Table 1.

The ORFs in and around mec DNA whose deduced products show similarities to extant protein sequences

ORFaLocation (nt positionb) start–stopSize (bp)Homology scorec% IdentitydGeneeDescription of gene productSpeciesf
CN009*10999–10556444635.242.3(kdpC)Potassium-transporting ATPase (C chain)C. acetobutylicum
CN01012996–109752,0224,878.656.5(kdpB)Potassium-transporting ATPase (B chain)C. acetobutylicum
CN012*13431–13018414758.145.9(kdpA)Potassium-transporting ATPase (A chain)C. acetobutylicum
CN013*14692–133581,3352,195.048.7(kdpA)Potassium-transporting ATPase (A chain)C. acetobutylicum
CN02634531–338007322,712.2100ermArRNA adenine N -6-methyltransferase
CN030*36670–36041630887.340.5(yrkJ)Protein with unknown functionB. subtilis
CN03136960–36685276660.252.3(yrkD)Protein with unknown functionB. subtilis
CN034*40759–396261,1343,134.264.2(xylR)Xylose repressorStaphylococcus xylosus
CN03641614–412433721,564.3100mecIMethicillin resistance protein MecIS. aureus
CN03743371–416141,7586,779.399.8mecR1Methicillin resistance protein MecR1S. aureus
CN039*46792–46160633657.532.4(ugpQ)Glycerophosphoryldiester phosphodiesteraseE. coli
(CN051)56817–563384801,121.659.7(yydA)Protein with unknown functionB. subtilis
(N001)423–683261698.250.0(yrkD)Protein with unknown functionB. subtilis
(N002)*683–1438756910.439.9(yrkJ)Protein with unknown functionB. subtilis
(N003)*1863–2198336744.772.8(yfjN)Protein with unknown functionB. subtilis
N021*14975–176292,6552,130.128.3(kdpD)Sensor protein KdpDC. acetobutylicum
N02217604–182996961,782.660.8(kdpE)KDP operon transcriptional regulatory protein KdpEC. acetobutylicum
N026*19527–19751225489.455.9(orfA)Putative transposaseB. anthracis
N027*19826–20179354587.644.2(orfB)Putative IS150-like transposaseB. anthracis
N028*20180–20578399801.355.6(orfB)Putative IS150-like transposaseB. anthracis
N03424137–254861,350400.726.5Integrase of bacteriophage TP901-1L. lactis
N03725508–271361,629720.137.4Integrase of bacteriophage TP901-1L. lactis
N044*28947–29264318517.141.6(orfB)Homologue of E. coli radC productB. subtilis
N04529383–304681,0864,270.599.7tnpATransposase A (transposon Tn554)
N04630465–323571,8937,043.1100tnpBTransposase B (transposon Tn554)
N04732364–327413781,282.4100tnpCTransposase C (transposon Tn554)
N04832892–336747832,873.2100spcAdenyltransferase (AAD9)
N05237081–381451,065879.149.4(yrkE)Protein with unknown functionB. subtilis
N05843471–454772,0077,319.4100mecAPenicillin binding protein 2′
N06248054–487286752,573.2100Transposase for insertion sequence-like element IS431mec
N06348921–496917713,393.2100aadDKanamycin nucleotidyltransferase
N06449914–503123991,629.4100bleBleomycin resistance protein (BRP)
N06650819–520811,2633,833.5100prePlasmid recombination enzyme
N068*52305–530997953,322.199.2repReplication protein
N069*53100–53309210954.5100repReplication protein
N07053400–540746752,573.2100Transposase for insertion sequence-like element IS431mec
  • a ORFs shown in parentheses were located outside of the mec DNA region. Asterisks signify incomplete ORFs that are potentially defective genes or pseudogenes containing either deletion, nonsense mutation, or frameshift mutation.

  • b Nucleotide (nt) position in the nucleotide sequence deposited under accession no. D86934 in the DDBJ, EMBL, and GenBank databases.

  • c Optimal z score in analysis with TFastA.

  • d Identity to the amino acid sequence of the best match revealed in the homology search of the GenBank and EMBL databases with TFastA.

  • e Genes shown in parentheses had deduced ORF with less than 70% amino acid identity to the ORF indicated.

  • f The species whose gene product had the best match to the ORF product.