2257552
−3
−
453
probable multiple
-none-
D23_1c2430
Neut_2211








antibiotic resistance











protein marC




fig|6666666.60966.peg.2438
CDS
2258357
2258229
−2
−
129
hypothetical protein
-none-
D23_1c2431
Neut_2212

fig|6666666.60966.peg.2440
CDS
2259106
2259264
1
+
159
hypothetical protein
-none-
D23_1c2432
NA

fig|6666666.60966.peg.2441
CDS
2259280
2260221
1
+
942
Ornithine
Arginine and Ornithine
D23_1c2433
Neut_2213








cyclodeaminase (EC
Degradation










4.3.1.12)




fig|6666666.60966.peg.2442
CDS
2260562
2261791
2
+
1230
hypothetical protein
-none-
D23_1c2434
Neut_2214

fig|6666666.60966.peg.2443
CDS
2262110
2262748
2
+
639
hypothetical protein
-none-
D23_1c2435
Neut_2232

fig|6666666.60966.peg.2444
CDS
2262936
2263406
3
+
471
FIG00858867:
-none-
D23_1c2436
Neut_2233








hypothetical protein




fig|6666666.60966.peg.2446
CDS
2264766
2263630
−3
−
1137
N-succinyl-L,L-
Arginine Biosynthesis--
D23_1c2437
Neut_2234








diaminopimelate
gjo; <br>Arginine










desuccinylase (EC
Biosynthesis extended;










3.5.1.18)
<br>Lysine Biosynthesis











DAP Pathway, GJO











scratch



fig|6666666.60966.peg.2447
CDS
2265597
2264815
−3
−
783
Methionine ABC
Methionine
D23_1c2438
Neut_2235








transporter ATP-binding
Biosynthesis;










protein
<br>Methionine











Degradation



fig|6666666.60966.peg.2448
CDS
2266742
2265597
−2
−
1146
ABC-type transport
-none-
D23_1c2439
Neut_2236








system involved in











resistance to organic











solvents, permease











component USSDB6A




fig|6666666.60966.peg.2449
CDS
2267603
2266767
−2
−
837
Prolipoprotein
Lipoprotein Biosynthesis
D23_1c2440
Neut_2237








diacylglyceryl











transferase (EC 2.4.99.—)




fig|6666666.60966.peg.2450
CDS
2267740
2269413
1
+
1674
Dihydroxy-acid
Branched-Chain Amino
D23_1c2441
Neut_2238








dehydratase (EC
Acid Biosynthesis










4.2.1.9)




fig|6666666.60966.peg.2451
CDS
2269430
2271499
2
+
2070
Thymidylate kinase (EC
pyrimidine conversions
D23_1c2442
Neut_2241








2.7.4.9)




fig|6666666.60966.peg.2452
CDS
2271523
2271834
1
+
312
Cytochrome c551/c552
Soluble cytochromes
D23_1c2443
Neut_2242









and functionally related











electron carriers



fig|6666666.60966.peg.2454
CDS
2272004
2272972
2
+
969
D-3-phosphoglycerate
Glycine and Serine
D23_1c2444
Neut_2243








dehydrogenase (EC
Utilization;










1.1.1.95)
<br>Pyridoxin (Vitamin











B6) Biosynthesis;











<br>Serine Biosynthesis



fig|6666666.60966.peg.2455
CDS
2273050
2273595
1
+
546
dTDP-4-
Rhamnose containing
D23_1c2445
Neut_2244








dehydrorhamnose 3,5-
glycans; <br>dTDP-










epimerase (EC 5.1.3.13)
rhamnose synthesis



fig|6666666.60966.peg.2456
CDS
2273700
2274983
3
+
1284
Permeases of the major
-none-
D23_1c2446
Neut_2245








facilitator superfamily




fig|6666666.60966.peg.2457
CDS
2275758
2274997
−3
−
762
hypothetical protein
-none-
D23_1c2447
NA

fig|6666666.60966.peg.2458
CDS
2275968
2276633
3
+
666
Chromosomal
Cell Division Subsystem
D23_1c2449
Neut_2247








replication initiator
including YidCD;










protein DnaA
<br>DNA replication











cluster 1



fig|6666666.60966.peg.2459
CDS
2276770
2277435
1
+
666
Phosphoserine
Glycine and Serine
D23_1c2450
Neut_2248








phosphatase (EC
Utilization; <br>Serine










3.1.3.3)
Biosynthesis; <br>Serine











Biosynthesis



fig|6666666.60966.peg.2460
CDS
2277481
2277846
1
+
366
FIG00859424:
-none-
D23_1c2451
Neut_2249








hypothetical protein




fig|6666666.60966.peg.2461
CDS
2277800
2277958
2
+
159
hypothetical protein
-none-
D23_1c2452
NA

fig|6666666.60966.peg.2462
CDS
2277971
2279434
2
+
1464
Inosine-5&#39;-
Purine conversions;
D23_1c2453
Neut_2250








monophosphate
<br>Purine salvage










dehydrogenase (EC
cluster










1.1.1.205)




fig|6666666.60966.peg.2463
CDS
2279447
2281006
2
+
1560
GMP synthase
GMP synthase; <br>GMP
D23_1c2454
Neut_2251








[glutamine-
synthase; <br>Purine










hydrolyzing],
conversions; <br>Purine










amidotransferase
conversions; <br>Purine










subunit (EC 6.3.5.2)/
salvage cluster;










GMP synthase
<br>Purine salvage










[glutamine-
cluster










hydrolyzing], ATP











pyrophosphatase











subunit (EC 6.3.5.2)




fig|6666666.60966.peg.2465
CDS
2282716
2281352
−1
−
1365
hypothetical protein
-none-
D23_1c2455
NA

fig|6666666.60966.peg.2466
CDS
2282899
2282762
−1
−
138
Mobile element protein
-none-
D23_1c2456
Neut_2501

fig|6666666.60966.peg.2467
CDS
2283609
2282872
−3
−
738
Mobile element protein
-none-
D23_1c2457
Neut_1888

fig|6666666.60966.peg.2468
CDS
2283851
2283666
−2
−
186
Mobile element protein
-none-
D23_1c2458
Neut_2500

fig|6666666.60966.peg.2469
CDS
2285015
2284020
−2
−
996
hypothetical protein
-none-
D23_1c2459
NA

fig|6666666.60966.peg.2470
CDS
2285305
2285048
−1
−
258
hypothetical protein
-none-
D23_1c2460
NA

fig|6666666.60966.peg.2471
CDS
2285448
2285573
3
+
126
hypothetical protein
-none-
D23_1c2461
NA

fig|6666666.60966.peg.2472
CDS
2285631
2286293
3
+
663
Thiopurine S-
-none-
D23_1c2462
Neut_2272








methyltransferase (EC











2.1.1.67)




fig|6666666.60966.peg.2473
CDS
2286615
2288795
3
+
2181
hypothetical protein
-none-
D23_1c2463
Neut_2273

fig|6666666.60966.peg.2474
CDS
2289016
2291046
1
+
2031
oligopeptide
-none-
D23_1c2464
Neut_2274








transporter




fig|6666666.60966.peg.2475
CDS
2291342
2291145
−2
−
198
FIG00859558:
-none-
D23_1c2465
Neut_2275








hypothetical protein




fig|6666666.60966.peg.2476
CDS
2291757
2291362
−3
−
396
FIG00859558:
-none-
D23_1c2466
Neut_2275








hypothetical protein




fig|6666666.60966.peg.2477
CDS
2292959
2291901
−2
−
1059
Putative permease
-none-
D23_1c2467
Neut_2276








often clustered with de











novo purine synthesis




fig|6666666.60966.peg.2478
CDS
2293039
2294097
1
+
1059
Phosphoribosylformylglycinamidine
De Novo Purine
D23_1c2468
Neut_2277








cyclo-ligase
Biosynthesis










(EC 6.3.3.1)




fig|6666666.60966.peg.2479
CDS
2294109
2294741
3
+
633
Phosphoribosylglycinamide
5-FCL-like protein;
D23_1c2469
Neut_2278








formyltransferase
<br>De Novo Purine










(EC 2.1.2.2)
Biosynthesis



fig|6666666.60966.peg.2480
CDS
2294738
2295460
2
+
723
FIG00859545:
-none-
D23_1c2470
Neut_2279








hypothetical protein




fig|6666666.60966.peg.2481
CDS
2295477
2296751
3
+
1275
Fmu (Sun)/eukaryotic
-none-
D23_1c2471
Neut_2280








nucleolar NOL1/Nop2p;











tRNAand rRNA











cytosine-C5-methylases




fig|6666666.60966.peg.2482
CDS
2297068
2296832
−1
−
237
hypothetical protein
-none-
D23_1c2472
Neut_2281








PA0941




fig|6666666.60966.peg.2483
CDS
2297785
2297237
−1
−
549
InterPro
-none-
D23_1c2473
Neut_2282








IPR000694:IPR001734




fig|6666666.60966.peg.2484
CDS
2297997
2297800
−3
−
198
hypothetical protein
-none-
D23_1c2474
Neut_2283

fig|6666666.60966.peg.2485
CDS
2298574
2299293
1
+
720
possible
-none-
D23_1c2475
Neut_2284








transmembrane protein




fig|6666666.60966.peg.2486
CDS
2299389
2301113
3
+
1725
Diguanylate
-none-
D23_1c2476
Neut_2285








cyclase/phosphodiesterase











domain 2 (EAL)




fig|6666666.60966.peg.2488
CDS
2301326
2301784
2
+
459
FKBP-type peptidyl-
-none-
D23_1c2477
Neut_2286








prolyl cis-trans











isomerase




fig|6666666.60966.peg.2489
CDS
2302743
2301856
−3
−
888
Ribosome small
Universal GTPases
D23_1c2478
Neut_2287








subunit-stimulated











GTPase EngC




fig|6666666.60966.peg.2490
CDS
2303060
2302782
−2
−
279
Pterin-4-alpha-
Pterin carbinolamine
D23_1c2479
Neut_2288








carbinolamine
dehydratase










dehydratase (EC











4.2.1.96)




fig|6666666.60966.peg.2491
CDS
2304388
2303120
−1
−
1269
macromolecule
-none-
D23_1c2480
Neut_2289








metabolism;











macromolecule











degradation;











degradation of proteins,











peptides, glycopeptides




fig|6666666.60966.peg.2492
CDS
2304540
2305085
3
+
546
3&#39;-to-5&#39;
RNA processing and
D23_1c2481
Neut_2290








oligoribonuclease (orn)
degradation, bacterial



fig|6666666.60966.peg.2493
CDS
2305123
2307678
1
+
2556
Glycogen
Glycogen metabolism
D23_1c2482
Neut_2291








phosphorylase (EC











2.4.1.1)




fig|6666666.60966.peg.2494
CDS
2308460
2307702
−2
−
759
Pantoate--beta-alanine
Coenzyme A
D23_1c2483
Neut_2292








ligase (EC 6.3.2.1)
Biosynthesis;











<br>Coenzyme A











Biosynthesis cluster



fig|6666666.60966.peg.2495
CDS
2309368
2308559
−1
−
810
3-methyl-2-
Coenzyme A
D23_1c2484
Neut_2293








oxobutanoate
Biosynthesis;










hydroxymethyltransferase
<br>Coenzyme A










(EC 2.1.2.11)
Biosynthesis cluster



fig|6666666.60966.peg.2496
CDS
2310016
2309372
−1
−
645
Deoxyadenosine kinase
Purine conversions;
D23_1c2485
Neut_2294








(EC 2.7.1.76)/
<br>Purine conversions










Deoxyguanosine kinase











(EC 2.7.1.113)




fig|6666666.60966.peg.2497
CDS
2310525
2310013
−3
−
513
2-amino-4-hydroxy-6-
Folate Biosynthesis
D23_1c2486
Neut_2295








hydroxymethyldihydropteridine











pyrophosphokinase (EC











2.7.6.3)




fig|6666666.60966.peg.2498
CDS
2311910
2310522
−2
−
1389
Poly(A) polymerase (EC
Polyadenylation
D23_1c2487
Neut_2296








2.7.7.19)
bacterial



fig|6666666.60966.peg.2499
CDS
2313230
2312073
−2
−
1158
Cardiolipin synthetase
Cardiolipin synthesis;
D23_1c2488
Neut_2297








(EC 2.7.8.—)
<br>Glycerolipid and











Glycerophospholipid











Metabolism in Bacteria



fig|6666666.60966.peg.2500
CDS
2314054
2313227
−1
−
828
Endonuclease/exonuclease/
-none-
D23_1c2489
Neut_2298








phosphatase family











protein




fig|6666666.60966.peg.2501
CDS
2315160
2314060
−3
−
1101
Quinolinate synthetase

Mycobacterium

D23_1c2490
Neut_2299








(EC 2.5.1.72)
virulence operon











possibly involved in











quinolinate biosynthesis;











<br>NAD and NADP











cofactor biosynthesis











global



fig|6666666.60966.peg.2502
CDS
2315495
2316031
2
+
537
FIG00859627:
-none-
D23_1c2491
Neut_2300








hypothetical protein




fig|6666666.60966.peg.2503
CDS
2316137
2316652
2
+
516
LptA, protein essential
Lipopolysaccharide
D23_1c2492
Neut_2301








for LPS transport across
assembly










the periplasm




fig|6666666.60966.peg.2504
CDS
2316704
2317426
2
+
723
Lipopolysaccharide ABC
Lipopolysaccharide
D23_1c2493
Neut_2302








transporter, ATP-
assembly










binding protein LptB




fig|6666666.60966.peg.2505
CDS
2317432
2318895
1
+
1464
RNA polymerase sigma-
Flagellar motility;
D23_1c2494
Neut_2303








54 factor RpoN
<br>Flagellum;











<br>Transcription











initiation, bacterial











sigma factors



fig|6666666.60966.peg.2506
CDS
2319070
2319405
1
+
336
Ribosome hibernation
Ribosome activity
D23_1c2495
Neut_2304








protein YhbH
modulation



fig|6666666.60966.peg.2507
CDS
2319646
2320116
1
+
471
PTS system nitrogen-
-none-
D23_1c2496
Neut_2305








specific IIA component,











PtsN




fig|6666666.60966.peg.2508
CDS
2320103
2321074
2
+
972
HPr
HPr catabolite
D23_1c2497
Neut_2306








kinase/phosphorylase
repression system










(EC 2.7.1.—) (EC 2.7.4.—)




fig|6666666.60966.peg.2509
CDS
2321107
2321223
1
+
117
hypothetical protein
-none-
D23_1c2498
NA

fig|6666666.60966.peg.2510
CDS
2321260
2321874
1
+
615
3-polyprenyl-4-
Ubiquinone
D23_1c2499
Neut_2307








hydroxybenzoate
Biosynthesis;










carboxy-lyase UbiX (EC
<br>Ubiquinone










4.1.1.—)
Biosynthesis-gjo



fig|6666666.60966.peg.2511
CDS
2322562
2321924
−1
−
639
5-
5-FCL-like protein;
D23_1c2500
Neut_2308








formyltetrahydrofolate
<br>Folate Biosynthesis;










cyclo-ligase (EC 6.3.3.2)
<br>One-carbon











metabolism by











tetrahydropterines



fig|6666666.60966.peg.2512
CDS
2323682
2322555
−2
−
1128
A/G-specific adenine
DNA repair, bacterial
D23_1c2501
Neut_2309








glycosylase (EC 3.2.2.—)




fig|6666666.60966.peg.2513
CDS
2324249
2323704
−2
−
546
Intracellular septation
CBSS-211586.9.peg.2729
D23_1c2503
Neut_2310








protein IspA




fig|6666666.60966.peg.2514
CDS
2326043
2324346
−2
−
1698
Lipid A export ATP-
KDO2-Lipid A
D23_1c2504
Neut_2311








binding/permease
biosynthesis cluster 2










protein MsbA (EC











3.6.3.25)




fig|6666666.60966.peg.2515
CDS
2327134
2326562
−1
−
573
hypothetical protein
-none-
D23_1c2505
Neut_2312

fig|6666666.60966.peg.2516
CDS
2329375
2327231
−1
−
2145
Copper resistance
Copper homeostasis
D23_1c2506
Neut_2313








protein D




fig|6666666.60966.peg.2517
CDS
2329755
2329381
−3
−
375
Copper resistance
-none-
D23_1c2507
Neut_2314








protein CopC precursor




fig|6666666.60966.peg.2518
CDS
2330496
2329909
−3
−
588
hypothetical protein
-none-
D23_1c2508
Neut_2074

fig|6666666.60966.peg.2519
CDS
2331308
2330568
−2
−
741
putative (U92432) ORF4
-none-
D23_1c2509
Neut_2316








