TABLE 1.

ORFs in SCCmec’s of CA05 and 8/6-3P

Strain (element) and ORFaLocation (position)bSize (bp) of geneDescription of gene product
CA05 (JCSC1968) (type IV SCCmec subtype a)
    CQ001Complement (1280-1900)621Hypothetical protein
    Q0012653-36571,005Hypothetical protein
    CQ002Complement (4281-5771)1,491Hypothetical protein
    CQ003Complement (6389-7438)1,050Conserved hypothetical protein
    Q0027577-7867291Conserved hypothetical protein
    Q0037867-96541,788Conserved hypothetical protein
    Q0059888-112371,350 (ccrA2.1)Cassette chromosome recombinase A
    Q00611259-128871,629 (ccrB2.1)Cassette chromosome recombinase B
    Q00713409-13759351Conserved hypothetical protein
    Q00813846-14157312Conserved hypothetical protein
    Q00914169-14678510Conserved hypothetical protein
    Q01014679-163371,659Putative transposase of IS 1272
    CQ004Complement (16560-17546)987 (ΔmecR1)Truncated signal transducer protein MecR1
    Q01117646-196522,007 (mecA)PBP 2′
    CQ005Complement (19698-20126)429Conserved hypothetical protein
    CQ007Complement (20223-20966)744 (ugpQ)Glycerophosphoryldiester phosphodiesterase
    Q01222268-22942675 tnpTransposase for insertion sequence-like element IS431mec
    CQ008Complement (22974-23213)240Conserved hypothetical protein
    CQ009Complement (23628-24659)1,032Truncated conserved hypothetical protein
    CQ010Complement (24509-24883)375Truncated conserved hypothetical protein
    (CQ011)Complement (25205-25684)480OrfX
8/6-3P (JCSC1978) (type IV SCCmec subtype b)
    CM001Complement (325-1446)1,122Hypothetical protein
    CM002Complement (1424-2194)771Hypothetical protein
    M0012311-37411,431Hypothetical protein
    M0023861-56511,791Conserved hypothetical protein
    M0045885-72341,350 (ccrA2.2)Cassette chromosome recombinase A
    M0057256-88841,629 (ccrB2.2)Cassette chromosome recombinase B
    M0069406-9756351Conserved hypothetical protein
    M0079843-10154312Conserved hypothetical protein
    M00810166-10675510Conserved hypothetical protein
    M00910676-123341,659Putative transposase of IS1272
    CM003Complement (12557-13543)987 (ΔmecR1)Truncated signal transducer protein MecR1
    M01013643-156492,007 (mecA)PBP 2′
    CM004Complement (15695-16123)429Conserved hypothetical protein
    CM006Complement (16220-16963)744 (ugpQ)Glycerophosphoryldiester phosphodiesterase
    M01118265-18939675 tnpTransposase for insertion sequence-like element IS431mec
    CM007Complement (18971-19210)240Conserved hypothetical protein
    CM008Complement (19625-20656)1,032Truncated conserved hypothetical protein
    CM009Complement (20506-20880)375Truncated conserved hypothetical protein
    CM010Complement (21204-21683)480OrfX
Homology to ORFs of type I SCCmecHomology to ORFs of type II SCCmecHomology to ORFs of type III SCCmecHomology to ORFs of type IV SCCmec subtype b
% IdentitycCorresponding ORF(s) (size [bp])% IdentitycCorresponding ORF(s) (size [bp])% IdentitycCorresponding ORF(s) (size [bp])% IdentitycCorresponding ORF(s) (size [bp])
96.4E024 (1329)72.4N053d (861)72.4Z025d (861)
77.8CZ002 (1,068)
46.2E025 (297)46N030 (297)45.7Z003 (288)
77.3E026 (1,770)85.3N031 (1,794)66.3Z004 (1,569)82.4M002 (1791)
75ccrA1 (1,350)97.6ccrA2 (1,350)72.4ccrA3 (1,350)98.2M004 (1350)
72.4ccrB1 (1,152)97.4ccrB2 (1,629)87.5ccrB3 (1,629)99.3M005 (1629)
85.3E031 (351)88.8N041 (351)51.3Z011 (351)100M006 (351)
85.4E032 (327)89.2N042 (312)47.2Z013 (396)100M007 (312)
97.6E033 (510)92.7N043 (318)61.3Z014 (522)100M008 (510)
100E034 (1,659)100M009 (1659)
100ΔmecR1NCTC10442 (987)100mecR1N315 (1,758)100ΔmecR185/2082 (114)100
99.9mecANCTC10442 (2,007)100mecAN315 (2,007)99.7mecA85/2082 (2007)100
99.3CE025 (429)100CN038 (429)100CZ029 (429)100CM004 (429)
100CE026 (744)100CN039 (744)100CZ030 (744)100
100E040 (675)100N062 and N070 (675)100, 99.6, 99.1, 99.1Z035, Z041, Z046, and Z058 (675)100
100CE029 (240)100CM007 (240)
100CE030 (1,296)100CN050 (1,296)100CM008 (1032)
98.4CE030 (1,296)98.4CN050 (1,296)100CM009 (375)
100orfX (480)100orfX (480)100orfX (480)100CM010 (480)
70.3E026 (1,770)80.7N031 (1,794)72.1Z004 (1,569)
75.2ccrA1 (1,350)96.2ccrA2 (1,350)73.5ccrA3 (1,350)
80.6ccrB1 (1,152)98.2ccrB2 (1,629)87.1ccrB3 (1,629)
85.3E031 (351)88.8N041 (351)5.3Z011 (351)
85.4E032 (327)89.2N042 (312)4.2Z013 (396)
97.6E033 (510)92.3N043 (318)61.3Z014 (522)
100E034 (1,659)
100ΔmecR1NCTC10442 (987)100mecR1N315 (1,758)100ΔmecR185/2082 (114)
99.9mecANCTC10442 (2,007)100mecAN315 (2,007)99.7mecA85/2082 (2,007)
99.3CE025 (429)100CN038 (429)100CZ029 (429)
100CE026 (744)100CN039 (744)100CZ030 (744)
100E040 (675)100N062 and N070 (675)100, 99.6, 99.1, 99.1Z035, Z041, Z046, and Z058 (675)
100CE029 (240)
100CE030 (1,296)100CN050 (1,296)
98.4CE030 (1,296)98.4CN050 (1,296)
100orfX (480)100orfX (480)100orfX (480)
  • a ORFs shown in parentheses were located outside of SCC mec.

  • b The nucleotide position in the nucleotide sequences deposited under DDBJ/EMBL/GenBank accession no. AB063172 (type IV subtype a) and AB063173 (type IV subtype b).

  • c Identity to amino acid sequences of each ORF.

  • d Incomplete ORFs that are potentially defective genes or pseudogenes containing either a deletion, a nonsense mutation, or a frameshift mutation.