TABLE 1.

Characteristics and closest relative of the predicted product of each CDS or gene from regions 1 and 2

CDS or genePosition (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)
    CDS3838438-37648HCM2.0120c, hypothetical, protein, S. enterica subsp. enterica serovar Typhi, plasmid pHCM2261/262 (99)NP_569592
    CDS3939737-38595HCM2.0121c, putative ribonucleoside diphosphate reductase beta subunit, S. enterica subsp. enterica serovar Typhi, plasmid pHCM2379/380 (99)NP_569593
    CDS4042160-39845HCM2.0122c, putative ribonucleoside diphosphate reductase alpha subunit, S. enterica subsp. enterica serovar Typhi, plasmid pHCM2769/771 (97)NP_569594
Region 2 (bp 81956 to 114573)
    traA82124-82480traA, prepropilin, E. coli K-12 strain CR63, plasmid F63/69 (91)NP_061453
    traL82631-82936traL, TraL, function in F pilus assembly, E. coli K-12 strain CR63, plasmid F87/99 (87)NP_061454
    traE82951-83517traE, TraE, function in F pilus assembly, E. coli K-12 strain CR63, plasmid F159/188 (84)NP_061455
    traK83504-84247traK, TraK, function in F pilus assembly, E. coli K-12 strain CR63, plasmid F173/224 (77)NP_061456
    traB84225-85628traB, TraB, function in pilus assembly, E. coli K-12 plasmid R100-1362/467 (77)AAB07770
    traV85650-86189traV, TraV, function in pilus biogenesis, Shigella flexneri 2b strain 222, plasmid R100114/163 (69)NP_052954
    traV86267-86533traR, TraR, conjugative transfer protein, S. enterica serovar Typhi, plasmid pED20855/88 (62)AAM90708
    orfX1 (CDS81)86537-86722orfX1, hypothetical protein, transfer region, S. enterica serovar Typhi, plasmid pED20854/60 (90)AAM90709
    orfX286604-87110orfX2, hypothetical protein, transfer region, S. enterica serovar Typhi, plasmid pED20873/95 (76)AAM90710
    traP87100-87666traP, conjugative transfer protein, Salmonella enterica serovar Typhimurium LT2, plasmid pSLT62/137 (45)NP_490568
    traC87659-90290Possible pseudogene, traC, E. coli K-12 strain CR63, plasmid F301/339 (88)NP_061463
    trbI90287-90634trbI, pilus assembly protein, S. enterica serovar Typhimurium LT2, plasmid pSLT78/91 (85)NP_490574
    traW90631-91281traW, pilus assembly protein, S. enterica serovar Typhimurium LT2, plasmid pSLT143/187 (76)NP_490575
    traU91278-92270traU, pilus assembly protein, S. enterica serovar Typhimurium LT2, plasmid pSLT276/320 (86)NP_490576
    trbC92462-92917trbC, hypothetical protein, S. flexneri 2b strain 222, plasmid R100111/151 (73)NP_052965
    traN92914-94764traN, mating pair stabilization protein, S. enterica serovar Typhimurium LT2, plasmid pSLT455/607 (74)NP_490579
    traF95017-95766traF, TraF, E. coli, plasmid R100-1193/234 (82)AAB61943
    traO95693-96031traQ, pilin chaperone, S. enterica serovar Typhimurium LT2, plasmid pSLT47/63 (74)NP_490582
    trbB95970-96566trbB, hypothetical protein, E. coli K-12 strain CR63, plasmid F139/179 (77)NP_061474
    traH96563-97936traH, pilus assembly protein, S. enterica serovar Typhimurium LT2, plasmid pSLT394/446 (88)NP_490584
    traG97936-100755traG, responsible for pilus biogenesis and stabilization of mating pairs, S. flexneri 2b strain 222, plasmid R100761/939 (81)NP_052976
    Y1062102083-100876Y1062, possible pseudogene, putative transposase IS285, Y. pestis KIM10+, plasmid pMT-1381/381 (100)AAC82722
    traD102087-104276traD, TraD, E. coli F sex factor547/705 (77)AAC44181
    traI104276-109516traI, TraI, function in oriT nicking and unwinding, E. coli K-12 strain CR63, plasmid F1,324/1,759 (75)NP_061483
    traX109380-110255traX, F pilin acetylation protein, S. flexneri, plasmid pWR501160/284 (56)NP_085416
    finO110322-111041finO, fertility inhibition protein, E. coli, plasmid F75/180 (41)P22707
    bcfH111028-111825bcfH, putative thiol disulfide isomerase, S. enterica serovar Typhimurium LT2138/244 (56)NP_459033
    nuc111973-112527nuc, endonuclease, Y. enterocolitica strain 15673 (biogroup 1A serogroup 0:5) pYV plasmid135/174 (77)CAA73744
    copB112418-112648copB, CopB, function in replication control, E. intermedius, plasmid pLV140236/46 (78)CAA08928
    copA112835-112750copA, small RNA, function in antisense control, E. coli, plasmid RI71/81 (87)V00326
    tapA112867-112944tapA, TapA, function in antisense control, E. intermedius, plasmid pLV140224/25 (96)CAA08929
    repA112925-113800repA, replication protein, E. intermedius, plasmid pLV1402234/287 (81)CAA08930
    SMR0139114351-114847SMR0139, possible pseudogene, ATP/GTP-binding protein, Serratia marcescens, plasmid R478143/164 (87)NP_941209