( Nitrosospira sp. NpAV)




fig|6666666.60966.peg.2520
CDS
2332640
2331375
−2
−
1266
Particulate methane
Particulate methane
D23_1c2510
Neut_2317








monooxygenase B-
monooxygenase










subunit (EC 1.14.13.25)
(pMMO)



fig|6666666.60966.peg.2521
CDS
2333470
2332640
−1
−
831
Particulate methane
Particulate methane
D23_1c2511
Neut_2318








monooxygenase A-
monooxygenase










subunit (EC 1.14.13.25)
(pMMO)



fig|6666666.60966.peg.2522
CDS
2334459
2333644
−3
−
816
Particulate methane
Particulate methane
D23_1c2512
Neut_2319








monooxygenase C-
monooxygenase










subunit (EC 1.14.13.25)
(pMMO)



fig|6666666.60966.peg.2523
CDS
2334883
2335908
1
+
1026
TsaC protein (YrdC-Sua5
-none-
D23_1c2513
Neut_2320








domains) required for











threonylcarbamoyladenosine











t(6)A37











modification in tRNA




fig|6666666.60966.peg.2524
CDS
2335923
2336666
3
+
744
Hypothetical protein
-none-
D23_1c2514
Neut_2321








CbbY




fig|6666666.60966.peg.2525
CDS
2337688
2336702
−1
−
987
Lipoprotein NlpD
Stationary phase repair
D23_1c2515
Neut_2322









cluster



fig|6666666.60966.peg.2526
CDS
2338471
2337803
−1
−
669
Protein-L-isoaspartate
Protein-L-isoaspartate O-
D23_1c2516
Neut_2323








O-methyltransferase
methyltransferase;










(EC 2.1.1.77)
<br>Stationary phase











repair cluster; <br>Ton











and Tol transport











systems



fig|6666666.60966.peg.2528
CDS
2339405
2338662
−2
−
744
5-nucleotidase SurE (EC
Housecleaning
D23_1c2517
Neut_2324








3.1.3.5) @
nucleoside triphosphate










Exopolyphosphatase
pyrophosphatases;










(EC 3.6.1.11)
<br>Phosphate











metabolism;











<br>Polyphosphate;











<br>Stationary phase











repair cluster



fig|6666666.60966.peg.2529
CDS
2340272
2339964
−2
−
309
Integration host factor
DNA structural proteins,
D23_1c2519
Neut_2325








alpha subunit
bacterial



fig|6666666.60966.peg.2530
CDS
2342785
2340485
−1
−
2301
Phenylalanyl-tRNA
tRNA aminoacylation,
D23_1c2520
Neut_2326








synthetase beta chain
Phe










(EC 6.1.1.20)




fig|6666666.60966.peg.2531
CDS
2343901
2342882
−1
−
1020
Phenylalanyl-tRNA
tRNA aminoacylation,
D23_1c2521
Neut_2327








synthetase alpha chain
Phe










(EC 6.1.1.20)




fig|6666666.60966.peg.2532
CDS
2344231
2343989
−1
−
243
LSU ribosomal protein
-none-
D23_1c2522
Neut_2328








L20p




fig|6666666.60966.peg.2533
CDS
2345202
2344723
−3
−
480
Translation initiation
Translation initiation
D23_1c2524
Neut_2330








factor 3
factors bacterial



fig|6666666.60966.peg.2534
CDS
2347209
2345302
−3
−
1908
Threonyl-tRNA
tRNA aminoacylation,
D23_1c2525
Neut_2331








synthetase (EC 6.1.1.3)
Thr



fig|6666666.60966.peg.2535
CDS
2348256
2347537
−3
−
720
Cytochrome c-type
-none-
D23_1c2526
Neut_1790








protein TorY




fig|6666666.60966.peg.2536
CDS
2348966
2348259
−2
−
708
Cytochrome c family
-none-
D23_1c2527
Neut_2333








protein




fig|6666666.60966.peg.2537
CDS
2350169
2349048
−2
−
1122
FIG00859557:
-none-
D23_1c2528
Neut_1792








hypothetical protein




fig|6666666.60966.peg.2538
CDS
2351878
2350166
−1
−
1713
Hydroxylamine
-none-
D23_1c2529
Neut_2335








oxidoreductase











precursor (EC 1.7.3.4)




fig|6666666.60966.peg.2539
CDS
2352170
2353255
2
+
1086
tRNA-specific 2-
RNA methylation
D23_1c2530
Neut_2336








thiouridylase MnmA




fig|6666666.60966.peg.2540
CDS
2354395
2353256
−1
−
1140
Twitching motility
-none-
D23_1c2531
Neut_2337








protein PilT




fig|6666666.60966.peg.2541
CDS
2355448
2354405
−1
−
1044
Twitching motility
-none-
D23_1c2532
Neut_2338








protein PilT




fig|6666666.60966.peg.2543
CDS
2355643
2356359
1
+
717
Hypothetical protein
A Hypothetical Protein
D23_1c2533
Neut_2339








YggS, proline synthase
Related to Proline










co-transcribed bacterial
Metabolism; <br>CBSS-










homolog PROSC
630.2.peg.3360



fig|6666666.60966.peg.2544
CDS
2356597
2356328
−1
−
270
4Fe—4S ferredoxin, iron-
Inorganic Sulfur
D23_1c2534
Neut_2340








sulfur binding
Assimilation



fig|6666666.60966.peg.2545
CDS
2357097
2356603
−3
−
495
Phosphopantetheine
CBSS-
D23_1c2535
Neut_2341








adenylyltransferase (EC
266117.6.peg.1260;










2.7.7.3)
<br>CBSS-269801.1.peg.1715;











<br>Coenzyme A











Biosynthesis



fig|6666666.60966.peg.2546
CDS
2357644
2357090
−1
−
555
16S rRNA
CBSS-
D23_1c2536
Neut_2342








(guanine(966)-N(2))-
266117.6.peg.1260;










methyltransferase (EC
<br>CBSS-










2.1.1.171) ## SSU rRNA
269801.1.peg.1715;










m(2)G966
<br>Heat shock Cell











division Proteases and a











Methyltransferase;











<br>RNA methylation



fig|6666666.60966.peg.2547
CDS
2358960
2357659
−3
−
1302
FIG015287: Zinc
Heat shock Cell division
D23_1c2537
Neut_2343








protease
Proteases and a











Methyltransferase



fig|6666666.60966.peg.2548
CDS
2359437
2359126
−3
−
312
Transposase
-none-
D23_1c2538
Neut_2344

fig|6666666.60966.peg.2549
CDS
2360187
2359819
−3
−
369
Mobile element protein
-none-
D23_1c2539
Neut_1814

fig|6666666.60966.peg.2550
CDS
2360570
2360247
−2
−
324
Putative periplasmic
-none-
D23_1c2540
Neut_2357








protein




fig|6666666.60966.peg.2551
CDS
2361073
2360771
−1
−
303
hypothetical protein
-none-
D23_1c2541
Neut_2349

fig|6666666.60966.peg.2552
CDS
2361307
2361110
−1
−
198
CsbD family protein
-none-
D23_1c2542
Neut_2359

fig|6666666.60966.peg.2553
CDS
2361551
2361384
−2
−
168
protein of unknown
-none-
D23_1c2543
NA








function DUF1328




fig|6666666.60966.peg.2554
CDS
2361863
2362066
2
+
204
Mobile element protein
-none-
D23_1c2544
Neut_2365

fig|6666666.60966.peg.2555
CDS
2362071
2362247
3
+
177
hypothetical protein
-none-
D23_1c2545
NA

fig|6666666.60966.peg.2556
CDS
2362394
2362957
2
+
564
Alkyl hydroperoxide
Thioredoxin-disulfide
D23_1c2546
Neut_2366








reductase protein C (EC
reductase










1.6.4.—)




fig|6666666.60966.peg.2557
CDS
2363052
2363633
3
+
582
putative lipoprotein
-none-
D23_1c2547
Neut_2367

fig|6666666.60966.peg.2558
CDS
2364440
2363661
−2
−
780
Putative
-none-
D23_1c2548
Neut_2368








stomatin/prohibitin-











family membrane











protease subunit











aq_911




fig|6666666.60966.peg.2559
CDS
2365869
2364442
−3
−
1428
Putative membrane-
-none-
D23_1c2549
Neut_2369








bound ClpP-class











protease associated











with aq_911




fig|6666666.60966.peg.2560
CDS
2366482
2365880
−1
−
603
ADP-ribose
CBSS-216591.1.peg.168;
D23_1c2550
Neut_2370








pyrophosphatase (EC
<br>NADand NADP










3.6.1.13)
cofactor biosynthesis











global; <br>Nudix











proteins (nucleoside











triphosphate hydrolases)



fig|6666666.60966.peg.2561
CDS
2367579
2366665
−3
−
915
putative membrane
-none-
D23_1c2551
Neut_2371








protein




fig|6666666.60966.peg.2562
CDS
2367673
2368539
1
+
867
Protein YicC
CBSS-323097.3.peg.2594
D23_1c2552
Neut_2372

fig|6666666.60966.peg.2563
CDS
2369652
2368633
−3
−
1020
C4-dicarboxylate
-none-
D23_1c2553
Neut_2373








transporter/malic acid











transport protein




fig|6666666.60966.peg.2564
CDS
2371015
2370053
−1
−
963
Mobile element protein
-none-
D23_1c2554
Neut_1746

fig|6666666.60966.peg.2565
CDS
2371724
2371065
−2
−
660
Glucose-1-phosphate
Rhamnose containing
D23_1c2555
Neut_2374








thymidylyltransferase
glycans; <br>dTDP-










(EC 2.7.7.24)
rhamnose synthesis



fig|6666666.60966.peg.2566
CDS
2372737
2371739
−1
−
999
COG3178: Predicted
-none-
D23_1c2556
Neut_2375








phosphotransferase











related to Ser/Thr











protein kinases




fig|6666666.60966.peg.2567
CDS
2372902
2373210
1
+
309
Putative cytoplasmic
-none-
D23_1c2557
Neut_2376








protein




fig|6666666.60966.peg.2568
CDS
2373276
2374775
3
+
1500
MG(2+) CHELATASE
-none-
D23_1c2559
Neut_2377








FAMILY PROTEIN/











ComM-related protein




fig|6666666.60966.peg.2569
CDS
2376191
2374794
−2
−
1398
Replicative DNA
-none-
D23_1c2560
Neut_2378








helicase (EC 3.6.1.—)




fig|6666666.60966.peg.2571
CDS
2376752
2376297
−2
−
456
LSU ribosomal protein
Primosomal replication
D23_1c2561
Neut_2379








L9p
protein N clusters with











ribosomal proteins



fig|6666666.60966.peg.2572
CDS
2377049
2376771
−2
−
279
SSU ribosomal protein
Primosomal replication
D23_1c2562
Neut_2380








S18p @ SSU ribosomal
protein N clusters with










protein S18p, zinc-
ribosomal proteins










independent




fig|6666666.60966.peg.2573
CDS
2377399
2377091
−1
−
309
Primosomal replication
Primosomal replication
D23_1c2563
Neut_2381








protein N
protein N clusters with











ribosomal proteins



fig|6666666.60966.peg.2574
CDS
2377721
2377401
−2
−
321
SSU ribosomal protein
Primosomal replication
D23_1c2564
Neut_2382








S6p
protein N clusters with











ribosomal proteins



fig|6666666.60966.peg.2576
CDS
2378765
2378340
−2
−
426
hypothetical protein
-none-
D23_1c2565
NA

fig|6666666.60966.peg.2578
CDS
2379069
2380031
3
+
963
Mobile element protein
-none-
D23_1c2566
Neut_1746

fig|6666666.60966.peg.2580
CDS
2380409
2380864
2
+
456
Mobile element protein
-none-
D23_1c2567
Neut_0883

fig|6666666.60966.peg.2581
CDS
2381862
2380975
−3
−
888
Acetylglutamate kinase
Arginine Biosynthesis--
D23_1c2568
Neut_2384








(EC 2.7.2.8)
gjo; <br>Arginine











Biosynthesis extended



fig|6666666.60966.peg.2582
CDS
2382398
2381919
−2
−
480
type IV pili signal
-none-
D23_1c2569
Neut_2385








transduction protein Pill




fig|6666666.60966.peg.2583
CDS
2382774
2382427
−3
−
348
twitching motility
-none-
D23_1c2570
Neut_2386








protein PilH




fig|6666666.60966.peg.2584
CDS
2383169
2383639
2
+
471
21 kDa hemolysin
CBSS-160492.1.peg.550
D23_1c2571
Neut_2387








precursor




fig|6666666.60966.peg.2585
CDS
2383676
2385043
2
+
1368
Fe—S protein, homolog
-none-
D23_1c2572
Neut_2388








of lactate











dehydrogenase SO1521




fig|6666666.60966.peg.2586
CDS
2386032
2385136
−3
−
897
Heme O synthase,
Biogenesis of
D23_1c2573
Neut_2389








protoheme IX
cytochrome c oxidases;










farnesyltransferase (EC
<br>CBSS-










2.5.1.—) COX10-CtaB
196164.1.peg.1690;











<br>CBSS-











316057.3.peg.563



fig|6666666.60966.peg.2587
CDS
2386422
2386123
−3
−
300
Probable
-none-
D23_1c2574
Neut_2390








transmembrane protein




fig|6666666.60966.peg.2588
CDS
2387398
2386679
−1
−
720
Cytochrome oxidase
Biogenesis of
D23_1c2575
Neut_2391








biogenesis protein
cytochrome c oxidases;










Surf1, facilitates heme
<br>CBSS-










A insertion
316057.3.peg.563



fig|6666666.60966.peg.2589
CDS
2388336
2387491
−3
−
846
Cytochrome c oxidase
CBSS-316057.3.peg.563;
D23_1c2576
Neut_2392








polypeptide III (EC
<br>Terminal










1.9.3.1)
cytochrome C oxidases



fig|6666666.60966.peg.2590
CDS
2389047
2388529
−3
−
519
Cytochrome oxidase
Biogenesis of cytochrome c oxidases;
D23_1c2577
Neut_2393








biogenesis protein
<br>CBSS-










Cox11-CtaG, copper
316057.3.peg.563










delivery to Cox1




fig|6666666.60966.peg.2591
CDS
2390759
2389182
−2
−
1578
Cytochrome c oxidase
Terminal cytochrome C
D23_1c2578
Neut_2394








polypeptide I (EC
oxidases










1.9.3.1)




fig|6666666.60966.peg.2592
CDS
2391643
2390819
−1
−
825
Cytochrome c oxidase
CBSS-316057.3.peg.563;
D23_1c2579
Neut_2395








polypeptide II (EC
<br>Terminal










1.9.3.1)
cytochrome C oxidases



fig|6666666.60966.peg.2594
CDS
2392145
2392567
2
+
423
Putative TEGT family
CBSS-326442.4.peg.1852
D23_1c2580
NA








carrier/transport











protein




fig|6666666.60966.peg.2595
CDS
2392600
2392884
1
+
285
Putative TEGT family
CBSS-326442.4.peg.1852
D23_1c2581
Neut_1715








carrier/transport











protein




fig|6666666.60966.peg.2596
CDS
2393084
2393302
2
+
219
Copper chaperone
Copper homeostasis
D23_1c2582
Neut_2397

fig|6666666.60966.peg.2597
CDS
2393426
2394394
2
+
969
Acetyl-coenzyme A
Fatty Acid Biosynthesis
D23_1c2583
Neut_2398








carboxyl transferase
FASII










alpha chain (EC 6.4.1.2)




fig|6666666.60966.peg.2598
CDS
2394357
2395742
3
+
1386
tRNA(Ile)-lysidine
-none-
D23_1c2584
Neut_2399








synthetase




fig|6666666.60966.peg.2599
CDS
2395746
2396807
3
+
1062
dTDP-glucose 4,6-
CBSS-
D23_1c2585
Neut_2400








dehydratase (EC
296591.1.peg.2330;










