TABLE 2.
Putative genes and their products, deduced from the plasmid nucleotide sequences
| Plasmid and gene | Codon
|
No. of amino acids | Best homolog (organism, GenBank accession no.) | % Identity (no. of amino acids overlapping) | Proposed function of gene product | |
|---|---|---|---|---|---|---|
| Start | Stopa | |||||
| pWCFS101 | ||||||
| rep | 163 | 1122 | 319 | Rep protein pLAB1000 (Lactobacillus hilgardii, E973099) | 71 (314) | Replication protein |
| orf2 | 1406 | 1260 C | 48 | No hits | Hypothetical protein | |
| orf3 | 1627 | 1809 | 60 | No hits | Hypothetical protein | |
| pWCFS102 | ||||||
| repB | 102 | 761 | 219 | RepB-like protein pLH2 (Lactobacillus helveticus, Q48562) | 88 (219) | Replication protein |
| orf2 | 1393 | 953 C | 146 | No hits | Hypothetical protein | |
| orf3 | 1889 | 1686 C | 67 | No hits | Hypothetical protein | |
| repA | 2242 | 35 | 52 | CopA pPSC22 (Lactobacillus plantarum, Q48820) | 60 (50) | Copy number control protein |
| pWCFS103 | ||||||
| orf1 | 51 | 35839 C | 93 | DinJ (Escherichia coli, Q47150) | 30 (80) | DNA-damage-inducible protein |
| repA | 610 | 302 C | 102 | RepA-like protein pSAK1 (Lactobacillus sakei, Q48860) | 53 (76)b | Replication protein |
| orf3 | 925 | 1257 C | 110 | No hits | Hypothetical protein | |
| repB | 2061 | 2861 | 266 | RepB pAD1 (Enterococcus faecalis, Q52229) | 39 (276) | Copy number control protein |
| orf5 | 2863 | 3213 | 116 | Hypothetical protein (Lactobacillus sakei, Q9AED4) | 33 (113) | Hypothetical protein |
| orf6 | 3344 | 3586 | 80 | No hits | Hypothetical protein | |
| tnpR1 | 4370 | 3816 C | 184 | Resolvase-like protein pMD136 (Pediococcus pentosus, Q9WW47) | 83 (184) | Putative resolvase |
| orf8 | 4649 | 4855 | 68 | No hits | Hypothetical protein | |
| orf9 | 5641 | 5378 C | 87 | No hits | Hypothetical protein | |
| arsR | 5713 | 6072 | 119 | ArsR-like protein pL1100 (Listeria innocua, Q926M3) | 48 (119) | Regulator of arsenical resistance operon |
| arsD1 | 6059 | 6421 | 120 | ArsD-like protein pL1100 (Listeria innocua, Q926M4) | 42 (123) | Repressor of arsenical resistance operon |
| arsA | 6505 | 8235 | 576 | ArsA-like protein pL1100 (Listeria innocua, Q926M2) | 65 (568) | Arsenical pump-driving ATPase |
| arsB | 8294 | 9589 | 431 | ArsB-like protein (Listeria monocytogenes, P96678) | 73 (427) | Arsenical pump membrane protein |
| orf14 | 9606 | 9935 | 109 | No hits | Hypothetical protein | |
| arsD2 | 9958 | 10257 | 99 | ArsD-like protein pL1100 (Listeria innocua, Q926M4) | 43 (95) | Repressor of arsenical resistance operon |
| nox | 10281 | 11681 | 466 | Hypothetical protein pL1100 (Listeria innocua, Q926L9) | 36 (450) | Putative NADH oxidase |
| cadC | 12031 | 12399 | 122 | Transcriptional regulator ArsR family (Chlorobium tepidum, Q8KE78) | 37 (97) | Putative positive regulator of cadmium resistance |
| cadD | 12401 | 13015 | 204 | CadD pUB101 (Staphylococcus aureus, Q8GNY9) | 50 (205) | Putative cadmium resistance protein |
