TABLE 2.
Genes important for biofilm formation in V. cholerae strains SIO and TP
| Strain | TIGR gene or genome region | Gene | Common name or conserved domainsa | Predicted function |
|---|---|---|---|---|
| Cell motility | ||||
| T1104 | VC2188 | flaA | Flagellin subunit A | Flagellar motility |
| T1106 | VC2131 | fliH | Flagellar assembly protein | Flagellar motility |
| T1108 | VC2190 | flgL | Flagellar hook-associated protein | Flagellar motility |
| T1109 | VC2194 | flgH | Flagellar L-ring protein precursor | Flagellar motility |
| T1116 | VC2125 | fliN | Flagellar motor switch | Flagellar motility |
| T1123 | VC0892 | pomA | Flagellar motor protein | Flagellar motility |
| T1139 | VC2059 | cheW | Purine-binding chemotaxis protein | Chemotaxis |
| T1141 | VC0414 | mshQ | MshQ | MSHA pilus biosynthesis |
| Amino acid transport and metabolism | ||||
| S1163 | VC1494 | pepN | Aminopeptidase N | Glutathione metabolism |
| S1168 | VC2492 | leuC | 3-Isopropylmalate dehydratase | Leucine metabolism |
| S1165 | VCA1100 | ABC transporter | Peptide/nickel transport | |
| S/T1101 | VCA0161a | tnaA | Tryptophanase | Tryptophan metabolism |
| T1124 | VCA0160 | mtr | Mtr | Tryptophan transport |
| T1133 | VC0391 | lysC | Aspartokinase III | Amino acid metabolism |
| Inorganic ion transport and metabolism | ||||
| S1164 | VC2215 | Cation transporter ATPase, E1-E2 family | Divalent ion transport | |
| T1114 | VC0378 | Zinc uptake regulation protein | Zinc transport | |
| T1127 | VC1437 | Cation transporter ATPase, E1-E2 family | Divalent ion transport | |
| T1132 | VC0609 | ABC transporter | Iron(III) transport | |
| Cell wall/membrane biogenesis | ||||
| S/T1105 | VC0927a | cpsF | UDP-N-acetyl-d-mannosamine transferase | EPS biosynthesis |
| S/T1128 | VC0921a | Polysaccharide export protein | EPS biosynthesis | |
| T1102 | VC0918 | epsD | UDP-N-acetyl-d-mannosaminuronic acid dehydrogenase | EPS biosynthesis |
| T1142 | VC0240 | rfaD | ADP-l-glycero-d-mannoheptose-6-epimerase | LPS biosynthesis |
| General function prediction only | ||||
| S1150 | VC0920a | epsF | Glycosyl transferase | EPS biosynthesis |
| T1130 | VCA0859a | Aldo/keto reductase 2 family | Phosphate starvation | |
| Coenzyme transport and metabolism | ||||
| T1118 | VC0105 | hemB | δ-Aminolevulinic acid dehydratase | Porphyrin metabolism |
| Transcription | ||||
| T1112 | VC2337 | lacI | LacI family transcriptional regulator | Transcription regulation |
| Replication, recombination, and repair | ||||
| T1122 | VC0345 | mutL | DNA mismatch repair protein | Hfq operon |
| Signal transduction mechanisms | ||||
| S1166 | VC1934 | Diguanylate cyclase/phosphodiesterase, GGDEF/EAL family | EPS biosynthesis and signaling | |
| Conserved hypothetical | ||||
| S1162 | VCA0094 | MarR transcriptional regulator domainb | Transcription regulation | |
| T1121 | VC0661 | O-Methyltransferase domainb | General | |
| T1131 | VCA0524 | Tellurite resistance protein domainb | Inorganic ion transport | |
| Hypothetical | ||||
| S1154 | VCA0051-GGDEF operon | TPR transcriptional regulator domainb | ||
| S1160 | VCA0075-GGDEF operon | |||
| S/T1103 | VC0922a-VPS operon | |||
| T1111 | VC1495- pepN operon | |||
| T1115 | VCA0817-mgtE operon | Small mechanosensitive channel domainb | ||
| T1120 | VCA0213 | Na/H transporter domainb | Energy production | |
| T1125 | VC0926-VPS operon | |||
| T1134 | VC0935-VPS operon | |||
| T1144 | VCA0109 | Conserved domain: DUF1316b | Unknown | |
| T1146 | VCA0936 | Deacylase/carboxypeptidase domainb | General | |
| Other | ||||
| T1143 | Tn5 transposase | |||
| T1140 | Vibrio phage VJK locus | |||
| T1138 | Putative LPS locus |
a
There are multiple mutations in the same locus.
b
Function assigned using the KEGG database.