4.2.1.46)
<br>Rhamnose











containing glycans;











<br>dTDP-rhamnose











synthesis



fig|6666666.60966.peg.2600
CDS
2396804
2397700
2
+
897
dTDP-4-
Rhamnose containing
D23_1c2586
Neut_2401








dehydrorhamnose
glycans; <br>dTDP-










reductase (EC
rhamnose synthesis










1.1.1.133)




fig|6666666.60966.peg.2601
CDS
2398663
2397710
−1
−
954
InterPro IPR002142
-none-
D23_1c2587
Neut_2402








COGs COG0616




fig|6666666.60966.peg.2602
CDS
2399353
2398691
−1
−
663
Outer membrane
Ton and Tol transport
D23_1c2588
Neut_2403








lipoprotein omp16
systems










precursor




fig|6666666.60966.peg.2603
CDS
2400398
2399562
−2
−
837
SH3, type 3 domain
-none-
D23_1c2590
Neut_2404








protein




fig|6666666.60966.peg.2604
CDS
2400602
2401477
2
+
876
esterase/lipase/thioesterase
-none-
D23_1c2591
Neut_2408








family active site




fig|6666666.60966.peg.2605
CDS
2402010
2401492
−3
−
519
Mobile element protein
-none-
D23_1c2592
Neut_2502

fig|6666666.60966.peg.2606
CDS
2402097
2403560
3
+
1464
hypothetical protein
-none-
D23_1c2593
Neut_2493

fig|6666666.60966.peg.2607
CDS
2403699
2404946
3
+
1248
Lipoprotein releasing
Lipopolysaccharide
D23_1c2594
Neut_2492








system transmembrane
assembly;










protein LolE
<br>Lipoprotein sorting











system



fig|6666666.60966.peg.2608
CDS
2404939
2405613
1
+
675
Lipoprotein releasing
Lipopolysaccharide
D23_1c2595
Neut_2491








system ATP-binding
assembly;










protein LolD
<br>Lipoprotein sorting











system



fig|6666666.60966.peg.2609
CDS
2406957
2405641
−3
−
1317
FIG065221: Holliday
CBSS-83333.1.peg.876
D23_1c2596
Neut_2490








junction DNA helicase




fig|6666666.60966.peg.2610
CDS
2407570
2406950
−1
−
621
Outer membrane
CBSS-83333.1.peg.876;
D23_1c2597
Neut_2489








lipoprotein carrier
<br>Lipopolysaccharide










protein LolA
assembly;











<br>Lipoprotein sorting











system



fig|6666666.60966.peg.2611
CDS
2409936
2407630
−3
−
2307
Cell division protein
Bacterial cell Division;
D23_1c2598
Neut_2488








FtsK
<br>Bacterial











cytoskeleton;











<br>Bacterial RNA-











metabolizing Zn-











dependent hydrolases;











<br>CBSS-











83333.1.peg.876



fig|6666666.60966.peg.2612
CDS
2411206
2410151
−1
−
1056
InterPro IPR002110
-none-
D23_1c2600
Neut_2487








COGs COG0666




fig|6666666.60966.peg.2613
CDS
2412939
2411203
−3
−
1737
Succinate
Succinate
D23_1c2601
Neut_2486








dehydrogenase
dehydrogenase;










flavoprotein subunit (EC
<br>TCA Cycle










1.3.99.1)




fig|6666666.60966.peg.2614
CDS
2413237
2412968
−1
−
270
Succinate
Succinate
D23_1c2602
Neut_2485








dehydrogenase
dehydrogenase










hydrophobic membrane











anchor protein




fig|6666666.60966.peg.2615
CDS
2413803
2413315
−3
−
489
Succinate
Succinate
D23_1c2603
Neut_2484








dehydrogenase
dehydrogenase










cytochrome b-556











subunit




fig|6666666.60966.peg.2616
CDS
2413889
2415583
2
+
1695
CTP synthase (EC
CTP synthase (EC
D23_1c2604
Neut_2483








6.3.4.2)
6.3.4.2) cluster;











<br>pyrimidine











conversions



fig|6666666.60966.peg.2617
CDS
2415872
2417158
2
+
1287
Enolase (EC 4.2.1.11)
Glycolysis and
D23_1c2605
Neut_2482









Gluconeogenesis



fig|6666666.60966.peg.2618
CDS
2417185
2417436
1
+
252
Cell division protein
Bacterial cell Division;
D23_1c2606
Neut_2481








DivIC (FtsB), stabilizes
<br>Bacterial










FtsL against RasP
cytoskeleton;










cleavage
<br>Stationary phase











repair cluster



fig|6666666.60966.peg.2619
CDS
2417726
2417860
2
+
135
hypothetical protein
-none-
D23_1c2607
NA

fig|6666666.60966.peg.2621
CDS
2419576
2418317
−1
−
1260
Transcription
Transcription factors
D23_1c2609
Neut_2479








termination factor Rho
bacterial



fig|6666666.60966.peg.2622
CDS
2420006
2419791
−2
−
216
Thioredoxin
-none-
D23_1c2610
Neut_2478

fig|6666666.60966.peg.2624
CDS
2420605
2421762
1
+
1158
Membrane-bound lytic
Murein Hydrolases;
D23_1c2611
Neut_2477








murein transglycosylase
<br>Peptidoglycan










B precursor (EC 3.2.1.—)
Biosynthesis



fig|6666666.60966.peg.2625
CDS
2422278
2421835
−3
−
444
Universal stress protein
-none-
D23_1c2612
Neut_2476








family COG0589




fig|6666666.60966.peg.2626
CDS
2424743
2422389
−2
−
2355
Partial urea carboxylase
Urea carboxylase and
D23_1c2613
Neut_2475








2 (EC 6.3.4.6)
Allophanate hydrolase











cluster; <br>Urea











decomposition



fig|6666666.60966.peg.2627
CDS
2425462
2424797
−1
−
666
Urea carboxylase-
Urea decomposition
D23_1c2614
Neut_2474








related











aminomethyltransferase











(EC 2.1.2.10)




fig|6666666.60966.peg.2628
CDS
2426187
2425459
−3
−
729
Urea carboxylase-
Urea decomposition
D23_1c2615
Neut_2473








related











aminomethyltransferase











(EC 2.1.2.10)




fig|6666666.60966.peg.2629
CDS
2427740
2426202
−2
−
1539
Urea carboxylase-
Urea decomposition
D23_1c2616
Neut_2472








related amino acid











permease




fig|6666666.60966.peg.2630
CDS
2427773
2427892
2
+
120
hypothetical protein
-none-
D23_1c2617
NA

fig|6666666.60966.peg.2631
CDS
2428128
2428319
3
+
192
hypothetical protein
-none-
D23_1c2618
NA

fig|6666666.60966.peg.2632
CDS
2428646
2428518
−2
−
129
hypothetical protein
-none-
D23_1c2620
NA

fig|6666666.60966.peg.2633
CDS
2428671
2432291
3
+
3621
Urea carboxylase (EC
Urea carboxylase and
D23_1c2621
Neut_2470








6.3.4.6)
Allophanate hydrolase











cluster; <br>Urea











decomposition



fig|6666666.60966.peg.2634
CDS
2433643
2432279
−1
−
1365
Membrane-bound lytic
CBSS-228410.1.peg.134;
D23_1c2622
Neut_2469








murein transglycosylase
<br>CBSS-










D precursor (EC 3.2.1.—)
342610.3.peg.1536;











<br>Murein Hydrolases



fig|6666666.60966.peg.2635
CDS
2434924
2433791
−1
−
1134
Ribonucleotide
Ribonucleotide
D23_1c2623
Neut_2468








reductase of class Ia
reduction










(aerobic), beta subunit











(EC 1.17.4.1)




fig|6666666.60966.peg.2636
CDS
2437918
2434976
−1
−
2943
Ribonucleotide
Ribonucleotide
D23_1c2624
Neut_2467








reductase of class Ia
reduction










(aerobic), alpha subunit











(EC 1.17.4.1)




fig|6666666.60966.peg.2637
CDS
2438096
2441536
2
+
3441
Long-chain-fatty-acid--
Biotin biosynthesis;
D23_1c2625
Neut_2466








CoA ligase (EC 6.2.1.3)
<br>Biotin synthesis











cluster; <br>Fatty acid











metabolism cluster



fig|6666666.60966.peg.2638
CDS
2441648
2441788
2
+
141
hypothetical protein
-none-
D23_1c2626
NA

fig|6666666.60966.peg.2639
CDS
2441958
2441845
−3
−
114
hypothetical protein
-none-
D23_1c2627
NA

fig|6666666.60966.peg.2640
CDS
2441984
2442337
2
+
354
S-adenosylmethionine
Polyamine Metabolism
D23_1c2628
Neut_2465








decarboxylase











proenzyme (EC











4.1.1.50), prokaryotic











class 1B




fig|6666666.60966.peg.2641
CDS
2442337
2443296
1
+
960
Spermidine synthase
Polyamine Metabolism
D23_1c2629
Neut_2464








(EC 2.5.1.16)




fig|6666666.60966.peg.2642
CDS
2444178
2443342
−3
−
837
Cytochrome c family
-none-
D23_1c2630
Neut_2463








protein




fig|6666666.60966.peg.2643
CDS
2446065
2444275
−3
−
1791
ABC transporter, fused
-none-
D23_1c2631
Neut_2462








permease and ATPase











domains




fig|6666666.60966.peg.2644
CDS
2446735
2446268
−1
−
468
Single-stranded DNA-
DNA repair, bacterial
D23_1c2632
Neut_2461








binding protein




fig|6666666.60966.peg.2645
CDS
2448142
2446736
−1
−
1407
Putative transport
-none-
D23_1c2633
Neut_2460








protein




fig|6666666.60966.peg.2646
CDS
2448217
2451054
1
+
2838
Excinuclease ABC
DNA repair, UvrABC
D23_1c2634
Neut_2459








subunit A
system



fig|6666666.60966.peg.2647
CDS
2451051
2452322
3
+
1272
D-glycerate 2-kinase (EC
Glycerate metabolism
D23_1c2635
Neut_2458








2.7.1.—)




fig|6666666.60966.peg.2648
CDS
2455286
2452443
−2
−
2844
Aconitate hydratase (EC
TCA Cycle
D23_1c2637
Neut_2457








4.2.1.3)




fig|6666666.60966.peg.2649
CDS
2455429
2456334
1
+
906
Aldose 1-epimerase
-none-
D23_1c2638
Neut_2456

fig|6666666.60966.peg.2650
CDS
2456378
2456941
2
+
564
NADPH-dependent
-none-
D23_1c2639
Neut_2455








FMN reductase




fig|6666666.60966.peg.2651
CDS
2457281
2457051
−2
−
231
HrgA protein
-none-
D23_1c2640
Neut_2454

fig|6666666.60966.peg.2652
CDS
2457998
2457480
−2
−
519
HrgA protein
-none-
D23_1c2641
NA

fig|6666666.60966.peg.2653
CDS
2459350
2458013
−1
−
1338
hypothetical protein
-none-
D23_1c2642
NA

fig|6666666.60966.peg.2654
CDS
2460249
2459347
−3
−
903
hypothetical protein
-none-
D23_1c2643
NA

fig|6666666.60966.peg.2655
CDS
2463305
2460264
−2
−
3042
Type I restriction-
Restriction-Modification
D23_1c2644
NA








modification system,
System; <br>Type I










restriction subunit R (EC
Restriction-Modification










3.1.21.3)




fig|6666666.60966.peg.2656
CDS
2463943
2463341
−1
−
603
hypothetical protein
-none-
D23_1c2645
NA

fig|6666666.60966.peg.2657
CDS
2465348
2463960
−2
−
1389
Type I restriction-
Restriction-Modification
D23_1c2646
NA








modification system,
System; <br>Type I










specificity subunit S (EC
Restriction-Modification










3.1.21.3)




fig|6666666.60966.peg.2658
CDS
2467567
2465348
−1
−
2220
Type I restriction-
Restriction-Modification
D23_1c2647
Neut_0541








modification system,
System; <br>Type I










DNA-methyltransferase
Restriction-Modification










subunit M (EC 2.1.1.72)




fig|6666666.60966.peg.2659
CDS
2468029
2467751
−1
−
279
Type I restriction-
Restriction-Modification
D23_1c2648
Neut_2448








modification system,
System; <br>Type I










DNA-methyltransferase
Restriction-Modification










subunit M (EC 2.1.1.72)




fig|6666666.60966.peg.2660
CDS
2468945
2468235
−2
−
711
RNA polymerase sigma
Flagellar motility;
D23_1c2650
Neut_2447








factor for flagellar
<br>Flagellum;










operon
<br>Transcription











initiation, bacterial











sigma factors



fig|6666666.60966.peg.2661
CDS
2469847
2468954
−1
−
894
Flagellar synthesis
Flagellar motility;
D23_1c2651
Neut_2446








regulator FleN
<br>Flagellum



fig|6666666.60966.peg.2662
CDS
2471090
2469840
−2
−
1251
Flagellar biosynthesis
Flagellar motility;
D23_1c2652
Neut_2445








protein FlhF
<br>Flagellum



fig|6666666.60966.peg.2663
CDS
2473171
2471087
−1
−
2085
Flagellar biosynthesis
Flagellar motility;
D23_1c2653
Neut_2444








protein FlhA
<br>Flagellum



fig|6666666.60966.peg.2664
CDS
2474349
2473219
−3
−
1131
Flagellar biosynthesis
Flagellar motility;
D23_1c2654
Neut_2443








protein FlhB
<br>Flagellum



fig|6666666.60966.peg.2665
CDS
2476208
2474601
−2
−
1608
Peptide chain release
Translation termination
D23_1c2655
Neut_2442








factor 3
factors bacterial



fig|6666666.60966.peg.2666
CDS
2478262
2476208
−1
−
2055
Dipeptide transport
ABC transporter
D23_1c2656
Neut_2441








ATP-binding protein
dipeptide (TC 3.A.1.5.2)










DppF (TC 3.A.1.5.2)




fig|6666666.60966.peg.2667
CDS
2479752
2478259
−3
−
1494
Oligopeptide transport
-none-
D23_1c2657
Neut_2440








system permease











protein




fig|6666666.60966.peg.2669
CDS
2480032
2480334
1
+
303
Negative regulator of
Flagellum
D23_1c2658
Neut_2439








flagellin synthesis




fig|6666666.60966.peg.2670
CDS
2480417
2480800
2
+
384
Flagellar biosynthesis
Flagellum
D23_1c2659
Neut_2438








protein FlgN




fig|6666666.60966.peg.2671
CDS
2481184
2483109
1
+
1926
tRNA uridine 5-
Cell Division Subsystem
D23_1c2660
Neut_2437








carboxymethylaminomethyl
including YidCD;










modification
<br>RNA modification










enzyme GidA
and chromosome











partitioning cluster;











<br>mnm5U34











biosynthesis bacteria;











<br>tRNA modification











Bacteria



fig|6666666.60966.peg.2672
CDS
2483084
2483728
2
+
645
rRNA small subunit 7-
Cell Division Subsystem
D23_1c2661
Neut_2436








methylguanosine (m7G)
including YidCD;










methyltransferase GidB
<br>RNA methylation;











<br>RNA modification











and chromosome











partitioning cluster



fig|6666666.60966.peg.2673
CDS
2483792
2484556
2
+
765
Chromosome (plasmid)
Bacterial Cell Division;
D23_1c2662
Neut_2435








partitioning protein
<br>Bacterial










ParA/Sporulation
Cytoskeleton;










initiation inhibitor
<br>Bacterial










protein Soj
Cytoskeleton; <br>Cell











Division Subsystem











including YidCD;











