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
 42379–264588ComplementlcrS(Y. pseudotuberculosis)
 53193–3540115ComplementlcrQ(Y. pseudotuberculosis) and yscM(Y. enterocolitica)
 63765–4430221ComplementyscL(Y. enterocolitica)
 74376–5005209ComplementyscK(Y. enterocolitica)
 85005–5739244ComplementyscJ(Y. enterocolitica)
 95746–6093115ComplementycsI(Y. enterocolitica) and lcrO (Y. pseudotuberculosis)
 106094–6591165ComplementyscH(Y. enterocolitica) and lcrP (Y. pseudotuberculosis)
 116588–6935115ComplementyscG(Y. enterocolitica)
 126937–720087ComplementyscF(Y. enterocolitica)
 137201–740166ComplementyscE(Y. enterocolitica)
 147398–8657419ComplementyscD(Y. enterocolitica)
 158654–10477607ComplementyscC(Y. enterocolitica)
 16a10483–10896137ComplementyscB(Y. enterocolitica)
 16b11121–1122032ComplementyscA(Y. enterocolitica)
 1711299–12114271ComplementlcrF(virF) transcription factor
 1812238–12633131ComplementvirG(Y. enterocolitica)
 1913209–14273354ComplementyscU(Y. enterocolitica)
 2014273–15058261ComplementyscT(Y. pseudotuberculosis)
 2115055–1532187ComplementyscS(Y. pseudotuberculosis)
 2215323–15976217ComplementyscR(Y. pestis)
 2315973–16896307ComplementyscQ(Y. pestis)
 2416893–18260455ComplementyscP(Y. pestis)
 2518260–18724154ComplementyscO(Y. pestis)
 2618721–20040439ComplementyscN (Yop secretion ATPase)
 2720238–21119293DirectyopN(Y. pseudotuberculosis)
 2821100–2137892DirectY. pseudotuberculosis hypothetical protein
 2921365–21736123DirectY. pseudotuberculosis and Y. enterocoliticahypothetical protein
 3021733–22101122DirectY. enterocolitica hypothetical protein
 3122098–22442114DirectY. enterocolitica hypothetical protein
 3222429–24543704DirectlcrD(Y. pseudotuberculosis and Y. enterocolitica)
 3324540–24980144DirectlcrR(Y. pestis)
 3425022–2530995DirectlcrG(Y. pestis)
 3525311–26291326DirectlcrV (V antigen)
 3626304–26810168DirectlcrH(sycD) (YopB and YopD chaperones)
 3726788–27993401DirectyopB(Y. pseudotuberculosis and Y. enterocolitica)
 3828012–28932306DirectyopD(Y. pseudotuberculosis and Y. enterocolitica)
 3929345–2951255ComplementY. pestis hypothetical protein
 4029778–3003887ComplementY. pseudotuberculosis transposase
 4130873–32102409DirectyopM(Y. pestis)
 4232145–3244499ComplementTransposase
 4334860–35828322ComplementY. enterocolitica hypothetical protein
 4436328–36876182DirectyopK(Y. pseudotuberculosis) and yopQ(Y. enterocolitica)
 45/4637360–3811036DirectylpApseudogene
 4738624–39016130DirectTransposase
 4840080–41288402DirectsopA (E. coli)
 4941417–42250277DirectsopB(E. coli)
 5044186–44845219ComplementyopE(Y. pestis)
 5145039–45431130DirectsycE (YopE chaperone)
 5245494–46123309ComplementTransposase
 5346241–47413390DirectTransposase
 5447413–47844143DirectTransposase
 5548188–48613141DirectsycH (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
 60/6154924–5622750DirectyadApseudogene
 6256488–5629763DirectHypothetical protein (Y. enterocolitica)
 6356928–57344138DirectDNA helicase I (E. coli plasmid F)
 6458681–5892982DirectEndonuclease (Y. enterocolitica)
 6559067–5932184DirectrepB(replication protein)
 6659618–60496292DirectrepA(replication protein)
 6763100–65298732DirectypkA (protein kinase) (Y. pseudotuberculosis and Y. enterocolitica)
 6865694–66557287DirectyopJ(Y. enterocolitica)
 6967146–67649167ComplementTransposase
 7068243–69649468DirectyopH(protein-tyrosine-phosphatase) (Y. pseudotuberculosisand Y. enterocolitica)
 7170502–70161113ComplementTransposase (partial)
Noncoding elements
1–1954ForwardIS100
2655–1961ReverseDesulfovibrio vulgarisinsertion sequence ISD1
5716–4973ReverseIS285
29501–30801ForwardY. pestis yopMgene, repeat region R1
32118–34817ForwardY. pestis yopMgene, repeat regions R2 and R3
36952–37179ForwardSalmonella enteritidis insertion element IS1351 andYersinia insertion element IS200
38717–39225ForwardShigella dysenteriaeinsertion sequence IS911
43032–43399ForwardErwinia herbicolaIS1327
46137–47226ForwardShigella sonnei insertion sequence IS640
46137–45463ReverseEnterobacter agglomerans nifJ gene and insertion sequence IS2222
49755–49521ReverseRhizobium insertion element ISR1
48647–48728ForwardIS285 (partial)
47600–47786ForwardDNA IS100 (partial)
53976–52230ReverseY. enterocolitica DNA, partial Tn3 homologue
60005–61324ForwardE. coli resistance plasmid R100; replication incompatibility, and copy number regions
70001–70145ReverseIS285(partial)
70504–70322ReverseS. enteritidis insertion element IS1351 andYersinia insertion element IS200