TABLE 1.
Characteristics and closest relative of the predicted product of each CDS or gene from regions 1 and 2
| CDS or gene | Position (bp) | Homologue found by BLAST (ORF or gene, product, organism/element) | No. of similar amino acids/total no. of amino acids (%) | Accession no. | ||
|---|---|---|---|---|---|---|
| Region 1 (bp 37546 to 42172) | ||||||
| CDS38 | 38438-37648 | HCM2.0120c, hypothetical, protein, S. enterica subsp. enterica serovar Typhi, plasmid pHCM2 | 261/262 (99) | NP_569592 | ||
| CDS39 | 39737-38595 | HCM2.0121c, putative ribonucleoside diphosphate reductase beta subunit, S. enterica subsp. enterica serovar Typhi, plasmid pHCM2 | 379/380 (99) | NP_569593 | ||
| CDS40 | 42160-39845 | HCM2.0122c, putative ribonucleoside diphosphate reductase alpha subunit, S. enterica subsp. enterica serovar Typhi, plasmid pHCM2 | 769/771 (97) | NP_569594 | ||
| Region 2 (bp 81956 to 114573) | ||||||
| traA | 82124-82480 | traA, prepropilin, E. coli K-12 strain CR63, plasmid F | 63/69 (91) | NP_061453 | ||
| traL | 82631-82936 | traL, TraL, function in F pilus assembly, E. coli K-12 strain CR63, plasmid F | 87/99 (87) | NP_061454 | ||
| traE | 82951-83517 | traE, TraE, function in F pilus assembly, E. coli K-12 strain CR63, plasmid F | 159/188 (84) | NP_061455 | ||
| traK | 83504-84247 | traK, TraK, function in F pilus assembly, E. coli K-12 strain CR63, plasmid F | 173/224 (77) | NP_061456 | ||
| traB | 84225-85628 | traB, TraB, function in pilus assembly, E. coli K-12 plasmid R100-1 | 362/467 (77) | AAB07770 | ||
| traV | 85650-86189 | traV, TraV, function in pilus biogenesis, Shigella flexneri 2b strain 222, plasmid R100 | 114/163 (69) | NP_052954 | ||
| traV | 86267-86533 | traR, TraR, conjugative transfer protein, S. enterica serovar Typhi, plasmid pED208 | 55/88 (62) | AAM90708 | ||
| orfX1 (CDS81) | 86537-86722 | orfX1, hypothetical protein, transfer region, S. enterica serovar Typhi, plasmid pED208 | 54/60 (90) | AAM90709 | ||
| orfX2 | 86604-87110 | orfX2, hypothetical protein, transfer region, S. enterica serovar Typhi, plasmid pED208 | 73/95 (76) | AAM90710 | ||
| traP | 87100-87666 | traP, conjugative transfer protein, Salmonella enterica serovar Typhimurium LT2, plasmid pSLT | 62/137 (45) | NP_490568 | ||
| traC | 87659-90290 | Possible pseudogene, traC, E. coli K-12 strain CR63, plasmid F | 301/339 (88) | NP_061463 | ||
| trbI | 90287-90634 | trbI, pilus assembly protein, S. enterica serovar Typhimurium LT2, plasmid pSLT | 78/91 (85) | NP_490574 | ||
| traW | 90631-91281 | traW, pilus assembly protein, S. enterica serovar Typhimurium LT2, plasmid pSLT | 143/187 (76) | NP_490575 | ||
| traU | 91278-92270 | traU, pilus assembly protein, S. enterica serovar Typhimurium LT2, plasmid pSLT | 276/320 (86) | NP_490576 | ||
| trbC | 92462-92917 | trbC, hypothetical protein, S. flexneri 2b strain 222, plasmid R100 | 111/151 (73) | NP_052965 | ||
| traN | 92914-94764 | traN, mating pair stabilization protein, S. enterica serovar Typhimurium LT2, plasmid pSLT | 455/607 (74) | NP_490579 | ||
| traF | 95017-95766 | traF, TraF, E. coli, plasmid R100-1 | 193/234 (82) | AAB61943 | ||
| traO | 95693-96031 | traQ, pilin chaperone, S. enterica serovar Typhimurium LT2, plasmid pSLT | 47/63 (74) | NP_490582 | ||
| trbB | 95970-96566 | trbB, hypothetical protein, E. coli K-12 strain CR63, plasmid F | 139/179 (77) | NP_061474 | ||
| traH | 96563-97936 | traH, pilus assembly protein, S. enterica serovar Typhimurium LT2, plasmid pSLT | 394/446 (88) | NP_490584 | ||
| traG | 97936-100755 | traG, responsible for pilus biogenesis and stabilization of mating pairs, S. flexneri 2b strain 222, plasmid R100 | 761/939 (81) | NP_052976 | ||
| Y1062 | 102083-100876 | Y1062, possible pseudogene, putative transposase IS285, Y. pestis KIM10+, plasmid pMT-1 | 381/381 (100) | AAC82722 | ||
| traD | 102087-104276 | traD, TraD, E. coli F sex factor | 547/705 (77) | AAC44181 | ||
| traI | 104276-109516 | traI, TraI, function in oriT nicking and unwinding, E. coli K-12 strain CR63, plasmid F | 1,324/1,759 (75) | NP_061483 | ||
| traX | 109380-110255 | traX, F pilin acetylation protein, S. flexneri, plasmid pWR501 | 160/284 (56) | NP_085416 | ||
| finO | 110322-111041 | finO, fertility inhibition protein, E. coli, plasmid F | 75/180 (41) | P22707 | ||
| bcfH | 111028-111825 | bcfH, putative thiol disulfide isomerase, S. enterica serovar Typhimurium LT2 | 138/244 (56) | NP_459033 | ||
| nuc | 111973-112527 | nuc, endonuclease, Y. enterocolitica strain 15673 (biogroup 1A serogroup 0:5) pYV plasmid | 135/174 (77) | CAA73744 | ||
| copB | 112418-112648 | copB, CopB, function in replication control, E. intermedius, plasmid pLV1402 | 36/46 (78) | CAA08928 | ||
| copA | 112835-112750 | copA, small RNA, function in antisense control, E. coli, plasmid RI | 71/81 (87) | V00326 | ||
| tapA | 112867-112944 | tapA, TapA, function in antisense control, E. intermedius, plasmid pLV1402 | 24/25 (96) | CAA08929 | ||
| repA | 112925-113800 | repA, replication protein, E. intermedius, plasmid pLV1402 | 234/287 (81) | CAA08930 | ||
| SMR0139 | 114351-114847 | SMR0139, possible pseudogene, ATP/GTP-binding protein, Serratia marcescens, plasmid R478 | 143/164 (87) | NP_941209 |