<br>RNA modification











and chromosome











partitioning cluster



fig|6666666.60966.peg.2674
CDS
2484637
2485440
1
+
804
Chromosome (plasmid)
Bacterial Cytoskeleton;
D23_1c2663
Neut_2434








partitioning protein
<br>Bacterial










ParB/Stage 0
Cytoskeleton; <br>Cell










sporulation protein J
Division Subsystem











including YidCD;











<br>RNA modification











and chromosome











partitioning cluster



fig|6666666.60966.peg.2675
CDS
2485777
2488083
1
+
2307
Glucose-6-phosphate
Glycolysis and
D23_1c2664
Neut_2433








isomerase (EC 5.3.1.9)
Gluconeogenesis



fig|6666666.60966.peg.2676
CDS
2488076
2489131
2
+
1056
6-phosphogluconate
D-gluconate and
D23_1c2665
Neut_2432








dehydrogenase,
ketogluconates










decarboxylating (EC
metabolism;










1.1.1.44)
<br>Pentose phosphate











pathway



fig|6666666.60966.peg.2677
CDS
2489149
2490591
1
+
1443
Glucose-6-phosphate 1-
Pentose phosphate
D23_1c2666
Neut_2431








dehydrogenase (EC
pathway










1.1.1.49)




fig|6666666.60966.peg.2678
CDS
2490598
2490741
1
+
144
hypothetical protein
-none-
D23_1c2667
NA

fig|6666666.60966.peg.2679
CDS
2491345
2490770
−1
−
576
putative membrane
-none-
D23_1c2668
Neut_2430








protein




fig|6666666.60966.peg.2680
CDS
2491701
2492270
3
+
570
DedA family inner
DedA family of inner
D23_1c2669
Neut_2429








membrane protein
membrane proteins










YohD




fig|6666666.60966.peg.2681
CDS
2492664
2492897
3
+
234
Mobile element protein
-none-
D23_1c2671
Neut_2428

fig|6666666.60966.peg.2682
CDS
2493050
2494789
2
+
1740
ABC-type anion
-none-
D23_1c2672
Neut_2427








transport system,











duplicated permease











component




fig|6666666.60966.peg.2683
CDS
2494811
2496100
2
+
1290
ABC-type
Alkanesulfonate
D23_1c2673
Neut_2426








nitrate/sulfonate/bicarbonate
assimilation










transport system,











ATPase component




fig|6666666.60966.peg.2684
CDS
2499268
2496263
−1
−
3006
Exonuclease SbcC
DNA repair, bacterial;
D23_1c2676
Neut_2425









<br>Rad50-Mre11 DNA











repair cluster



fig|6666666.60966.peg.2685
CDS
2499230
2499520
2
+
291
hypothetical protein
-none-
D23_1c2677
NA

fig|6666666.60966.peg.2686
CDS
2500770
2499526
−3
−
1245
Exonuclease SbcD
DNA repair, bacterial;
D23_1c2678
Neut_2424









<br>Rad50-Mre11 DNA











repair cluster



fig|6666666.60966.peg.2687
CDS
2501402
2500767
−2
−
636
FIG01057587:
-none-
D23_1c2679
NA








hypothetical protein




fig|6666666.60966.peg.2688
CDS
2501615
2502037
2
+
423
Mobile element protein
-none-
D23_1c2680
Neut_2450

fig|6666666.60966.peg.2689
CDS
2502217
2502050
−1
−
168
hypothetical protein
-none-
D23_1c2681
NA

fig|6666666.60966.peg.2691
CDS
2503677
2502628
−3
−
1050
hypothetical protein
-none-
D23_1c2682
Neut_2415

fig|6666666.60966.peg.2692
CDS
2503893
2504105
3
+
213
hypothetical protein
-none-
D23_1c2683
NA

fig|6666666.60966.peg.2693
CDS
2505239
2504595
−2
−
645
hypothetical protein
-none-
D23_1c2685
NA

fig|6666666.60966.peg.2694
CDS
2506092
2505229
−3
−
864
Mobile element protein
-none-
D23_1c2686
Neut_2192

fig|6666666.60966.peg.2695
CDS
2506385
2506089
−2
−
297
Mobile element protein
-none-
D23_1c2687
Neut_2193

fig|6666666.60966.peg.2696
CDS
2506924
2506445
−1
−
480
DNA primase/helicase,
Phage replication
D23_1c2688
NA








phage-associated




fig|6666666.60966.peg.2697
CDS
2507166
2506921
−3
−
246
hypothetical protein
-none-
D23_1c2689
NA

fig|6666666.60966.peg.2698
CDS
2507393
2507166
−2
−
228
hypothetical protein
-none-
D23_1c2690
NA

fig|6666666.60966.peg.2699
CDS
2507735
2508577
2
+
843
hypothetical protein
-none-
D23_1c2691
NA

fig|6666666.60966.peg.2700
CDS
2508650
2509111
2
+
462
Putative bacteriophage-
-none-
D23_1c2692
NA








related protein




fig|6666666.60966.peg.2701
CDS
2509108
2510448
1
+
1341
probable DNA invertase
-none-
D23_1c2693
Neut_2563

fig|6666666.60966.peg.2702
CDS
2510478
2510897
3
+
420
elements of external
-none-
D23_1c2694
NA








origin; phage-related











functions and











prophages




fig|6666666.60966.peg.2703
CDS
2512240
2511590
−1
−
651
Similar to
2-phosphoglycolate
D23_1c2696
Neut_2506








phosphoglycolate
salvage










phosphatase, clustered











with ubiquinone











biosynthesis SAM-











dependent O-











methyltransferase




fig|6666666.60966.peg.2704
CDS
2512973
2512269
−2
−
705
3-demethylubiquinol 3-
Ubiquinone
D23_1c2697
Neut_2507








O-methyltransferase
Biosynthesis;










(EC 2.1.1.64)
<br>Ubiquinone











Biosynthesis-gjo



fig|6666666.60966.peg.2705
CDS
2513079
2512963
−3
−
117
hypothetical protein
-none-
D23_1c2698
NA

fig|6666666.60966.peg.2706
CDS
2513892
2513197
−3
−
696
Outer membrane
Osmoregulation
D23_1c2699
Neut_2508








protein A precursor




fig|6666666.60966.peg.2708
CDS
2514251
2515009
2
+
759
ABC-type multidrug
CBSS-196164.1.peg.1690
D23_1c2700
Neut_2509








transport system,











ATPase component




fig|6666666.60966.peg.2709
CDS
2515006
2515752
1
+
747
gliding motility protein
-none-
D23_1c2701
Neut_2510








GldF




fig|6666666.60966.peg.2710
CDS
2515776
2517128
3
+
1353
Mucin 2 precursor
-none-
D23_1c2702
Neut_2511

fig|6666666.60966.peg.2711
CDS
2517144
2517959
3
+
816
Formamidopyrimidine-
DNA Repair Base
D23_1c2703
Neut_2512








DNA glycosylase (EC
Excision










3.2.2.23)




fig|6666666.60966.peg.2712
CDS
2518479
2517994
−3
−
486
Thioredoxin
-none-
D23_1c2704
Neut_2513

fig|6666666.60966.peg.2713
CDS
2520458
2518644
−2
−
1815
GTP-binding protein
Universal GTPases
D23_1c2705
Neut_2514








TypA/BipA




fig|6666666.60966.peg.2714
CDS
2520591
2521196
3
+
606
Riboflavin synthase
Riboflavin, FMN and FAD
D23_1c2706
Neut_2515








eubacterial/eukaryotic
metabolism;










(EC 2.5.1.9)
<br>Riboflavin, FMN and











FAD metabolism in











plants; <br>Riboflavin











synthesis cluster;











<br>riboflavin to FAD



fig|6666666.60966.peg.2715
CDS
2521193
2522302
2
+
1110
3,4-dihydroxy-2-
Riboflavin, FMN and FAD
D23_1c2707
Neut_2516








butanone 4-phosphate
metabolism;










synthase (EC 4.1.99.12)/
<br>Riboflavin, FMN and










GTP cyclohydrolase II
FAD metabolism;










(EC 3.5.4.25)
<br>Riboflavin, FMN and











FAD metabolism in











plants; <br>Riboflavin,











FMN and FAD











metabolism in plants;











<br>Riboflavin synthesis











cluster; <br>Riboflavin











synthesis cluster;











<br>riboflavin to FAD



fig|6666666.60966.peg.2716
CDS
2522529
2523026
3
+
498
6,7-dimethyl-8-
Possible RNA
D23_1c2708
Neut_2517








ribityllumazine synthase
degradation cluster;










(EC 2.5.1.78)
<br>Riboflavin, FMN and











FAD metabolism;











<br>Riboflavin, FMN and











FAD metabolism in











plants; <br>Riboflavin











synthesis cluster



fig|6666666.60966.peg.2717
CDS
2523023
2523526
2
+
504
Transcription
Riboflavin synthesis
D23_1c2709
Neut_2518








termination protein
cluster;










NusB
<br>Transcription











factors bacterial



fig|6666666.60966.peg.2719
CDS
2523801
2524787
3
+
987
Thiamine-
5-FCL-like protein;
D23_1c2710
Neut_2519








monophosphate kinase
<br>Riboflavin synthesis










(EC 2.7.4.16)
cluster; <br>Thiamin











biosynthesis



fig|6666666.60966.peg.2720
CDS
2524864
2525307
1
+
444
Phosphatidylglycerophosphatase
Glycerolipid and
D23_1c2711
Neut_2520








A (EC 3.1.3.27)
Glycerophospholipid











Metabolism in Bacteria;











<br>Riboflavin synthesis











cluster



fig|6666666.60966.peg.2721
CDS
2525304
2525846
3
+
543
C-terminal domain of
DNA repair system
D23_1c2712
Neut_2521








CinA type S; Protein
including RecA, MutS










Implicated in DNA
and a hypothetical










repair function with
protein; <br>NAD and










RecA and MutS
NADP cofactor











biosynthesis global;











<br>NAD and NADP











cofactor biosynthesis











global; <br>Possible RNA











degradation cluster;











<br>Riboflavin, FMN and











FAD metabolism in











plants; <br>Riboflavin











synthesis cluster



fig|6666666.60966.peg.2722
CDS
2527502
2526306
−2
−
1197
FIG00859610:
-none-
D23_1c2713
Neut_2522








hypothetical protein




fig|6666666.60966.peg.2723
CDS
2529448
2527829
−1
−
1620
ATP-dependent DNA
-none-
D23_1c2714
Neut_2523








helicase RecQ




fig|6666666.60966.peg.2724
CDS
2529855
2529445
−3
−
411
Ribosome-associated
DNA replication cluster
D23_1c2715
Neut_2524








heat shock protein
1; <br>Heat shock dnaK










implicated in the
gene cluster extended










recycling of the 50S











subunit (S4 paralog)




fig|6666666.60966.peg.2725
CDS
2530686
2529877
−3
−
810
InterPro IPR002781
-none-
D23_1c2716
Neut_2525








COGs COG0730




fig|6666666.60966.peg.2726
CDS
2532376
2530694
−1
−
1683
FIG003847:
CBSS-269482.4.peg.5018
D23_1c2717
Neut_2526








Oxidoreductase











(flavoprotein)




fig|6666666.60966.peg.2727
CDS
2532913
2532488
−1
−
426
Transcriptional
-none-
D23_1c2718
Neut_2527








regulator, ArsR family




fig|6666666.60966.peg.2728
CDS
2533377
2532910
−3
−
468
GENE II AND X
-none-
D23_1c2719
Neut_2528








PROTEINS




fig|6666666.60966.peg.2729
CDS
2533835
2533407
−2
−
429
Probable
-none-
D23_1c2720
Neut_2529








transmembrane protein




fig|6666666.60966.peg.2730
CDS
2533940
2534806
2
+
867
FIG146518: Zn-
CBSS-269482.4.peg.5018
D23_1c2721
Neut_2530








dependent hydrolases,











including glyoxylases




fig|6666666.60966.peg.2731
CDS
2535475
2534891
−1
−
585
FIG001587: exported
-none-
D23_1c2722
Neut_2531








protein




fig|6666666.60966.peg.2732
CDS
2537039
2535534
−2
−
1506
FIG00859025:
-none-
D23_1c2723
Neut_2532








hypothetical protein




fig|6666666.60966.peg.2733
CDS
2537388
2537077
−3
−
312
hypothetical protein
-none-
D23_1c2724
NA

