Table 1.

ORFs identified in Y. pestis pMT1 DNA sequence by classificationa

ORF classDesignationFunction or commentsOrganism or element (gene if known)Accession no.Location (bp)
DNA metabolismORF1IS100 Y. pestis IS100(orfB) U59875 73885–74661
ORF2LigaseBacteriophage T3 X05031 74680–75777
ORF12Integrase Vibrio cholera U39068 82931–84109
ORF16DNA Pol III E. coli M19334 88955–92479
ORF26RecA Bacteroides fragilis M63029 96910–97986
ORF34RepA E. coli plasmid ColV L01250 Complement, 717–1781   
ORF41 exoA Bacteriophage T4 X01804 4968–6053
ORF43 exoB Bacteriophage T4 X01804 6271–8199
ORF46IS200 IS200 U22457 9675–10184
ORF60Rep-like Coxiella burnetti L34077 16197–16895
ORF61SpoJ-like Streptococcus pneumoniae AF000658 16862–17563
ORF69Gene 17-likeBacteriophage T4 X52394 20457–21713
ORF93IS100 Y. pestisIS100(orfB) U59875 Complement, 46449–47231
ORF94IS100 Y. pestisIS100(orfA) U59875 Complement, 47228–48250
ORF101IS285 Y. pestisIS285 (orf2) X78303 51013–52221
ORF102Transposase Enterobacter U60777 52648–53712
ORF108Membrane endonuclease E. coliplasmid-pKM101 (nuc) U09868 Complement, 57629–58117
ORF111Resolvase Pseudomonas syringae(stbA) L48985 Complement, 60161–60781
ORF113ParABacteriophage P1 X02954 61767–63041
ORF114ParBBacteriophage P1 K02380 63038–64009
ORF123Adenine-specific DNA methylase E. coli pEC156 EcoVIII methylase U48806 66648–67325
ORF128Antirestriction E. coli Z34467 69208–69714
ORF135DNA partitioning Rhizobium meliloti (Orf1 and Orf2 of pRmeGR4a) X69105 70730–72739
Shigella sonnei (psiB) U82272
Streptococcus pneumoniae(spoOJ) AF000658
ORF136IS100 Y. pestisIS100 (orfA) U59875 72863–73882
Protein metabolismORF28HflC-like Vibrio parahaemolyticus U09005 98281–99111
ORF63ABC transporter/ATP binding Archaeglobus fulgidus(AF1064) AE001029 17500–18198
ORF75L12 ribosomal protein L12e Haloferax volcanii X58924 25927–26361
Gene regulationORF5Caf1R Y. pestis(caf1R) X61996 Complement, 77118–78041
ORF22PrpB-like Pseudomonas putida X80272 94557–95636
ORF56Repressor of flagellum synthesis Salmonella abony(fljA) D26167 Complement, 13278–13841
Known virulenceORF6Caf1M Y. pestis (caf1M) X61996 78318–79127
ORF8Caf1A Y. pestis(caf1A) X61996 79152–81653
ORF9Caf1 Y. pestis(caf1) X61996 81734–82246
ORF107Murine toxin Y. pestis(ymt) X92727 Complement, 55788–57551
Lambda-likeORF80aV major tail fiberBacteriophage lambda P03733 28560–29303
Intimin E. coli O157:H7 (eae) P43261
ORF84H tail fiberBacteriophage lambda AF007380 30041–34618
ORF85M minor tail fiberBacteriophage lambda P03737 34660–34995
ORF86L minor tail fiberBacteriophage lambda P03738 35052–35783
ORF87aK tail assemblyBacteriophage lambda P03729 35815–36570
ORF88I tail assemblyBacteriophage lambda P03730 36561–37148
ORF89J host specificityBacteriophage lambda P03749 37164–41801
ORF91Hypothetical protein ORF314Bacteriophage lambda P03745 42469–45405
ORF92Tail fiber assemblyBacteriophage lambda (tfa)22593145707–46315
Hypothetical in databaseb ORF15CobT Pseudomonas denitrificans (cobT) P29934 85075–87441
ORF15aCobS Pseudomonas denitrificans(cobS) P29933 87539–88771
ORF29HypotheticalBacteriophage P22 X78401 99265–99636
ORF33aHypothetical regulatoryBacteriophage P176816100922–147
ORF38Hypothetical lipoprotein Bacillus subtilis (orfK yzeA) L16808,Z93102 Complement, 3530–4552  
ORF59Long hypothetical protein Pyrococcus horikoshii(PHBW005) AB009472 Complement, 14573–16132
ORF73SRPI hypothetical protein SynechococcusPCC7942 pANL Q55032 24271–25146
ORF104Hypothetical protein E. coli U70214 Complement, 54408–54803
ORF105Hypothetical protein E. coli U70214 Complement, 54694–55002
ORF116Hypothetical SphingomonasS88 U51197 64388–65785
ORF131Hypothetical E. coli AE000133 70427–70657
Fragmentsc ORF23DNA polymerase Lactococcus lactis U78771 95646–96641
ORF33Type II Helicobacter pylori AE000647 100590–100925
ORF99Hypothetical protein Methanobacterium thermo-autotrophicum AE000913 Complement, 49210–50004
ORF103Hypothetical transposase Salmonella typhimurium Z29513 Complement, 53911–54234
ORF103aIS600 Shigella sonnei X05952 54281–54481
ORF106Hypothetical Shigella flexneri U97489 55073–55543
ORF106aIS801 Pseudomonas syringae X57269 55589–55729
ORF110Hypothetical Salmonella typhimurium Z29513 Complement, 59154–60140
ORF115aSamB-like Salmonella typhimurium D90202 87539–88771
  • a ORFs listed were assigned a putative function according to our criteria outlined in the general overview section of Results and Discussion. Classification then was based on these putative functions.

  • b Homology above our criteria with proteins in the database that have not been assigned a function.

  • c ORFs that appear to be remnants of larger proteins in the database.