TABLE 3.
Distribution of citrate fermentation over 156 sequenced bacterial genomes (207 strains)
| Phylum and class | na | Bacterium | Presence of:
|
Transporter family | Gene organizationb | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| CitM | OAD
|
CitR | CitAB | ||||||||
| A | D | B | G | ||||||||
| Firmicutes | 38 | ||||||||||
| Bacillales | 23 | Lactococcus lactis | x | x | [st326]2HCT | (R-T)cM><R<>C-DEF-X-G | |||||
| Lactobacillus plantarum | x | x | [st303]AIT | G-4-MDH-T><R<>M-C-DEF-FU-FR-2-X | |||||||
| Lactobacillus acidophilus | x | [st303]AIT | FU-FR-MDH-1-T-1-C-DEF-1><5-RXG | ||||||||
| Streptococcus mutans | x | x | x | [st301]CITM | C-G-1-T<>1-D-B-DEF-X-A | ||||||
| Streptococcus pyogenes | x | x | x | [st301]CITM | G-1-T-1-D-B-DEF-X-A-C | ||||||
| Enterococcus faecalis | x | x | x | x | [st301]CITM | T-1-D-B-1-C-DEF-X-A-M-G | |||||
| Clostridia | 4 | Clostridium perfringens | x | x | [st326]2HCT | R-G-C-DEF-X-M-T | |||||
| Clostridium tetani | - | DEF-C-X-Gd | |||||||||
| Clostridium tetani | x | [st313]AITC | DEF-T-1-Md | ||||||||
| Fusobacteria | 1 | Fusobacterium nucleatum | x | [st326]2HCT | C-XT-A-G-DEF | ||||||
| Proteobacteria | 74 | ||||||||||
| Gamma subdivision | 34 | Photobacterium profundum | x | x | x | x | x | [st326]2HCT | BA-B-A:D-oG-T<>C-DEF-X-Gd | ||
| Salmonella typhimurium | x | x | x | x | x | [st326]2HCT | BA-B-A:D-oG-T<>C-DEF-X-G | ||||
| Salmonella enterica | x | x | x | x | x | [st326]2HCT | BA-B-A:D-oG-T<>C-DEF-X-G | ||||
| Vibrio cholerae | x | x | x | x | x | [st326]2HCT | BA-B-A:D-oG-T<>C-DEF-X-G | ||||
| Escherichia coli | x | [st303]AIT | BA<>C-DEF-X-G-T | ||||||||
| Salmonella typhimurium | x | [st303]AIT | BA<>C-DEF-X-G-T | ||||||||
| Salmonella enterica | x | [st303]AIT | BA<>C-DEF-X-G-T | ||||||||
| Haemophilus influenza | [st303]AIT | C-DEF-X:G-T | |||||||||
| Haemophilus ducreyi | x | [st303]AIT | C-DEF-X:G-T-M | ||||||||
| Shigella flexneri | [st303]AIT | C-DEF-X-G-Te | |||||||||
| Erwinia carotovora | x | [st326]2HCT | BA<>T-1-C-DEF-X-G | ||||||||
| Spirochaetales | 5 | Treponema denticola | x | x | x | [st326]2HCT? | A:D-BC-X:GDEFT | ||||
Number of completed genomes available at http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complete.html. For the remaining completed genomes, see Table 2.
abbreviations: R, transcriptional regulator CitR; T, transporter; M, malic enzyme CitM; C, DEF, X, and G, citrate lyase subunits and accessory proteins (see Fig. 3C); MDH, malate dehydrogenase; FU, fumarase; FR, fumarate reductase; D, B, and A, subunits of the oxaloacetate decarboxylase OadDBA (see Fig. 3B); oG, γ subunit of oxaloacetate decarboxylase; BA, two-component signal transduction system CitAB. Adjacent genes are connected by a dash, adjacent but divergently transcribed genes by angle brackets, and distant genes by a space. Numbers indicate intergenic open reading frames. A “:” indicates that the genes are fused in one open reading frame.
Plasmidic.
oadG and/or citD erroneously annotated or not annotated in the database.
T not annotated in the database.