fig|6666666.60966.rna.11
RNA
226254
226324
3
+
71
tRNA-Gly-CCC
tRNAs
NA
NA

fig|6666666.60966.rna.2
RNA
6795
6868
3
+
74
tRNA-Cys-GCA
tRNAs
NA
NA

fig|6666666.60966.rna.39
RNA
1810921
1810848
−1
−
74
tRNA-Gly-TCC
-none-
NA
NA

fig|6666666.60966.rna.23
RNA
969765
969839
3
+
75
tRNA-Gln-TTG
-none-
NA
NA

fig|6666666.60966.rna.36
RNA
1758968
1759042
2
+
75
tRNA-Val-CAC
tRNAs
NA
NA

fig|6666666.60966.rna.38
RNA
1810812
1810738
−3
−
75
tRNA-Thr-GGT
-none-
NA
NA

fig|6666666.60966.rna.1
RNA
6614
6689
2
+
76
tRNA-Gly-GCC
tRNAs
NA
NA

fig|6666666.60966.rna.7
RNA
120428
120503
2
+
76
tRNA-Ala-TGC
-none-
NA
NA

fig|6666666.60966.rna.12
RNA
284547
284472
−3
−
76
tRNA-Glu-TTC
-none-
NA
NA

fig|6666666.60966.rna.13
RNA
284648
284573
−2
−
76
tRNA-Ala-GGC
tRNAs
NA
NA

fig|6666666.60966.rna.14
RNA
493566
493641
3
+
76
tRNA-Thr-CGT
-none-
NA
NA

fig|6666666.60966.rna.16
RNA
561828
561903
3
+
76
tRNA-Val-TAC
-none-
NA
NA

fig|6666666.60966.rna.20
RNA
859357
859282
−1
−
76
tRNA-Lys-TTT
-none-
NA
NA

fig|6666666.60966.rna.21
RNA
948801
948876
3
+
76
tRNA-Thr-TGT
-none-
NA
NA

fig|6666666.60966.rna.24
RNA
1157662
1157587
−1
−
76
tRNA-Arg-CCT
-none-
NA
NA

fig|6666666.60966.rna.25
RNA
1199325
1199250
−3
−
76
tRNA-His-GTG
-none-
NA
NA

fig|6666666.60966.rna.29
RNA
1470510
1470435
−3
−
76
tRNA-Asn-GTT
-none-
NA
NA

fig|6666666.60966.rna.33
RNA
1618239
1618314
3
+
76
tRNA-Met-CAT
-none-
NA
NA

fig|6666666.60966.rna.34
RNA
1673498
1673423
−2
−
76
tRNA-Arg-CCG
tRNAs
NA
NA

fig|6666666.60966.rna.37
RNA
1809438
1809363
−3
−
76
tRNA-Trp-CCA
tRNAs
NA
NA

fig|6666666.60966.rna.42
RNA
2107281
2107356
3
+
76
tRNA-Phe-GAA
tRNAs
NA
NA

fig|6666666.60966.rna.6
RNA
120349
120425
1
+
77
tRNA-Ile-GAT
-none-
NA
NA

fig|6666666.60966.rna.10
RNA
196762
196838
1
+
77
tRNA-Met-CAT
-none-
NA
NA

fig|6666666.60966.rna.15
RNA
524553
524629
3
+
77
tRNA-Val-GAC
tRNAs
NA
NA

fig|6666666.60966.rna.17
RNA
561963
562039
3
+
77
tRNA-Asp-GTC
-none-
NA
NA

fig|6666666.60966.rna.18
RNA
728392
728316
−1
−
77
tRNA-Pro-CGG
tRNAs
NA
NA

fig|6666666.60966.rna.26
RNA
1199452
1199376
−1
−
77
tRNA-Arg-TCT
-none-
NA
NA

fig|6666666.60966.rna.27
RNA
1199573
1199497
−2
−
77
tRNA-Pro-TGG
-none-
NA
NA

fig|6666666.60966.rna.28
RNA
1427736
1427812
3
+
77
tRNA-Met-CAT
-none-
NA
NA

fig|6666666.60966.rna.41
RNA
2107137
2107213
3
+
77
tRNA-Arg-ACG
tRNAs
NA
NA

fig|6666666.60966.rna.44
RNA
2339644
2339568
−1
−
77
tRNA-Pro-GGG
tRNAs
NA
NA

fig|6666666.60966.rna.19
RNA
835520
835604
2
+
85
tRNA-Leu-GAG
tRNAs
NA
NA

fig|6666666.60966.rna.32
RNA
1597631
1597715
2
+
85
tRNA-Leu-CAG
tRNAs
NA
NA

fig|6666666.60966.rna.40
RNA
1811116
1811032
−1
−
85
tRNA-Tyr-GTA
-none-
NA
NA

fig|6666666.60966.rna.4
RNA
97072
96987
−1
−
86
tRNA-Leu-TAG
-none-
NA
NA

fig|6666666.60966.rna.31
RNA
1574940
1574854
−3
−
87
tRNA-Leu-CAA
tRNAs
NA
NA

fig|6666666.60966.rna.30
RNA
1550222
1550135
−2
−
88
tRNA-Ser-TGA
-none-
NA
NA

fig|6666666.60966.rna.3
RNA
6894
6982
3
+
89
tRNA-Leu-TAA
-none-
NA
NA

fig|6666666.60966.rna.22
RNA
956464
956374
−1
−
91
tRNA-Ser-GGA
tRNAs
NA
NA

fig|6666666.60966.rna.35
RNA
1757250
1757342
3
+
93
tRNA-Ser-CGA
tRNAs
NA
NA

fig|6666666.60966.rna.43
RNA
2120297
2120205
−2
−
93
tRNA-Ser-GCT
-none-
NA
NA

fig|6666666.60966.peg.111
CDS
108515
108628
2
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.353
CDS
326760
326647
−3
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.404
CDS
375917
375804
−2
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.432
CDS
397539
397426
−3
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.509
CDS
474482
474369
−2
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.589
CDS
543008
543121
2
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.838
CDS
770105
770218
2
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.923
CDS
855159
855046
−3
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.943
CDS
873193
873306
1
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1081
CDS
1010260
1010373
1
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1333
CDS
1235666
1235779
2
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1414
CDS
1326350
1326463
2
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1695
CDS
1575540
1575653
3
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1875
CDS
1749599
1749486
−2
−
114
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.2082
CDS
1936491
1936378
−3
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2205
CDS
2047715
2047828
2
+
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2370
CDS
2201390
2201277
−2
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2413
CDS
2236764
2236651
−3
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2577
CDS
2379043
2378930
−1
−
114
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.421
CDS
392634
392518
−3
−
117
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.431
CDS
397234
397350
1
+
117
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1104
CDS
1033773
1033889
3
+
117
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1856
CDS
1730271
1730155
−3
−
117
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2044
CDS
1907891
1907775
−2
−
117
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2046
CDS
1908400
1908516
1
+
117
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2250
CDS
2086632
2086516
−3
−
117
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2378
CDS
2209362
2209246
−3
−
117
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.28
CDS
31960
31841
−1
−
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.536
CDS
496598
496717
2
+
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.866
CDS
794273
794392
2
+
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1031
CDS
956342
956223
−2
−
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1238
CDS
1152349
1152230
−1
−
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1279
CDS
1184453
1184572
2
+
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1566
CDS
1462529
1462410
−2
−
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1604
CDS
1492079
1491960
−2
−
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1610
CDS
1495100
1495219
2
+
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1938
CDS
1820165
1820046
−2
−
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1940
CDS
1820392
1820511
1
+
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2194
CDS
2040715
2040596
−1
−
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2229
CDS
2069192
2069073
−2
−
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2542
CDS
2355482
2355601
2
+
120
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.477
CDS
444630
444508
−3
−
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.634
CDS
579242
579364
2
+
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.927
CDS
859107
859229
3
+
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1015
CDS
941818
941940
1
+
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1388
CDS
1298114
1298236
2
+
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1755
CDS
1633195
1633073
−1
−
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2224
CDS
2067753
2067631
−3
−
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2271
CDS
2103666
2103788
3
+
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2336
CDS
2170340
2170462
2
+
123
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2415
CDS
2237130
2237008
−3
−
123
Hydroxyacylglutathione
CBSS-228410.1.peg.134;
NA
NA








hydrolase (EC 3.1.2.6)
<br>CBSS-











342610.3.peg.1536;











<br>Glutathione: Non-











redox reactions;











<br>Methylglyoxal











Metabolism



fig|6666666.60966.peg.82
CDS
79801
79676
−1
−
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.585
CDS
541998
542123
3
+
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1268
CDS
1176741
1176866
3
+
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1473
CDS
1385674
1385799
1
+
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1510
CDS
1423155
1423030
−3
−
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1690
CDS
1573599
1573474
−3
−
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1758
CDS
1635456
1635331
−3
−
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1935
CDS
1816227
1816352
3
+
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1966
CDS
1832788
1832913
1
+
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2285
CDS
2119314
2119439
3
+
126
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.21
CDS
28650
28522
−3
−
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.27
CDS
31632
31760
3
+
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.247
CDS
231537
231665
3
+
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.300
CDS
272364
272492
3
+
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.864
CDS
792354
792226
−3
−
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1166
CDS
1092637
1092509
−1
−
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1314
CDS
1216530
1216658
3
+
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1730
CDS
1612183
1612311
1
+
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2328
CDS
2162434
2162306
−1
−
129
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.122
CDS
124194
124063
−3
−
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.154
CDS
155514
155645
3
+
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.874
CDS
801546
801677
3
+
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.894
CDS
823808
823939
2
+
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.960
CDS
886681
886550
−1
−
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1188
CDS
1108861
1108730
−1
−
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1578
CDS
1468706
1468837
2
+
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1950
CDS
1824304
1824435
1
+
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1983
CDS
1850338
1850469
1
+
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2066
CDS
1923319
1923450
1
+
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2445
CDS
2263603
2263472
−1
−
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2570
CDS
2376200
2376331
2
+
132
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.296
CDS
267656
267790
2
+
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1086
CDS
1016149
1016015
−1
−
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1167
CDS
1092703
1092837
1
+
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1560
CDS
1459112
1459246
2
+
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1597
CDS
1486647
1486513
−3
−
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1949
CDS
1824258
1824124
−3
−
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2059
CDS
1916861
1916995
2
+
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2151
CDS
1995848
1995982
2
+
135
FIG00858674:
-none-
NA
NA








hypothetical protein




fig|6666666.60966.peg.2230
CDS
2069201
2069335
2
+
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2363
CDS
2194044
2194178
3
+
135
LSU ribosomal protein
Cell Division Subsystem
NA
NA








L34p
including YidCD;











<br>RNA modification











cluster



fig|6666666.60966.peg.2527
CDS
2338623
2338489
−3
−
135
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1276
CDS
1182314
1182177
−2
−
138
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1317
CDS
1218021
1218158
3
+
138
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1606
CDS
1493209
1493072
−1
−
138
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1867
CDS
1739233
1739370
1
+
138
Error-prone, lesion
-none-
NA
NA








bypass DNA polymerase











V(UmuC)




fig|6666666.60966.peg.2117
CDS
1966387
1966250
−1
−
138
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2227
CDS
2068598
2068735
2
+
138
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.163
CDS
160970
160830
−2
−
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.173
CDS
168825
168965
3
+
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1286
CDS
1189481
1189621
2
+
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1416
CDS
1328534
1328674
2
+
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1422
CDS
1330733
1330873
2
+
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1759
CDS
1635699
1635839
3
+
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1775
CDS
1649712
1649572
−3
−
141
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.1984
CDS
1850712
1850572
−3
−
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2003
CDS
1866906
1867046
3
+
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2080
CDS
1935668
1935808
2
+
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2487
CDS
2301272
2301132
−2
−
141
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.369
CDS
342367
342224
−1
−
144
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.635
CDS
579509
579652
2
+
144
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1001
CDS
928837
928980
1
+
144
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1642
CDS
1524746
1524603
−2
−
144
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2114
CDS
1962886
1963029
1
+
144
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2593
CDS
2391861
2392004
3
+
144
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.205
CDS
197036
196890
−2
−
147
Integrase
-none-
NA
NA

fig|6666666.60966.peg.284
CDS
260995
261141
1
+
147
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1885
CDS
1759287
1759141
−3
−
147
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2453
CDS
2272001
2271855
−2
−
147
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2620
CDS
2417974
2417828
−1
−
147
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2623
CDS
2420545
2420399
−1
−
147
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.108
CDS
106117
106266
1
+
150
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.813
CDS
746234
746085
−2
−
150
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1296
CDS
1205130
1205279
3
+
150
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1334
CDS
1235992
1235843
−1
−
150
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2300
CDS
2134634
2134485
−2
−
150
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.35
CDS
36062
35910
−2
−
153
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1312
CDS
1215961
1216113
1
+
153
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2143
CDS
1990257
1990105
−3
−
153
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.359
CDS
335237
335392
2
+
156
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.546
CDS
506105
505950
−2
−
156
FIG00858972:
-none-
NA
NA








hypothetical protein




fig|6666666.60966.peg.1174
CDS
1095978
1095823
−3
−
156
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.1384
CDS
1296435
1296280
−3
−
156
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2575
CDS
2378324
2378169
−2
−
156
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.89
CDS
85217
85059
−2
−
159
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.556
CDS
516983
516825
−2
−
159
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.562
CDS
523304
523462
2
+
159
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1099
CDS
1029431
1029589
2
+
159
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1571
CDS
1466563
1466405
−1
−
159
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.613
CDS
562226
562065
−2
−
162
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.886
CDS
814562
814401
−2
−
162
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1114
CDS
1043720
1043559
−2
−
162
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.291
CDS
265661
265825
2
+
165
FIG00856904:
-none-
NA
NA








hypothetical protein




fig|6666666.60966.peg.2077
CDS
1934012
1933848
−2
−
165
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.620
CDS
568234
568401
1
+
168
Methyltransferase (EC
-none-
NA
NA








2.1.1.—)




fig|6666666.60966.peg.2317
CDS
2149354
2149521
1
+
168
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.2420
CDS
2241817
2241650
−1
−
168
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.856
CDS
785317
785147
−1
−
171
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1487
CDS
1401876
1401706
−3
−
171
FIG00858878:
-none-
NA
NA








hypothetical protein




fig|6666666.60966.peg.2286
CDS
2119703
2119873
2
+
171
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2707
CDS
2514260
2514090
−2
−
171
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.862
CDS
790885
790712
−1
−
174
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1450
CDS
1360555
1360382
−1
−
174
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.1572
CDS
1466783
1466956
2
+
174
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1608
CDS
1494659
1494835
2
+
177
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2416
CDS
2237303
2237127
−2
−
177
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2668
CDS
2479940
2479764
−2
−
177
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.748
CDS
694556
694377
−2
−
180
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1667
CDS
1550475
1550296
−3
−
180
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2116
CDS
1965779
1965600
−2
−
180
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2144
CDS
1990362
1990541
3
+
180
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.2400
CDS
2229074
2228895
−2
−
180
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.287
CDS
262264
262446
1
+
183
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.422
CDS
392649
392831
3
+
183
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1562
CDS
1459862
1460044
2
+
183
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2388
CDS
2218996
2219178
1
+
183
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.338
CDS
308508
308323
−3
−
186
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1842
CDS
1720173
1719988
−3
−
186
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.286
CDS
262147
261959
−1
−
189
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1202
CDS
1125016
1124828
−1
−
189
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1304
CDS
1209919
1209731
−1
−
189
FIG00858878:
-none-
NA
NA








hypothetical protein




fig|6666666.60966.peg.2395
CDS
2224520
2224332
−2
−
189
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.250
CDS
233011
233202
1
+
192
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.794
CDS
729662
729471
−2
−
192
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1764
CDS
1639415
1639606
2
+
192
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.808
CDS
741018
740824
−3
−
195
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.276
CDS
255673
255870
1
+
198
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.749
CDS
694591
694788
1
+
198
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2718
CDS
2523733
2523536
−1
−
198
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.217
CDS
203959
204159
1
+
201
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.682
CDS
631759
631959
1
+
201
FIG00859622:
-none-
NA
NA








hypothetical protein




fig|6666666.60966.peg.208
CDS
199189
199392
1
+
204
Cold shock protein CspA
Cold shock, CspA family
NA
NA









of proteins



fig|6666666.60966.peg.380
CDS
348880
348677
−1
−
204
SSU ribosomal protein
-none-
NA
NA








S16p




fig|6666666.60966.peg.2149
CDS
1995706
1995503
−1
−
204
dTDP-4-
Rhamnose containing
NA
NA








dehydrorhamnose
glycans; <br>dTDP-










reductase (EC
rhamnose synthesis










1.1.1.133)




fig|6666666.60966.peg.1148
CDS
1073050
1073259
1
+
210
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2464
CDS
2281343
2281134
−2
−
210
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.522
CDS
484104
484316
3
+
213
LSU ribosomal protein
-none-
NA
NA








L29p (L35e)




fig|6666666.60966.peg.1481
CDS
1395113
1394901
−2
−
213
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.292
CDS
265809
266024
3
+
216
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.511
CDS
475254
475469
3
+
216
SSU ribosomal protein

Mycobacterium

NA
NA








S12p (S23e)
virulence operon











involved in protein











synthesis (SSU ribosomal











proteins);











<br>Ribosomal protein











S12p Asp











methylthiotransferase



fig|6666666.60966.peg.529
CDS
490129
490347
1
+
219
Translation initiation
Translation initiation
NA
NA








factor 1
factors bacterial



fig|6666666.60966.peg.2374
CDS
2207422
2207640
1
+
219
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2105
CDS
1956719
1956940
2
+
222
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2690
CDS
2502317
2502538
2
+
222
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2153
CDS
1996354
1996578
1
+
225
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2138
CDS
1985283
1985510
3
+
228
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.442
CDS
405529
405299
−1
−
231
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1716
CDS
1598000
1597770
−2
−
231
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2439
CDS
2259000
2258770
−3
−
231
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1111
CDS
1042874
1043110
2
+
237
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.1999
CDS
1865704
1865468
−1
−
237
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1214
CDS
1136308
1136069
−1
−
240
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1733
CDS
1614273
1614031
−3
−
243
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.48
CDS
47253
47498
3
+
246
Alpha-L-Rha alpha-1,3-
Rhamnose containing
NA
NA








L-rhamnosyltransferase
glycans










(EC 2.4.1.—)




fig|6666666.60966.peg.423
CDS
393586
393338
−1
−
249
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.429
CDS
396754
396506
−1
−
249
Transglycosylase-
-none-
NA
NA








associated protein




fig|6666666.60966.peg.1147
CDS
1072594
1072842
1
+
249
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1951
CDS
1824656
1824408
−2
−
249
Plasmid stabilization
-none-
NA
NA








system protein




fig|6666666.60966.peg.2579
CDS
2380195
2380446
1
+
252
Mobile element protein
-none-
NA
NA

fig|6666666.60966.peg.523
CDS
484294
484548
1
+
255
SSU ribosomal protein
-none-
NA
NA








S17p (S11e)




fig|6666666.60966.peg.1022
CDS
948522
948782
3
+
261
Stringent starvation
Carbon Starvation
NA
NA








protein B




fig|6666666.60966.peg.1957
CDS
1826664
1826936
3
+
273
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2273
CDS
2108052
2108336
3
+
285
putative DNA transport
-none-
NA
NA








competence protein




fig|6666666.60966.peg.46
CDS
46807
46481
−1
−
327
Conserved domain
-none-
NA
NA








protein




fig|6666666.60966.peg.2109
CDS
1959886
1960239
1
+
354
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.2429
CDS
2248841
2248488
−2
−
354
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.1579
CDS
1468834
1469334
1
+
501
hypothetical protein
-none-
NA
NA

fig|6666666.60966.peg.293
CDS
266114
266689
2
+
576
hypothetical protein
-none-
NA
NA






















































