Table 2.

Localization and description of ORFs and noncoding elements in pCD1

ORF or noncoding elementPosition no.Size (amino acid residues)Strand or directionDescription (homologue by BLAST)
ORFs
 187–1109340DirectTransposase
 21109–1888259DirectTransposase
 31939–2343134ComplementTransposase
 42379–264588Complement lcrS(Y. pseudotuberculosis)
 53193–3540115Complement lcrQ(Y. pseudotuberculosis) and yscM(Y. enterocolitica)
 63765–4430221Complement yscL(Y. enterocolitica)
 74376–5005209Complement yscK(Y. enterocolitica)
 85005–5739244Complement yscJ(Y. enterocolitica)
 95746–6093115Complement ycsI(Y. enterocolitica) and lcrO (Y. pseudotuberculosis)
 106094–6591165Complement yscH(Y. enterocolitica) and lcrP (Y. pseudotuberculosis)
 116588–6935115Complement yscG(Y. enterocolitica)
 126937–720087Complement yscF(Y. enterocolitica)
 137201–740166Complement yscE(Y. enterocolitica)
 147398–8657419Complement yscD(Y. enterocolitica)
 158654–10477607Complement yscC(Y. enterocolitica)
 16a10483–10896137Complement yscB(Y. enterocolitica)
 16b11121–1122032Complement yscA(Y. enterocolitica)
 1711299–12114271Complement lcrF(virF) transcription factor
 1812238–12633131Complement virG(Y. enterocolitica)
 1913209–14273354Complement yscU(Y. enterocolitica)
 2014273–15058261Complement yscT(Y. pseudotuberculosis)
 2115055–1532187Complement yscS(Y. pseudotuberculosis)
 2215323–15976217Complement yscR(Y. pestis)
 2315973–16896307Complement yscQ(Y. pestis)
 2416893–18260455Complement yscP(Y. pestis)
 2518260–18724154Complement yscO(Y. pestis)
 2618721–20040439Complement yscN (Yop secretion ATPase)
 2720238–21119293Direct yopN(Y. pseudotuberculosis)
 2821100–2137892Direct Y. pseudotuberculosis hypothetical protein
 2921365–21736123Direct Y. pseudotuberculosis and Y. enterocoliticahypothetical protein
 3021733–22101122Direct Y. enterocolitica hypothetical protein
 3122098–22442114Direct Y. enterocolitica hypothetical protein
 3222429–24543704Direct lcrD(Y. pseudotuberculosis and Y. enterocolitica)
 3324540–24980144Direct lcrR(Y. pestis)
 3425022–2530995Direct lcrG(Y. pestis)
 3525311–26291326Direct lcrV (V antigen)
 3626304–26810168Direct lcrH(sycD) (YopB and YopD chaperones)
 3726788–27993401Direct yopB(Y. pseudotuberculosis and Y. enterocolitica)
 3828012–28932306Direct yopD(Y. pseudotuberculosis and Y. enterocolitica)
 3929345–2951255Complement Y. pestis hypothetical protein
 4029778–3003887Complement Y. pseudotuberculosis transposase
 4130873–32102409Direct yopM(Y. pestis)
 4232145–3244499ComplementTransposase
 4334860–35828322Complement Y. enterocolitica hypothetical protein
 4436328–36876182Direct yopK(Y. pseudotuberculosis) and yopQ(Y. enterocolitica)
 45/4637360–3811036Direct ylpApseudogene
 4738624–39016130DirectTransposase
 4840080–41288402Direct sopA (E. coli)
 4941417–42250277Direct sopB(E. coli)
 5044186–44845219Complement yopE(Y. pestis)
 5145039–45431130Direct sycE (YopE chaperone)
 5245494–46123309ComplementTransposase
 5346241–47413390DirectTransposase
 5447413–47844143DirectTransposase
 5548188–48613141Direct sycH (YopH chaperone) (Y. pseudotuberculosis and Y. enterocolitica)
 5649594–4986088ComplementTransposase
 5750911–51462183ComplementTransposon gamma-delta resolvase and tnpR (Y. enterocolitica)
 5851626–53941771DirectTransposase andtnpA (Y. enterocolitica)
 5953938–54318206ComplementTransposase
 60/6154924–5622750Direct yadApseudogene
 6256488–5629763DirectHypothetical protein (Y. enterocolitica)
 6356928–57344138DirectDNA helicase I (E. coli plasmid F)
 6458681–5892982DirectEndonuclease (Y. enterocolitica)
 6559067–5932184Direct repB(replication protein)
 6659618–60496292Direct repA(replication protein)
 6763100–65298732Direct ypkA (protein kinase) (Y. pseudotuberculosis and Y. enterocolitica)
 6865694–66557287Direct yopJ(Y. enterocolitica)
 6967146–67649167ComplementTransposase
 7068243–69649468Direct yopH(protein-tyrosine-phosphatase) (Y. pseudotuberculosisand Y. enterocolitica)
 7170502–70161113ComplementTransposase (partial)
Noncoding elements
1–1954ForwardIS100
2655–1961Reverse Desulfovibrio vulgarisinsertion sequence ISD1
5716–4973ReverseIS285
29501–30801Forward Y. pestis yopMgene, repeat region R1
32118–34817Forward Y. pestis yopMgene, repeat regions R2 and R3
36952–37179Forward Salmonella enteritidis insertion element IS1351 andYersinia insertion element IS200
38717–39225Forward Shigella dysenteriaeinsertion sequence IS911
43032–43399Forward Erwinia herbicolaIS1327
46137–47226Forward Shigella sonnei insertion sequence IS640
46137–45463Reverse Enterobacter agglomerans nifJ gene and insertion sequence IS2222
49755–49521Reverse Rhizobium insertion element ISR1
48647–48728ForwardIS285 (partial)
47600–47786ForwardDNA IS100 (partial)
53976–52230Reverse Y. enterocolitica DNA, partial Tn3 homologue
60005–61324Forward E. coli resistance plasmid R100; replication incompatibility, and copy number regions
70001–70145ReverseIS285(partial)
70504–70322Reverse S. enteritidis insertion element IS1351 andYersinia insertion element IS200