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
CN02634531–338007322,712.2100 ermA rRNA adenine N -6-methyltransferase
CN030* 36670–36041630887.340.5(yrkJ)Protein with unknown function B. subtilis
CN03136960–36685276660.252.3(yrkD)Protein with unknown function B. subtilis
CN034* 40759–396261,1343,134.264.2(xylR)Xylose repressor Staphylococcus xylosus
CN03641614–412433721,564.3100 mecI Methicillin resistance protein MecI S. aureus
CN03743371–416141,7586,779.399.8 mecR1 Methicillin resistance protein MecR1 S. aureus
CN039* 46792–46160633657.532.4(ugpQ)Glycerophosphoryldiester phosphodiesterase E. coli
(CN051)56817–563384801,121.659.7(yydA)Protein with unknown function B. subtilis
(N001)423–683261698.250.0(yrkD)Protein with unknown function B. subtilis
(N002)* 683–1438756910.439.9(yrkJ)Protein with unknown function B. subtilis
(N003)* 1863–2198336744.772.8(yfjN)Protein with unknown function B. subtilis
N021* 14975–176292,6552,130.128.3(kdpD)Sensor protein KdpD C. acetobutylicum
N02217604–182996961,782.660.8(kdpE)KDP operon transcriptional regulatory protein KdpE C. acetobutylicum
N026* 19527–19751225489.455.9(orfA)Putative transposase B. anthracis
N027* 19826–20179354587.644.2(orfB)Putative IS150-like transposase B. anthracis
N028* 20180–20578399801.355.6(orfB)Putative IS150-like transposase B. anthracis
N03424137–254861,350400.726.5Integrase of bacteriophage TP901-1 L. lactis
N03725508–271361,629720.137.4Integrase of bacteriophage TP901-1 L. lactis
N044* 28947–29264318517.141.6(orfB)Homologue of E. coli radC product B. subtilis
N04529383–304681,0864,270.599.7 tnpA Transposase A (transposon Tn554)
N04630465–323571,8937,043.1100 tnpB Transposase B (transposon Tn554)
N04732364–327413781,282.4100 tnpC Transposase C (transposon Tn554)
N04832892–336747832,873.2100 spc Adenyltransferase (AAD9)
N05237081–381451,065879.149.4(yrkE)Protein with unknown function B. subtilis
N05843471–454772,0077,319.4100 mecA Penicillin binding protein 2′
N06248054–487286752,573.2100Transposase for insertion sequence-like element IS431mec
N06348921–496917713,393.2100 aadD Kanamycin nucleotidyltransferase
N06449914–503123991,629.4100 ble Bleomycin resistance protein (BRP)
N06650819–520811,2633,833.5100 pre Plasmid recombination enzyme
N068* 52305–530997953,322.199.2 rep Replication protein
N069* 53100–53309210954.5100 rep Replication 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.