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































SUPPLEMENTARY TABLE 2



Selected D23 sequences





SEQ ID



and



length
Description
Sequence



SEQ ID
amoC1
MATTLGTSSASSVSSRGYDMSLWYDSKFYKFGLITMLLVAIFWVWYQRYF

NO: 4
(D23_1c22
AYSHGMDSMEPEFDRVWMGLWRVHMAIMPLFALVTWGWIWKTRDTEEQLN

(271
72)
NLDPKLEIKRYFYYMMWLGVYIFGVYWGGSFFTEQDASWHQVIIRDTSFT

aa)
protein
PSHVVVFYGSFPMYIVCGVATYLYAMTRLPLFHRGISFPLVMAIAGPLMI



LPNVGLNEWGHAFWFMEELFSAPLHWGFVVLGWAGLFQGGVAAQIITRYS



NLTDVVWNNQSKEILNNRVVA



SEQ ID
amoC1
ATGGCAACTACGTTAGGAACGAGCAGTGCCTCATCAGTCTCATCAAGAGG

NO: 5
(D23_1c22
CTATGACATGTCACTGTGGTATGACTCCAAATTTTATAAATTTGGTTTAA

(816
72) DNA
TAACCATGTTGTTGGTAGCGATATTCTGGGTATGGTATCAACGTTACTTT

nt)

GCCTATTCACACGGAATGGATTCAATGGAACCAGAGTTTGACCGTGTATG



GATGGGCCTGTGGCGTGTGCACATGGCCATTATGCCGCTGTTTGCACTGG



TAACCTGGGGCTGGATCTGGAAAACACGTGATACAGAAGAGCAATTGAAT



AACCTGGATCCGAAACTGGAAATCAAACGCTACTTCTACTACATGATGTG



GCTGGGTGTATACATTTTTGGTGTTTACTGGGGTGGTAGCTTCTTTACGG



AGCAAGATGCCTCCTGGCACCAGGTGATTATTCGTGACACCAGCTTTACA



CCAAGTCACGTAGTCGTGTTTTATGGATCATTTCCGATGTACATCGTCTG



CGGAGTTGCAACCTATCTGTATGCAATGACCCGTCTGCCGCTGTTTCATC



GTGGAATTTCTTTCCCACTGGTGATGGCGATTGCAGGTCCTCTGATGATT



CTGCCAAACGTTGGTCTGAATGAATGGGGTCATGCTTTCTGGTTCATGGA



AGAGCTGTTCAGCGCACCGCTGCATTGGGGTTTTGTAGTGCTCGGTTGGG



CTGGGTTATTCCAGGGTGGAGTTGCTGCCCAAATCATTACCCGTTATTCC



AACCTGACTGACGTGGTCTGGAATAATCAAAGCAAAGAAATTCTGAATAA



CCGGGTTGTAGCTTAG



SEQ ID
amoA1
VSIFRTEEILKAAKMPPEAVHMSRLIDAVYFPILVVLLVGTYHMHFMLLA

NO: 6
(D23_1c22
GDWDFWMDWKDRQWWPVVTPIVGITYCSAIMYYLWVNYRQPFGATLCVVC

(276
71)
LLIGEWLTRYWGFYWWSHYPLNFVTPGIMLPGALMLDFTMYLTRNWLVTA

aa)
protein
LVGGGFFGLLFYPGNWAIFGPTHLPIVVEGTLLSMADYMGHLYVRTGTPE



YVRHIEQGSLRTFGGHTTVIAAFFAAFVSMLMFAVWWYLGKVYCTAFFYV



KGKRGRIVQRNDVTAFGEEGFPEGIK



SEQ ID
amoA1
GTGAGTATATTTAGAACAGAAGAGATCCTGAAAGCGGCCAAGATGCCGCC

NO: 7
(D23_1c22
GGAAGCGGTCCATATGTCACGCCTGATTGATGCGGTTTATTTTCCGATTC

(831
71) DNA
TGGTTGTTCTGTTGGTAGGTACCTACCATATGCACTTCATGTTGTTGGCA

nt)

GGTGACTGGGATTTCTGGATGGACTGGAAAGATCGTCAATGGTGGCCTGT



AGTAACACCTATTGTAGGCATTACCTATTGCTCGGCAATTATGTATTACC



TGTGGGTCAACTACCGTCAACCATTTGGTGCGACTCTGTGCGTAGTGTGT



TTGCTGATAGGTGAGTGGCTGACACGTTACTGGGGTTTCTACTGGTGGTC



ACACTATCCACTCAATTTTGTAACCCCAGGTATCATGCTCCCGGGTGCAT



TGATGTTGGATTTCACAATGTATCTGACACGTAACTGGTTGGTGACTGCA



TTGGTTGGGGGTGGATTCTTTGGTCTGCTGTTTTACCCGGGTAACTGGGC



AATCTTTGGTCCGACCCATCTGCCAATCGTTGTAGAAGGAACACTGTTGT



CGATGGCTGACTATATGGGTCACCTGTATGTTCGTACGGGTACACCTGAG



TATGTTCGTCATATTGAACAAGGTTCATTACGTACCTTTGGTGGTCACAC



CACAGTTATTGCAGCATTCTTCGCTGCGTTTGTATCCATGCTGATGTTTG



CAGTCTGGTGGTATCTTGGAAAAGTTTACTGCACAGCCTTCTTCTACGTT



AAAGGTAAAAGAGGACGTATCGTGCAGCGCAATGATGTTACGGCATTTGG



TGAAGAAGGGTTTCCAGAGGGGATCAAATAA



SEQ ID
amoB1
MGIKNLYKRGMMGLCGVAVYAMAALTMTVTLDVSTVAAHGERSQEPFLRM

NO: 8
(D23_1c22
RTVQWYDVKWGPEVTKVNENAQITGKFHLAEDWPRAAARPDFAFFNVGSP

(421
70)
SSVYVRLSTKINGHPWFISGPLQIGRDYAFEVQLRARIPGRHHMHAMLNV

aa)
protein
KDAGPIAGPGAWMNITGSWDDFTNPLKLLTGETIDSETFNLSNGIFWHIL



WMSIGIFWIGIFVARPMFLPRSRVLLAYGDDLLLDPMDKKITWVLAILTL



AIVWGGYRYTETKHPYTVPIQAGQSKVAPLPVAPNPVAIKITDANYDVPG



RALRVSMEVTNNGDTPVTFGEFTTAGIRFVNSTGRKYLDPQYPRELVAVG



LNFDDDGAIQPGETKQLRMEAKDALWEIQRLMALLGDPESRFGGLLMSWD



SEGNRHINSIAGPVIPVFTKL



SEQ ID
amoB1
ATGGGTATCAAGAACCTTTATAAACGTGGAATGATGGGACTTTGTGGCGT

NO: 9
(D23_1c22
TGCTGTTTATGCAATGGCGGCACTGACCATGACAGTGACACTAGATGTCT

(1266
70) DNA
CAACAGTAGCAGCCCATGGAGAACGATCCCAGGAACCGTTTCTTCGGATG

nt)

CGTACAGTACAGTGGTACGATGTTAAGTGGGGTCCGGAAGTAACCAAAGT



CAATGAGAATGCCCAAATTACCGGCAAATTTCACTTGGCTGAAGACTGGC



CGCGTGCGGCAGCAAGACCGGATTTCGCATTCTTTAACGTAGGTAGCCCA



AGCTCGGTATACGTGCGTTTGAGTACGAAGATTAATGGCCACCCATGGTT



TATTTCAGGTCCGCTGCAAATTGGTCGTGACTATGCGTTCGAAGTTCAGC



TGAGAGCACGTATTCCAGGACGCCATCACATGCACGCCATGTTAAACGTT



AAAGATGCAGGTCCAATTGCAGGACCGGGTGCATGGATGAACATTACCGG



AAGCTGGGATGATTTTACTAATCCACTCAAGCTGCTGACAGGCGAAACAA



TTGACTCAGAAACATTCAACCTGTCAAACGGTATTTTCTGGCATATTCTC



TGGATGTCAATTGGTATATTTTGGATTGGTATCTTTGTAGCGCGTCCGAT



GTTCCTGCCACGTAGCCGGGTATTGCTCGCTTATGGTGATGATCTGTTGC



TGGATCCGATGGATAAGAAAATCACCTGGGTACTTGCAATCCTGACCTTG



GCTATAGTATGGGGTGGATACCGCTATACAGAAACCAAGCATCCATACAC



AGTACCTATCCAGGCTGGTCAATCCAAAGTTGCACCATTACCGGTAGCAC



CAAATCCGGTAGCAATCAAAATTACAGATGCTAACTATGACGTACCGGGA



CGTGCACTGCGTGTATCGATGGAAGTAACCAACAACGGTGATACACCAGT



CACATTTGGTGAATTTACCACAGCAGGTATTCGTTTCGTTAACAGTACCG



GCCGCAAGTACCTGGATCCACAGTATCCTCGTGAACTGGTTGCAGTAGGC



TTGAATTTTGATGATGATGGTGCAATTCAGCCAGGCGAGACCAAGCAATT



GAGGATGGAAGCCAAAGATGCTCTGTGGGAAATCCAACGTCTGATGGCGT



TGCTGGGTGACCCGGAAAGCCGTTTTGGTGGACTGTTAATGTCTTGGGAT



TCAGAAGGTAATCGCCATATCAACAGTATTGCTGGTCCGGTGATTCCAGT



CTTTACCAAGCTCTAA



SEQ ID
amoC2
MATTLGTSSASSVSSRGYDMSLWYDSKFYKFGLITMLLVAIFWVWYQRYF

NO: 10
(D23_1c25
AYSHGMDSMEPEFDRVWMGLWRVHMAIMPLFALVTWGWIWKTRDTEEQLN

(271
12)
NLDPKLEIKRYFYYMMWLGVYIFGVYWGGSFFTEQDASWHQVIIRDTSFT

aa)
protein
PSHVVVFYGSFPMYIVCGVATYLYAMTRLPLFHRGISFPLVMAIAGPLMI



LPNVGLNEWGHAFWFMEELFSAPLHWGFVVLGWAGLFQGGVAAQIITRYS



NLTDVVWNNQSKEILNNRVVA



SEQ ID
amoC2
ATGGCAACTACGTTAGGAACGAGCAGTGCCTCATCAGTCTCATCAAGAGG

NO: 11
(D23_1c25
CTATGACATGTCACTGTGGTATGACTCCAAATTTTATAAATTTGGTTTAA

(816
12) DNA
TAACCATGTTGTTGGTAGCGATATTCTGGGTATGGTATCAACGTTACTTT

nt)

GCCTATTCACACGGAATGGATTCAATGGAACCAGAGTTTGACCGTGTATG



GATGGGCCTGTGGCGTGTGCACATGGCCATTATGCCGCTGTTTGCACTGG



TAACCTGGGGCTGGATCTGGAAAACACGTGATACAGAAGAGCAATTGAAT



AACCTGGATCCGAAACTGGAAATCAAACGCTACTTCTACTACATGATGTG



GCTGGGTGTATACATTTTTGGTGTTTACTGGGGTGGTAGCTTCTTTACGG



AGCAAGATGCCTCCTGGCACCAGGTGATTATTCGTGACACCAGCTTTACA



CCAAGTCACGTAGTCGTGTTTTATGGATCATTTCCGATGTACATCGTCTG



CGGAGTTGCAACCTATCTGTATGCAATGACCCGTCTGCCGCTGTTTCATC



GTGGAATTTCTTTCCCACTGGTGATGGCGATTGCAGGTCCTCTGATGATT



CTGCCAAACGTTGGTCTGAATGAATGGGGTCATGCTTTCTGGTTCATGGA



AGAGCTGTTCAGCGCACCGCTGCATTGGGGTTTTGTAGTGCTCGGTTGGG



CTGGGTTATTCCAGGGTGGAGTTGCTGCCCAAATCATTACCCGTTATTCC



AACCTGACTGACGTGGTCTGGAATAATCAAAGCAAAGAAATTCTGAATAA



CCGGGTTGTAGCTTAG



SEQ ID
amoA2
VSIFRTEEILKAAKMPPEAVHMSRLIDAVYFPILVVLLVGTYHMHFMLLA

NO: 12
(D23_1c25
GDWDFWMDWKDRQWWPVVTPIVGITYCSAIMYYLWVNYRQPFGATLCVVC

(276
11)
LLIGEWLTRYWGFYWWSHYPLNFVTPGIMLPGALMLDFTMYLTRNWLVTA

aa)
protein
LVGGGFFGLLFYPGNWAIFGPTHLPIVVEGTLLSMADYMGHLYVRTGTPE



YVRHIEQGSLRTFGGHTTVIAAFFAAFVSMLMFAVWWYLGKVYCTAFFYV



KGKRGRIVQRNDVTAFGEEGFPEGIK



SEQ ID
amoA2
GTGAGTATATTTAGAACAGAAGAGATCCTGAAAGCGGCCAAGATGCCGCC

NO: 13
(D23_1c25
GGAAGCGGTCCATATGTCACGCCTGATTGATGCGGTTTATTTTCCGATTC

(831
11) DNA
TGGTTGTTCTGTTGGTAGGTACCTACCATATGCACTTCATGTTGTTGGCA

nt)

GGTGACTGGGATTTCTGGATGGACTGGAAAGATCGTCAATGGTGGCCTGT



AGTAACACCTATTGTAGGCATTACCTATTGCTCGGCAATTATGTATTACC



TGTGGGTCAACTACCGTCAACCATTTGGTGCGACTCTGTGCGTAGTGTGT



TTGCTGATAGGTGAGTGGCTGACACGTTACTGGGGTTTCTACTGGTGGTC



ACACTATCCACTCAATTTTGTAACCCCAGGTATCATGCTCCCGGGTGCAT



TGATGTTGGATTTCACAATGTATCTGACACGTAACTGGTTGGTGACTGCA



TTGGTTGGGGGTGGATTCTTTGGTCTGCTGTTTTACCCGGGTAACTGGGC



AATCTTTGGTCCGACCCATCTGCCAATCGTTGTAGAAGGAACACTGTTGT



CGATGGCTGACTATATGGGTCACCTGTATGTTCGTACGGGTACACCTGAG



TATGTTCGTCATATTGAACAAGGTTCATTACGTACCTTTGGTGGTCACAC



CACAGTTATTGCAGCATTCTTCGCTGCGTTTGTATCCATGCTGATGTTTG



CAGTCTGGTGGTATCTTGGAAAAGTTTACTGCACAGCCTTCTTCTACGTT



AAAGGTAAAAGAGGACGTATCGTGCAGCGCAATGATGTTACGGCATTTGG



TGAAGAAGGGTTTCCAGAGGGGATCAAATAA



SEQ ID
amoB2
MGIKNLYKRGMMGLCGVAVYAMAALTMTVTLDVSTVAAHGERSQEPFLRM

NO: 14
(D23_1c25
RTVQWYDVKWGPEVTKVNENAQITGKFHLAEDWPRAAARPDFAFFNVGSP

(421
10)
SSVYVRLSTKINGHPWFISGPLQIGRDYAFEVQLRARIPGRHHMHAMLNV

aa)
protein
KDAGPIAGPGAWMNITGSWDDFTNPLKLLTGETIDSETFNLSNGIFWHIL



WMSIGIFWIGIFVARPMFLPRSRVLLAYGDDLLLDPMDKKITWVLAILTL



AIVWGGYRYTETKHPYTVPIQAGQSKVAPLPVAPNPVAIKITDANYDVPG



RALRVSMEVTNNGDTPVTFGEFTTAGIRFVNSTGRKYLDPQYPRELVAVG



LNFDDDGAIQPGETKQLRMEAKDALWEIQRLMALLGDPESRFGGLLMSWD



SEGNRHINSIAGPVIPVFTKL



SEQ ID
amoB2
ATGGGTATCAAGAACCTTTATAAACGTGGAATGATGGGACTTTGTGGCGT

NO: 15
(D23_1c25
TGCTGTTTATGCAATGGCGGCACTGACCATGACAGTGACACTAGATGTCT

(1266
10) DNA
CAACAGTAGCAGCCCATGGAGAACGATCCCAGGAACCGTTTCTTCGGATG

nt)

