TABLE 2.
Deduced functions of ORFs in the TCA biosynthetic gene cluster
| Gene | Sizea | Protein, homolog,b and origin | % Identity/similarity | Proposed function |
|---|---|---|---|---|
| orf(−4)c | 134 | CBG1971 (CAE72536.1); Caenorhabditis briggsae | 36/47 | Hypothetical protein |
| orf(−3)c | 296 | CitA (ZP_00616833.1); Kineococcus radiotolerans SRS30216 | 52/63 | ATP-binding region, ATPase-like |
| orf(−2)c | 186 | CitB (NP_629572.1); Streptomyces coelicolor A3(2) | 58/67 | Two-component response regulator |
| orf(−1)c | 1,031 | DnaE (ZP_01650120.1); Salinispora arenicola CNS205 | 87/93 | DNA polymerase III, alpha subunit |
| orf(0)c | 105 | Unknown protein | ||
| tcaT1 | 370 | STIAU_3104 (ZP_01461407); Stigmatella aurantiaca DW4/3-1 | 30/42 | GT |
| TcaC | 186 | RHA1_ro09012 (YP_708214); Rhodococcus sp. RHA1 | 55/68 | Flavin reductase |
| tcaU1 | 109 | Strop_3510 (5059984); Salinispora tropica CNB-440 | 65/69 | Unknown protein |
| tcaU2 | 146 | CLOL250_02534 (EDO56846); Clostridium sp. strain L2-50 | 32/56 | Unknown protein |
| tcaU3 | 312 | Unknown protein | ||
| tcaR1 | 267 | ChlF2 (AAZ77687); S. antibioticus | 44/59 | Pathway-specific activator |
| tcaB5 | 197 | TylCVII (AAD41825); Streptomyces fradiae | 60/73 | Sugar (3,)5-epimerase |
| tcaB4 | 332 | ChlC4 (AAZ77681); S. antibioticus | 56/69 | Sugar 3-ketoreductase |
| tcaT2 | 392 | ChlC7 (AAZ77672); S. antibioticus | 37/53 | GT |
| tcaB11 | 263 | Methyltransferase (ZP_01650637); S. arenicola CNS205 | 38/53 | SAM-dependent N-methyltransferase |
| tcaB7 | 380 | SpnR (AAG23279); Sacharopolyspora spinosa SpnQ (AAG23278); S. spinosa | 55/71 26/50 | Sugar aminotransferase/3,4-dehydratase |
| TcaM | 380 | Srm6 (CM96572); Streptomyces ambofaciens | 40/56 | O-Acyltransferase |
| tcaB1 | 295 | AclY (AAK83289); Steptomyces galilaeus | 62/75 | TDP-d-glucose synthase |
| tcaB2 | 332 | AprE (AAG18457); Streptomyces tenebrarius | 74/83 | TDP-glucose 4,6-dehydratase |
| tcaB10 | 434 | RubN8 (CAI94696); Streptomyces achromogenes subsp. Rubradiris | 61/74 | Oxidoreductase |
| tcaB8 | 373 | Med-ORF20 (BAC79028); Streptomyces sp. strain AM-7161 | 80/86 | Sugar 3-aminotransferase |
| tcaB9 | 414 | PCZA361.22 (CAA11777); Amycolatopsis orientalis | 69/79 | Sugar 3-methyltransferase |
| tcaU4 | 164 | YD repeat (ZP_00573146); Frankia sp. strain EAN1pec | 41/52 | PAS/PAC sensor hybrid histidine kinase |
| tcaA1 | 6,330 | FRAAL4072 (YP_714269); Frankia alni ACN14a | 44/55 | Type I polyketide synthase |
| tcaA2 | 7,007 | FscC (AAQ82564); Streptomyces sp. strain FR-008 | 49/61 | Type I polyketide synthase |
| tcaA4 | 1,840 | HbmAII (AAY28226); Streptomyces hygroscopicus | 49/62 | Type I polyketide synthase |
| tcaA5 | 1,537 | ChlA6 (AAZ77699); S. antibioticus | 51/62 | Type I polyketide synthase |
| tcaE1 | 491 | ChlE3 (AAZ77700); S. antibioticus | 48/61 | FAD-dependent oxidoreductase |
| tcaD4 | 350 | ChlM (AAZ77702); S. antibioticus | 65/76 | Ketosynthase III-like condensation protein |
| tcaD1 | 633 | ChlD1 (AAZ77703); S. antibioticus | 60/70 | Acyltransferase and phosphotase |
| tcaD2 | 75 | ChlD2 (AAZ77704); S. antibioticus | 57/72 | ACP |
| tcaD3 | 616 | N-terminal domain to ChlD3 (AAZ77705); S. antibioticus C-terminal domain to ChlD4 (AAZ77706); S. antibioticus | 58/74 55/71 | Dihydrolipoamide acyltransferase and hydrolase |
| tcaR2 | 192 | SACE_3583 (YP_001105782); Sacharopolyspora erythraea NRRL 2338 | 40/56 | TetR family transcriptional regulator |
| tcaT3 | 398 | ChlC7 (AAZ77672); S. antibioticus | 41/55 | GT |
| tcaT4 | 379 | ChlC7 (AAZ77672); S. antibioticus | 42/57 | GT |
| tcaE2 | 505 | MitR (AAD28454); Streptomyces lavendulae | 49/65 | Flavin-dependent oxidoreductase |
| TcaF | 254 | SAV407 (AAD28454); S. avermitilis MA-4680 | 54/70 | Thioesterase |
| tcaB3 | 487 | ORF26 (AAP85341); Streptomyces griseoruber | 53/64 | Sugar 2,3-dehydratase |
| tcaA3 | 3,964 | ChlA5 (AAZ77698); S. antibioticus | 55/66 | Type I polyketide synthase |
| tcaB6 | 289 | SCO3730 (NP_627921); S. coelicolor A3(2) | 59/71 | NAD(P)H-dependent aldo/keto reductase |
| TcaG | 490 | ChlG (AAZ77686); S. antibioticus | 43/61 | Multidrug export protein |
| orf37c | 275 | STIAU_2740 (ZP_01466190.1); Stigmatella aurantiaca DW4/3-1 | 39/53 | M23 peptidase domain protein |
| orf38c | 222 | CHAP (ZP_00532045.1)Chlorobium phaeobacteroides BS1 | 32/52 | Integrin alpha chain |
| orf39c | 132 | mll5401 (NP_106072.1); Mesorhizobium loti MAFF303099 | 40/52 | Hypothetical protein |
| orf40c | 106 | ArsR (YP_001135161.1); Mycobacterium gilvum PYR-GCK | 78/84 | Regulatory protein |
| orf4c | 243 | MMT1 (YP_001135160.1); M.m gilvum PYR-GCK | 76/83 | Co/Zn/Cd cation transporter-like protein |
| orf42c | 148 | PldB (YP_286985.1); Dechloromonas aromatica RCB | 41/57 | Alpha/beta hydrolase fold |
a
The size of each protein is shown as the number of amino acids.
b
NCBI accession numbers are given in parentheses.
c
ORF beyond the tca gene cluster.