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 metabolismORF1IS100Y. pestis IS100(orfB)U5987573885–74661
ORF2LigaseBacteriophage T3X0503174680–75777
ORF12IntegraseVibrio choleraU3906882931–84109
ORF16DNA Pol IIIE. coliM1933488955–92479
ORF26RecABacteroides fragilisM6302996910–97986
ORF34RepAE. coli plasmid ColVL01250Complement, 717–1781   
ORF41exoABacteriophage T4X018044968–6053
ORF43exoBBacteriophage T4X018046271–8199
ORF46IS200IS200U224579675–10184
ORF60Rep-likeCoxiella burnettiL3407716197–16895
ORF61SpoJ-likeStreptococcus pneumoniaeAF00065816862–17563
ORF69Gene 17-likeBacteriophage T4X5239420457–21713
ORF93IS100Y. pestisIS100(orfB)U59875Complement, 46449–47231
ORF94IS100Y. pestisIS100(orfA)U59875Complement, 47228–48250
ORF101IS285Y. pestisIS285 (orf2)X7830351013–52221
ORF102TransposaseEnterobacterU6077752648–53712
ORF108Membrane endonucleaseE. coliplasmid-pKM101 (nuc)U09868Complement, 57629–58117
ORF111ResolvasePseudomonas syringae(stbA)L48985Complement, 60161–60781
ORF113ParABacteriophage P1X0295461767–63041
ORF114ParBBacteriophage P1K0238063038–64009
ORF123Adenine-specific DNA methylaseE. coli pEC156 EcoVIII methylaseU4880666648–67325
ORF128AntirestrictionE. coliZ3446769208–69714
ORF135DNA partitioningRhizobium meliloti (Orf1 and Orf2 of pRmeGR4a)X6910570730–72739
Shigella sonnei (psiB)U82272
Streptococcus pneumoniae(spoOJ)AF000658
ORF136IS100Y. pestisIS100 (orfA)U5987572863–73882
Protein metabolismORF28HflC-likeVibrio parahaemolyticusU0900598281–99111
ORF63ABC transporter/ATP bindingArchaeglobus fulgidus(AF1064)AE00102917500–18198
ORF75L12 ribosomal protein L12eHaloferax volcaniiX5892425927–26361
Gene regulationORF5Caf1RY. pestis(caf1R)X61996Complement, 77118–78041
ORF22PrpB-likePseudomonas putidaX8027294557–95636
ORF56Repressor of flagellum synthesisSalmonella abony(fljA)D26167Complement, 13278–13841
Known virulenceORF6Caf1MY. pestis (caf1M)X6199678318–79127
ORF8Caf1AY. pestis(caf1A)X6199679152–81653
ORF9Caf1Y. pestis(caf1)X6199681734–82246
ORF107Murine toxinY. pestis(ymt)X92727Complement, 55788–57551
Lambda-likeORF80aV major tail fiberBacteriophage lambdaP0373328560–29303
IntiminE. coli O157:H7 (eae)P43261
ORF84H tail fiberBacteriophage lambdaAF00738030041–34618
ORF85M minor tail fiberBacteriophage lambdaP0373734660–34995
ORF86L minor tail fiberBacteriophage lambdaP0373835052–35783
ORF87aK tail assemblyBacteriophage lambdaP0372935815–36570
ORF88I tail assemblyBacteriophage lambdaP0373036561–37148
ORF89J host specificityBacteriophage lambdaP0374937164–41801
ORF91Hypothetical protein ORF314Bacteriophage lambdaP0374542469–45405
ORF92Tail fiber assemblyBacteriophage lambda (tfa)22593145707–46315
Hypothetical in databasebORF15CobTPseudomonas denitrificans (cobT)P2993485075–87441
ORF15aCobSPseudomonas denitrificans(cobS)P2993387539–88771
ORF29HypotheticalBacteriophage P22X7840199265–99636
ORF33aHypothetical regulatoryBacteriophage P176816100922–147
ORF38Hypothetical lipoproteinBacillus subtilis (orfK yzeA)L16808 ,Z93102Complement, 3530–4552  
ORF59Long hypothetical proteinPyrococcus horikoshii(PHBW005)AB009472Complement, 14573–16132
ORF73SRPI hypothetical proteinSynechococcusPCC7942 pANLQ5503224271–25146
ORF104Hypothetical proteinE. coliU70214Complement, 54408–54803
ORF105Hypothetical proteinE. coliU70214Complement, 54694–55002
ORF116HypotheticalSphingomonasS88U5119764388–65785
ORF131HypotheticalE. coliAE00013370427–70657
FragmentscORF23DNA polymeraseLactococcus lactisU7877195646–96641
ORF33Type IIHelicobacter pyloriAE000647100590–100925
ORF99Hypothetical proteinMethanobacterium thermo-autotrophicumAE000913Complement, 49210–50004
ORF103Hypothetical transposaseSalmonella typhimuriumZ29513Complement, 53911–54234
ORF103aIS600Shigella sonneiX0595254281–54481
ORF106HypotheticalShigella flexneriU9748955073–55543
ORF106aIS801Pseudomonas syringaeX5726955589–55729
ORF110HypotheticalSalmonella typhimuriumZ29513Complement, 59154–60140
ORF115aSamB-likeSalmonella typhimuriumD9020287539–88771
  • 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.