CGTACAGTACAGTGGTACGATGTTAAGTGGGGTCCGGAAGTAACCAAAGT



CAATGAGAATGCCCAAATTACCGGCAAATTTCACTTGGCTGAAGACTGGC



CGCGTGCGGCAGCAAGACCGGATTTCGCATTCTTTAACGTAGGTAGCCCA



AGCTCGGTATACGTGCGTTTGAGTACGAAGATTAATGGCCACCCATGGTT



TATTTCAGGTCCGCTGCAAATTGGTCGTGACTATGCGTTCGAAGTTCAGC



TGAGAGCACGTATTCCAGGACGCCATCACATGCACGCCATGTTAAACGTT



AAAGATGCAGGTCCAATTGCAGGACCGGGTGCATGGATGAACATTACCGG



AAGCTGGGATGATTTTACTAATCCACTCAAGCTGCTGACAGGCGAAACAA



TTGACTCAGAAACATTCAACCTGTCAAACGGTATTTTCTGGCATATTCTC



TGGATGTCAATTGGTATATTTTGGATTGGTATCTTTGTAGCGCGTCCGAT



GTTCCTGCCACGTAGCCGGGTATTGCTCGCTTATGGTGATGATCTGTTGC



TGGATCCGATGGATAAGAAAATCACCTGGGTACTTGCAATCCTGACCTTG



GCTATAGTATGGGGTGGATACCGCTATACAGAAACCAAGCATCCATACAC



AGTACCTATCCAGGCTGGTCAATCCAAAGTTGCACCATTACCGGTAGCAC



CAAATCCGGTAGCAATCAAAATTACAGATGCTAACTATGACGTACCGGGA



CGTGCACTGCGTGTATCGATGGAAGTAACCAACAACGGTGATACACCAGT



CACATTTGGTGAATTTACCACAGCAGGTATTCGTTTCGTTAACAGTACCG



GCCGCAAGTACCTGGATCCACAGTATCCTCGTGAACTGGTTGCAGTAGGC



TTGAATTTTGATGATGATGGTGCAATTCAGCCAGGCGAGACCAAGCAATT



GAGGATGGAAGCCAAAGATGCTCTGTGGGAAATCCAACGTCTGATGGCGT



TGCTGGGTGACCCGGAAAGCCGTTTTGGTGGACTGTTAATGTCTTGGGAT



TCAGAAGGTAATCGCCATATCAACAGTATTGCTGGTCCGGTGATTCCAGT



CTTTACCAAGCTCTAA



SEQ ID
amoC3
MATNILKDKAAQQVADKPTYDKSEWFDAKYYKFGLLPILAVAVMWVYFQR

NO: 16
(D23_1c16
TYAYSHGMDSMEPEFDRIWMGLWRVQMAALPLIALFTWGWLYKTRNTAEQ

(274
05)
LANLTPKQEIKRYFYFLMWLGVYIFAVYWGSSFFTEQDASWHQVIIRDTS

aa)
protein
FTPSHIPLFYGSFPVYIIMGVSMIIYANTRLPLYNKGWSFPLIMTVAGPL



MSLPNVGLNEWGHAFWFMEELFSAPLHWGFVILAWAALFQGGLAVQIIAR



FSNLLDVEWNKQDRAILDDVVTAP



SEQ ID
amoC3
ATGGCTACAAATATATTAAAAGACAAAGCTGCACAGCAGGTTGCTGATAA

NO: 17
(D23_1c16
ACCAACTTATGATAAATCCGAGTGGTTTGATGCTAAATACTATAAATTCG

(825
05) DNA
GGCTGCTACCTATCTTAGCTGTAGCTGTGATGTGGGTTTATTTCCAGCGC

nt)

ACATACGCCTATTCTCACGGCATGGATTCAATGGAACCGGAATTTGACCG



GATCTGGATGGGCTTGTGGCGTGTTCAAATGGCCGCTCTGCCTCTTATAG



CACTTTTTACGTGGGGATGGTTATATAAAACCCGCAATACTGCAGAACAG



CTTGCCAATCTGACTCCAAAGCAGGAAATAAAGCGGTATTTCTATTTCCT



CATGTGGCTTGGGGTCTATATATTTGCAGTTTACTGGGGATCAAGCTTCT



TTACCGAGCAGGACGCTTCATGGCACCAGGTGATTATCAGGGATACAAGT



TTTACTCCTAGCCATATTCCTCTGTTTTATGGTTCATTCCCGGTATACAT



CATCATGGGAGTATCGATGATTATTTACGCCAACACCCGGTTGCCGCTGT



ACAACAAAGGGTGGTCATTCCCTCTGATCATGACCGTAGCAGGACCGTTG



ATGAGTCTGCCTAACGTTGGCCTGAACGAGTGGGGACACGCCTTCTGGTT



CATGGAAGAACTTTTCAGCGCACCGCTGCACTGGGGCTTCGTGATTCTGG



CTTGGGCTGCCCTGTTCCAGGGTGGGCTTGCAGTACAGATCATAGCTCGC



TTTTCCAACTTGCTTGACGTGGAGTGGAATAAACAAGACAGAGCCATATT



GGACGATGTCGTAACTGCTCCTTAA



SEQ ID
hao1
MRLGEYLKGMLLCAGLLLIGPVQADISTVPDETYEALKLDRSKATPKETY

NO: 18
(D23_1c25
DALVKRYKDPAHGAGKGTMGDYWEPIALSIYMDPSTFYKPPVSPKEIAER

(570
29)
KDCVECHSDETPVWVRAWKRSTHANLDKIRNLKPEDPLFYKKGKLEEVEN

aa)
protein
NLRSMGKLGEKEALKEVGCIDCHVDINAKKKADHTKDVRMPTADVCGTCH



LREFAERESERDTMIWPNGQWPDGRPSHALDYTANIETTVWAAMPQREVA



EGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNYEAYIM



SKHGKLAEMNRENWNWNVRLKDAFSKGGQTAPTCAACHMEYEGEYTHNIT



RKTRWANYPFVPGIAENITSDWSEARLDSWVVTCTQCHSERFARSYLDLM



DKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPAPEKPGFGIFTQ



LFWSKGNNPASLELKVLEMAENNLAKMHVGLAHVNPGGWTYTEGWGPMNR



AYVEIQDEYTKMQEMTALQARVNKLEGKKTSLLDLKGAGEKISLGGLGGG



MLLAGAIALIGWRKRKQTQA



SEQ ID
hao1
ATGAGATTAGGGGAGTATTTGAAGGGGATGCTGCTGTGTGCGGGCCTGTT

NO: 19
(D23_1c25
GTTGATTGGGCCGGTACAGGCGGATATATCGACGGTACCGGATGAGACGT

(1713
29) DNA
ATGAAGCATTGAAGCTGGATCGCAGCAAAGCCACGCCGAAAGAGACCTAT

nt)

GATGCGCTGGTGAAGCGTTACAAGGATCCTGCACATGGTGCTGGCAAGGG



CACGATGGGAGACTACTGGGAACCGATAGCGCTTAGTATCTACATGGACC



CGAGCACCTTTTACAAACCACCGGTTTCCCCGAAAGAAATTGCTGAGCGC



AAAGACTGCGTTGAATGCCACTCTGATGAAACGCCGGTTTGGGTAAGAGC



ATGGAAACGCAGCACCCACGCCAACCTGGACAAAATACGCAACCTCAAGC



CGGAAGATCCGCTTTTTTACAAAAAAGGCAAGCTGGAAGAAGTTGAGAAC



AACCTGCGCTCCATGGGCAAACTTGGAGAGAAGGAAGCGCTCAAGGAAGT



AGGCTGTATTGACTGTCACGTTGACATCAACGCCAAAAAGAAAGCAGATC



ACACCAAAGACGTACGCATGCCTACAGCTGACGTTTGCGGAACCTGTCAC



CTGAGAGAATTTGCCGAGCGTGAATCCGAGCGTGACACCATGATCTGGCC



GAATGGCCAGTGGCCTGACGGACGTCCATCCCACGCACTGGACTACACAG



CCAACATTGAAACCACCGTTTGGGCAGCCATGCCGCAACGTGAAGTGGCA



GAAGGTTGCACCATGTGCCACACCAACCAGAACAAATGCGACAACTGCCA



TACCCGCCATGAATTTTCGGCGGCAGAATCCCGCAAACCGGAAGCCTGTG



CCACCTGTCACAGCGGCGTGGATCATAATAACTATGAAGCCTACATTATG



TCCAAGCACGGCAAACTGGCTGAAATGAACCGGGAGAACTGGAACTGGAA



TGTTCGTCTGAAAGACGCCTTCTCCAAAGGAGGTCAGACCGCACCGACCT



GTGCAGCCTGCCACATGGAATACGAAGGGGAATATACCCATAACATCACC



CGTAAGACCCGCTGGGCAAACTACCCGTTTGTTCCGGGGATTGCAGAAAA



CATCACCAGCGACTGGTCAGAAGCTCGTCTGGATTCCTGGGTTGTGACCT



GTACCCAATGTCACTCGGAACGGTTTGCCCGCTCCTACCTGGATCTCATG



GACAAAGGTACCCTGGAAGGGTTGGCTAAATACCAGGAAGCCAATGCCAT



TGTTCACAAAATGTATGAAGACGGCACCCTGACTGGTCAAAAAACCAATC



GTCCGAATCCACCGGCGCCAGAGAAACCGGGTTTTGGTATCTTCACCCAA



CTGTTCTGGTCCAAGGGTAACAACCCGGCCTCACTTGAACTGAAAGTGCT



GGAAATGGCAGAAAACAACCTGGCCAAAATGCACGTAGGACTGGCACACG



TTAATCCAGGTGGCTGGACATATACCGAAGGTTGGGGCCCGATGAACCGT



GCCTATGTTGAAATCCAGGATGAATACACCAAGATGCAGGAAATGACAGC



TCTGCAAGCGCGTGTTAACAAACTGGAAGGTAAAAAAACCAGCCTGCTTG



ACCTCAAGGGAGCGGGAGAAAAGATCTCGCTGGGAGGACTGGGAGGTGGC



ATGTTGCTGGCGGGAGCGATTGCTCTGATTGGCTGGCGTAAACGTAAGCA



AACGCAAGCTTGA



SEQ ID
hao2
MRLGEYLKGMLLCAGLLLIGPVQADISTVPDETYEALKLDRSKATPKETY

NO: 20
(D23_1c19
DALVKRYKDPAHGAGKGTMGDYWEPIALSIYMDPSTFYKPPVSPKEIAER

(570
26)
KDCVECHSDETPVWVRAWKRSTHANLDKIRNLKPEDPLFYKKGKLEEVEN

aa)
protein
NLRSMGKLGEKEALKEVGCIDCHVDINAKKKADHTKDVRMPTADVCGTCH



LREFAERESERDTMIWPNGQWPDGRPSHALDYTANIETTVWAAMPQREVA



EGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNYEAYIM



SKHGKLAEMNRENWNWNVRLKDAFSKGGQTAPTCAACHMEYEGEYTHNIT



RKTRWANYPFVPGIAENITSDWSEARLDSWVVTCTQCHSERFARSYLDLM



DKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPAPEKPGFGIFTQ



LFWSKGNNPASLELKVLEMAENNLAKMHVGLAHVNPGGWTYTEGWGPMNR



AYVEIQDEYTKMQEMTALQARVNKLEGKKTSLLDLKGAGEKISLGGLGGG



MLLAGAIALIGWRKRKQTQA



SEQ ID
hao2
ATGAGATTAGGGGAGTATTTGAAGGGGATGCTGCTGTGTGCGGGCCTGTT

NO: 21
(D23_1c19
GTTGATTGGGCCGGTACAGGCGGATATATCGACGGTACCGGATGAGACGT

(1713
26) DNA
ATGAAGCATTGAAGCTGGATCGCAGCAAAGCCACGCCGAAAGAGACCTAT

nt)

GATGCGCTGGTGAAGCGTTACAAGGATCCTGCACATGGTGCTGGCAAGGG



CACGATGGGAGACTACTGGGAACCGATAGCGCTTAGTATCTACATGGACC



CGAGCACCTTTTACAAACCACCGGTTTCCCCGAAAGAAATTGCTGAGCGC



AAAGACTGCGTTGAATGCCACTCTGATGAAACGCCGGTTTGGGTAAGAGC



ATGGAAACGCAGCACCCACGCCAACCTGGACAAAATACGCAACCTCAAGC



CGGAAGATCCGCTTTTTTACAAAAAAGGCAAGCTGGAAGAAGTTGAGAAC



AACCTGCGCTCCATGGGCAAACTTGGAGAGAAGGAAGCGCTCAAGGAAGT



AGGCTGTATTGACTGTCACGTTGACATCAACGCCAAAAAGAAAGCAGATC



ACACCAAAGACGTACGCATGCCTACAGCTGACGTTTGCGGAACCTGTCAC



CTGAGAGAATTTGCCGAGCGTGAATCCGAGCGTGACACCATGATCTGGCC



GAATGGCCAGTGGCCTGACGGACGTCCATCCCACGCACTGGACTACACAG



CCAACATTGAAACCACCGTTTGGGCAGCCATGCCGCAACGTGAAGTGGCA



GAAGGTTGCACCATGTGCCACACCAACCAGAACAAATGCGACAACTGCCA



TACCCGCCATGAATTTTCGGCGGCAGAATCCCGCAAACCGGAAGCCTGTG



CCACCTGTCACAGCGGCGTGGATCATAATAACTATGAAGCCTACATTATG



TCCAAGCACGGCAAACTGGCTGAAATGAACCGGGAGAACTGGAACTGGAA



TGTTCGTCTGAAAGACGCCTTCTCCAAAGGAGGTCAGACCGCACCGACCT



GTGCAGCCTGCCACATGGAATACGAAGGGGAATATACCCATAACATCACC



CGTAAGACCCGCTGGGCAAACTACCCGTTTGTTCCGGGGATTGCAGAAAA



CATCACCAGCGACTGGTCAGAAGCTCGTCTGGATTCCTGGGTTGTGACCT



GTACCCAATGTCACTCGGAACGGTTTGCCCGCTCCTACCTGGATCTCATG



GACAAAGGTACCCTGGAAGGGTTGGCTAAATACCAGGAAGCCAATGCCAT



TGTTCACAAAATGTATGAAGACGGCACCCTGACTGGTCAAAAAACCAATC



GTCCGAATCCACCGGCGCCAGAGAAACCGGGTTTTGGTATCTTCACCCAA



CTGTTCTGGTCCAAGGGTAACAACCCGGCCTCACTTGAACTGAAAGTGCT



GGAAATGGCAGAAAACAACCTGGCCAAAATGCACGTAGGACTGGCACACG



TTAATCCAGGTGGCTGGACATATACCGAAGGTTGGGGCCCGATGAACCGT



GCCTATGTTGAAATCCAGGATGAATACACCAAGATGCAGGAAATGACAGC



TCTGCAAGCGCGTGTTAACAAACTGGAAGGTAAAAAAACCAGCCTGCTTG



ACCTCAAGGGAGCGGGAGAAAAGATCTCGCTGGGAGGACTGGGAGGTGGC



ATGTTGCTGGCGGGAGCGATTGCTCTGATTGGCTGGCGTAAACGTAAGCA



AACGCAAGCTTGA



SEQ ID
hao3
MRLGEYLKGMLLCAGLLLIGPVQADISTVPDETYEALKLDRSKATPKETY

NO: 22
(D23_1c17
DALVKRYKDPAHGAGKGTMGDYWEPIALSIYMDPSTFYKPPVSPKEIAER

(570
88)
KDCVECHSDETPVWVRAWKRSTHANLDKIRNLKPEDPLFYKKGKLEEVEN

aa)
protein
NLRSMGKLGEKEALKEVGCIDCHVDINAKKKADHTKDVRMPTADVCGTCH



LREFAERESERDTMIWPNGQWPDGRPSHALDYTANIETTVWAAMPQREVA



EGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNYEAYIM



SKHGKLAEMNRENWNWNVRLKDAFSKGGQTAPTCAACHMEYEGEYTHNIT



RKTRWANYPFVPGIAENITSDWSEARLDSWVVTCTQCHSERFARSYLDLM



DKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPAPEKPGFGIFTQ



LFWSKGNNPASLELKVLEMAENNLAKMHVGLAHVNPGGWTYTEGWGPMNR



AYVEIQDEYTKMQEMTALQARVNKLEGKKTSLLDLKGAGEKISLGGLGGG



MLLAGAIALIGWRKRKQTQA



SEQ ID
hao3
ATGAGATTAGGGGAGTATTTGAAGGGGATGCTGCTGTGTGCGGGCCTGTT

NO: 23
(D23_1c17
GTTGATTGGGCCGGTACAGGCGGATATATCGACGGTACCGGATGAGACGT

(1713
88) DNA
ATGAAGCATTGAAGCTGGATCGCAGCAAAGCCACGCCGAAAGAGACCTAT

nt)