| orf19 | 14131 | 13100 C | 344 | Transposase (Lactobacillus delbrueckii, Q93L10) | 41 (338) | Putative transposase |
| orf20 | 14404 | 14240 C | 54 | LtrC pMRC01 (Lactococcus lactis, O87224) | 61 (49)c | Hypothetical protein |
| orf21 | 14623 | 14408 C | 71 | Hypothetical 8.0-kDa protein pMRC01 (Lactococcus lactis, O87223) | 57 (70) | Hypothetical protein |
| tra1 | 16881 | 14746 C | 711 | Trs1 pMRC01 (Lactococcus lactis, O87222) | 60 (722) | DNA topoisomerase |
| orf23 | 17298 | 16888 C | 136 | No hits | Hypothetical protein | |
| traL | 18170 | 17313 C | 285 | TrsL pMRC01 (Lactococcus lactisO87221) | 44 (277) | Conjugation protein |
| orf25 | 18565 | 18176 C | 129 | Hypothetical 14.7-kDa protein pMRC01 (Lactococcus lactis, O87220) | 32 (126) | Hypothetical protein |
| traK | 20076 | 18565 C | 503 | TraK pMRC01 (Lactococcus lactis, O87219) | 76 (503) | Conjugation protein |
| traJ | 20548 | 20078 C | 156 | TrsJ pMRC01 (Lactococcus lactis, O87218) | 48 (150) | Conjugation protein |
| orf28 | 20917 | 20549 C | 122 | Hypothetical protein pMRC01 (Lactococcus lactis, O87217) | 42 (118) | Hypothetical protein |
| orf29 | 21521 | 20904 C | 205 | Hypothetical 23.3-kDa protein pMRC01 (Lactococcus lactis, O87216) | 48 (204) | Hypothetical protein |
| orf30 | 22690 | 21536 C | 384 | Hypothetical protein pMRC01 (Lactococcus lactis, O87215) | 54 (395) | Hypothetical protein |
| traF | 24109 | 22691 C | 472 | TrsF pMRC01 (Lactococcus lactis, O87214) | 50 (471) | Conjugation protein |
| traE | 26120 | 24102 C | 672 | TrsE pMRC01 (Lactococcus lactis, O87213) | 82 (671) | Conjugation protein |
| traE | 26791 | 26132 C | 219 | TrsD pMRC01 (Lactococcus lactis, O87212) | 80 (219) | Conjugation protein |
| traC | 27122 | 27760 C | 120 | TrsC pMRC01 (Lactococcus lactis, O87211) | 73 (115) | Conjugation protein |
| traB | 27478 | 27143 C | 111 | TrsB pMRC01 (Lactococcus lactis, O87210) | 72 (107) | Conjugation protein |
| orf36 | 28094 | 27480 C | 204 | Hypothetical 23.2-kDa protein pMRC01 (Lactococcus lactis, O97209) | 51 (201) | Hypothetical protein |
| orf37 | 28471 | 28133 C | 112 | Hypothetical 13.1-kDa protein pMRC01 (Lactococcus lactis, O87208) | 46 (90) | Hypothetical protein |
| traA | 30584 | 28524 C | 686 | TraA pMRC01 (Lactococcus lactis, O87207) | 49 (677) | Nickase |
| orf39 | 30856 | 31065 | 69 | Hypothetical 10.9-kDa protein pMRC01 (Lactococcus lactis, O87206) | 56 (66) | Hypothetical protein |
| orf40 | 31088 | 31366 | 92 | Hypothetical 10.6-kDa protein pMRC01 (Lactococcus lactis, O87204) | 50 (88) | Hypothetical protein |
| orf41 | 31356 | 31670 C | 104 | No hits | Hypothetical protein | |
| tnpR2 | 32466 | 31880 C | 195 | TnpR transposon Tn551 (Staphylococcus aureus, TNR7_ENTFA) | 40 (181) | Putative resolvase |
| tnpA | 32645 | 35638 | 997 | Transposase pAM373 (Enterococcus faecalis, Q9F117) | 64 (987) | Putative transposase |
a
C, complementary sequence.
b
Homologous to C-terminal part of protein.
c
Homologous to N-terminal part of protein.