GATGCGCTGGTGAAGCGTTACAAGGATCCTGCGCATGGTGCTGGCAAGGG



CACGATGGGAGACTACTGGGAACCGATAGCGCTTAGTATCTACATGGACC



CGAGCACCTTTTACAAACCACCGGTTTCCCCGAAAGAAATTGCTGAGCGC



AAAGACTGCGTTGAATGCCACTCTGATGAAACGCCGGTTTGGGTAAGAGC



ATGGAAACGCAGCACCCACGCCAACCTGGACAAAATACGCAACCTCAAGC



CGGAAGATCCGCTTTTTTACAAAAAAGGCAAGCTGGAAGAAGTTGAGAAC



AACCTGCGCTCCATGGGCAAACTTGGAGAGAAGGAAGCGCTCAAGGAAGT



AGGCTGTATTGACTGTCACGTTGACATCAACGCCAAAAAGAAAGCAGATC



ACACCAAAGACGTACGCATGCCTACAGCTGACGTTTGCGGAACCTGTCAC



CTGAGAGAATTTGCCGAGCGTGAATCCGAGCGTGACACCATGATCTGGCC



GAATGGCCAGTGGCCTGACGGACGTCCATCCCACGCACTGGACTACACAG



CCAACATTGAAACCACCGTTTGGGCAGCCATGCCGCAACGTGAAGTGGCA



GAAGGTTGCACCATGTGCCACACCAACCAGAACAAATGCGACAACTGCCA



TACCCGCCATGAATTTTCGGCGGCAGAATCCCGCAAACCGGAAGCCTGTG



CCACCTGTCACAGCGGCGTGGATCATAATAACTATGAAGCCTACATTATG



TCCAAGCACGGCAAACTGGCTGAAATGAACCGGGAGAACTGGAACTGGAA



TGTTCGTCTGAAAGACGCCTTCTCCAAAGGAGGTCAGACCGCACCGACCT



GTGCAGCCTGCCACATGGAATACGAAGGGGAATATACCCATAACATCACC



CGTAAGACCCGCTGGGCAAACTACCCGTTTGTTCCGGGGATTGCAGAAAA



CATCACCAGCGACTGGTCAGAAGCTCGTCTGGATTCCTGGGTTGTGACCT



GTACCCAATGTCACTCGGAACGGTTTGCCCGCTCCTACCTGGATCTCATG



GACAAAGGTACCCTGGAAGGGTTGGCTAAATACCAGGAAGCCAATGCCAT



TGTTCACAAAATGTATGAAGACGGCACCCTGACTGGTCAAAAAACCAATC



GTCCGAATCCACCGGCGCCAGAGAAACCGGGTTTTGGTATCTTCACCCAA



CTGTTCTGGTCCAAGGGTAACAACCCGGCCTCACTTGAACTGAAAGTGCT



GGAAATGGCAGAAAACAACCTGGCCAAAATGCACGTAGGACTGGCACACG



TTAATCCAGGTGGCTGGACATATACCGAAGGTTGGGGCCCGATGAACCGT



GCCTATGTTGAAATCCAGGATGAATACACCAAGATGCAGGAAATGACAGC



TCTGCAAGCGCGTGTTAACAAACTGGAAGGTAAAAAAACCAGCCTGCTTG



ACCTCAAGGGAGCGGGAGAAAAGATCTCGCTGGGAGGACTGGGAGGTGGC



ATGTTGCTGGCGGGAGCGATTGCTCTGATTGGCTGGCGTAAACGTAAGCA



AACGCAAGCTTGA



SEQ ID
c554
MKIIIACGLVAAALFTLTSGQSLAADAPFEGRKKCSSCHKPQAQSWKHTA

NO: 24
cycA1
HAKAMESLKPNVKVEAKQKAKLDPTKDYTQDKDCVGCHVDGFGQKGGYTI

(235
(D23_1c25
DSPKPMLTGVGCESCHGPGRKYRGDHRKAGQAFEKSGKKAPRKTLASKGQ

aa)
27)
DFNFEERCSACHLNYEGSPWKGAKPPYTPYTPEVDPKYTFKFDEMVKDVK


protein
AMHEHYKLDGVFDGEPKFKFHDEFQANAKTAKKGK



SEQ ID
c554
ATGAAAATAATAATAGCCTGCGGACTGGTTGCTGCAGCCCTGTTCACCCT

NO: 25
cycA1
GACAAGTGGGCAGAGTCTGGCAGCGGATGCTCCGTTTGAAGGTCGGAAAA

(708
(D23_1c25
AGTGCAGTTCCTGTCACAAACCACAAGCCCAGTCGTGGAAACATACTGCC

nt)
27) DNA
CACGCCAAGGCGATGGAATCGCTCAAGCCCAATGTCAAAGTGGAAGCCAA



ACAAAAAGCCAAACTGGATCCTACCAAGGACTACACCCAGGACAAAGACT



GCGTAGGTTGCCACGTGGATGGATTTGGCCAGAAAGGCGGCTACACGATA



GACTCCCCCAAACCCATGCTGACTGGCGTAGGCTGTGAATCCTGCCACGG



GCCTGGACGTAAATACCGGGGAGATCACCGCAAGGCCGGGCAAGCATTTG



AGAAATCGGGCAAAAAAGCGCCGCGCAAGACCCTGGCAAGCAAGGGGCAA



GACTTTAATTTTGAAGAACGTTGCAGCGCCTGCCATCTGAACTATGAAGG



GTCACCCTGGAAAGGAGCAAAACCTCCCTATACCCCGTATACACCGGAAG



TGGATCCGAAATACACCTTCAAGTTTGACGAGATGGTAAAAGACGTCAAA



GCCATGCACGAGCATTACAAACTGGATGGCGTATTTGACGGAGAGCCTAA



ATTCAAGTTCCATGACGAATTCCAGGCCAACGCTAAAACTGCCAAAAAAG



GAAAATAG



SEQ ID
cycA2
MKIIIACGLVAAALFTLTSGQSLAADAPFEGRKKCSSCHKPQAQSWKHTA

NO: 26
(D23_1c19
HAKAMESLKPNVKVEAKQKAKLDPTKDYTQDKDCVGCHVDGFGQKGGYTI

(235
24)
DSPKPMLTGVGCESCHGPGRKYRGDHRKAGQAFEKSGKKAPRKTLASKGQ

aa)
protein
DFNFEERCSACHLNYEGSPWKGAKPPYTPYTPEVDPKYTFKFDEMVKDVK



AMHEHYKLDGVFDGEPKFKFHDEFQANAKTAKKGK



SEQ ID
cycA2
ATGAAAATAATAATAGCCTGCGGACTGGTTGCTGCAGCCCTGTTCACCCT

NO: 27
(D23_1c19
GACAAGTGGGCAGAGTCTGGCAGCGGATGCTCCGTTTGAAGGTCGGAAAA

(708
24) DNA
AGTGCAGTTCCTGTCACAAACCACAAGCCCAGTCGTGGAAACATACTGCC

nt)

CACGCCAAGGCGATGGAATCGCTCAAGCCCAATGTCAAAGTGGAAGCCAA



ACAAAAAGCCAAACTGGATCCTACCAAGGACTACACCCAGGACAAAGACT



GCGTAGGTTGCCACGTGGATGGATTTGGCCAGAAAGGCGGCTACACGATA



GACTCCCCCAAACCCATGCTGACTGGCGTAGGCTGTGAATCCTGCCACGG



GCCTGGACGTAAATACCGGGGAGATCACCGCAAGGCTGGGCAAGCATTTG



AGAAATCGGGCAAAAAAGCGCCGCGCAAGACCCTGGCAAGCAAGGGGCAA



GACTTTAATTTTGAAGAACGTTGCAGCGCCTGCCATCTGAACTATGAAGG



GTCACCCTGGAAAGGAGCAAAACCTCCCTATACCCCGTATACACCGGAAG



TGGATCCGAAATACACCTTCAAGTTTGACGAGATGGTAAAAGACGTCAAA



GCCATGCACGAGCATTACAAACTGGATGGCGTATTTGACGGAGAGCCTAA



ATTCAAGTTCCATGACGAATTCCAGGCCAACGCTAAAACTGCCAAAAAAG



GAAAATAG



SEQ ID
cycA3
MKIIIACGLVAAALFTLTSGQSLAADAPFEGRKKCSSCHKPQAQSWKHTA

NO: 28
(D23_1c17
HAKAMESLKPNVKVEAKQKAKLDPTKDYTQDKDCVGCHVDGFGQKGGYTI

(235
86)
DSPKPMLTGVGCESCHGPGRKYRGDHRKAGQAFEKSGKKAPRKTLASKGQ

aa)
protein
DFNFEERCSACHLNYEGSPWKGAKPPYTPYTPEVDPKYTFKFDEMVKDVK



AMHEHYKLDGVFDGEPKFKFHDEFQANAKTAKKGK



SEQ ID
cycA3
ATGAAAATAATAATAGCCTGCGGACTGGTTGCTGCAGCCCTGTTCACCCT

NO: 29
(D23_1c17
GACAAGTGGGCAGAGTCTGGCAGCGGATGCTCCGTTTGAAGGTCGGAAAA

(708
86) DNA
AGTGCAGTTCCTGTCACAAACCACAAGCCCAGTCGTGGAAACATACTGCC

nt)

CACGCCAAGGCGATGGAATCGCTCAAGCCCAATGTCAAAGTGGAAGCCAA



ACAAAAAGCCAAACTGGATCCTACCAAGGACTACACCCAGGACAAAGACT



GCGTAGGTTGCCACGTGGATGGATTTGGCCAGAAAGGCGGCTACACGATA



GACTCCCCCAAACCCATGCTGACTGGCGTAGGCTGTGAATCCTGCCACGG



GCCTGGACGTAAATACCGGGGAGATCACCGCAAGGCTGGGCAAGCATTTG



AGAAATCGGGCAAAAAAGCGCCGCGCAAGACCCTGGCAAGCAAGGGGCAA



GACTTTAATTTTGAAGAACGTTGCAGCGCCTGCCATCTGAACTATGAAGG



GTCACCCTGGAAAGGAGCAAAACCTCCCTATACCCCGTATACACCGGAAG



TGGATCCGAAATACACCTTCAAGTTTGACGAGATGGTAAAAGACGTCAAA



GCCATGCACGAGCATTACAAACTGGATGGCGTATTTGACGGAGAGCCTAA



ATTCAAGTTCCATGACGAATTCCAGGCCAACGCTAAAACTGCCAAAAAAG



GAAAATAG



SEQ ID
cM552
MTRLQKGSIGTLLTGALLGIALVAVVFGGEAALSTEEFCTSCHSMSYPQS

NO: 30
cycB1
ELKESTHYGALGVNPTCKDCHIPQGIENFHLAVATHVVDGARELWLEMVN

(239
(D23_1c19
DYSTLEKFNERRLEMAHDARMNLKKWDSITCRTCHVKPAPPGESAQAEHK

aa)
23)
KMETEGATCIDCHQNLVHEEAPMTDLNASLAAGKLVLKPEEGDGDDDDDV


protein
DVDDEEEDEEVEVEVEETETADDSDSASSSNHDDDSDDE



SEQ ID
cM552
ATGACTAGACTGCAAAAAGGATCAATTGGTACTTTACTGACAGGAGCTCT

NO: 31
cycB1
GCTGGGAATAGCATTGGTGGCTGTGGTTTTTGGTGGGGAAGCTGCGTTAT

(720
(D23_1c19
CGACCGAAGAGTTTTGTACCAGCTGTCATTCCATGTCATACCCACAGAGT

nt)
23) DNA
GAATTAAAAGAATCCACCCACTATGGTGCATTGGGGGTTAATCCGACTTG



TAAAGACTGTCATATTCCACAAGGGATAGAAAATTTCCACCTGGCAGTAG



CAACTCACGTGGTTGATGGTGCCAGAGAACTTTGGTTGGAGATGGTCAAT



GACTACTCCACCCTGGAGAAGTTCAACGAAAGAAGATTGGAAATGGCGCA



TGATGCCCGGATGAACCTCAAGAAATGGGACAGCATCACCTGCCGTACCT



GTCATGTAAAACCAGCTCCTCCGGGAGAAAGCGCCCAGGCGGAACATAAG



AAAATGGAAACGGAAGGAGCAACCTGCATAGACTGTCATCAGAATCTGGT



GCATGAAGAAGCGCCGATGACAGATTTGAATGCAAGTCTTGCTGCAGGCA



AGCTGGTATTAAAGCCAGAAGAGGGTGACGGTGACGATGACGATGACGTT



GACGTTGATGACGAGGAGGAGGATGAAGAAGTCGAGGTGGAAGTTGAAGA



AACTGAAACAGCTGACGACAGCGACTCCGCTTCCTCCAGCAACCATGATG



ACGATAGTGATGATGAGTAA



SEQ ID
cycB2
MTRLQKGSIGTLLTGALLGIALVAVVFGGEAALSTEEFCTSCHSMSYPQS

NO: 32
(D23_1c25
ELKESTHYGALGVNPTCKDCHIPQGIENFHLAVATHVVDGARELWLEMVN

(239
26)
DYSTLEKFNERRLEMAHDARMNLKKWDSITCRTCHVKPAPPGESAQAEHK

aa)
protein
KMETEGATCIDCHQNLVHEEAPMTDLNASLAAGKLVLKPEEGDDDDDDDV



DVDDEEEDEEVEVEVEETETADDSDSASSSNHDDDSDDE



SEQ ID
cycB2
ATGACTAGACTGCAAAAAGGATCAATTGGCACTTTACTGACAGGAGCTCT

NO: 33
(D23_1c25
GCTGGGAATAGCATTGGTGGCTGTGGTTTTTGGTGGGGAAGCTGCGTTAT

(720
26) DNA
CGACCGAAGAGTTTTGTACCAGCTGTCATTCCATGTCATACCCACAGAGT

nt)

GAATTAAAAGAATCCACCCACTATGGTGCATTGGGGGTTAATCCGACTTG



TAAAGACTGTCATATTCCACAAGGGATAGAAAATTTCCACCTGGCAGTAG



CAACTCACGTGGTTGATGGTGCCAGAGAACTTTGGTTGGAGATGGTCAAT



GACTACTCCACCCTGGAGAAGTTCAACGAAAGAAGATTGGAAATGGCGCA



TGATGCCCGGATGAACCTCAAGAAATGGGACAGCATCACCTGCCGTACCT



GTCATGTAAAACCAGCTCCTCCGGGAGAAAGCGCCCAGGCGGAACATAAG



AAAATGGAAACGGAAGGAGCAACCTGCATAGACTGTCATCAGAATCTGGT



GCATGAAGAAGCGCCGATGACAGATTTGAATGCAAGTCTTGCTGCAGGCA



AGCTGGTATTAAAGCCAGAAGAGGGTGACGATGACGATGACGATGACGTT



GACGTTGATGACGAGGAGGAGGATGAAGAAGTCGAGGTGGAAGTTGAAGA



AACTGAAACAGCTGACGACAGCGACTCCGCTTCCTCCAGCAACCATGATG



ACGATAGTGATGATGAGTAA





























































































































































































































































































































































































































































































INCORPORATION BY REFERENCE
All publications and patents mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference.
While specific embodiments of the subject invention have been discussed, the above specification is illustrative and not restrictive. Many variations of the invention will become apparent to those skilled in the art upon review of this specification and the claims below. The full scope of the invention should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations.
Certain embodiments are within the following claims.