TABLE 1.

ORFs encoded on SCCmecZH47

Coding sequence no.NameaPosition (bp)Identity (%)bHomolog(s)cInformationd
DR-L754-771Integration site sequence of SCCmec, A→G substitution at position 16 of left direct repeat
IR-L757-764Integration site sequence of SCCmec; left inverted repeat
1ZH021017-132298CZ078 (85/2082)Hypothetical protein, predicted restriction endonuclease domain (COG 3183)
2ZH031887-2384100CZ077 (85/2082)Conserved hypothetical protein (COG 3680)
3ZH042468-3967100CZ076 (85/2082)Hypothetical protein
4ZH054193-5293100CZ075 (85/2082)Hypothetical protein; DNA polymerase A family domain (Pfam 00476.12)
5ZH065286-565794CZ074 (85/2082)Hypothetical protein (DUF 1092)
6ZH075654-72731003 half: CG008 (85/3907)Hypothetical protein; POX_D5 domain associated with viral DNA replication (Pfam 03288.11)
1005 half: unnamed ORF (TSGH17)
7ccrC7498-917494ccrC2 (TSGH17)Cassette chromosome recombinase C
89ccrC3 (85/2082)
8ZH099280-961898SSP0034 (ATCC 15305)Hypothetical protein
9ZH109714-1002590SSP0032 (ATCC 15305)Hypothetical protein, contains SmaI restriction site
10ZH1110041-1054790CZ068 (85/2082)Conserved in gram-positive and -negative bacteria but of unknown function (COG 4333)
11IS43110696-1137099IS431 (SCCmec types I-IV)Insertion sequence IS431
12ZH1311628-11795100ORF CN041 (N315) and in SCCmec types I-VPutative HMG-coenzyme A-synthase (cholesterol biosynthesis)
13ugpQ12712-13455100ugpQ (all SCCmec types)Glycerophosphoryl diester phosphodiesterase
14ZH1513552-13980100SA0037 (N315) and in SCCmec types I-VHypothetical protein, MaoC-like domain (Pfam 01575.11)
15mecA14026-16032100WIS (SCCmec type V) and TSGH17 (SCCmec type VT)Penicillin-binding protein PBP2a
16ΔmecR1′16132-16958100ΔmecR1 from mec complex BFirst 826 bp of ΔmecR1, truncated signal transducer MecR1 from mec complex B
DRTn400116951-16958Repeated region generated by transposon integration
IRTn400116959-17059Repeated region generated by transposon integration
17IS256L17060-18232100Tn4001IS of Tn4001
18aac18235-18681100Tn4001Putative N-acyltransferase, GNAT family
19aac(2′)-aph(6")18682-20121100Tn4001Aminoglycoside-(2′)-acetyltransferase-aminoglycoside-(6")-phosphotransferase
20IS256R20251-21423100Tn4001IS of Tn4001
IRTn400121424-21524Repeated region generated by transposon integration
DRTn400121525-21532Repeated region generated by transposon integration
21ΔmecR1"21533-21692100ΔmecR1 from mec complex BRemainder of ΔmecR1, interrupted by Tn4001 insertion
22ZH2221595-21924100ΔhsdR (MW2)Truncated hypothetical protein, similar to type I restriction endonuclease
23ZH2321915-23438100IS1272 transposase from mec complex Baa 1-102: transposase and inactivated derivatives (COG 3666)
aa 185-459: transposase DDE domain
24ZH2423574-24083100Various type IV SCCmecsHypothetical protein
25ZH2524095-24406100Various type IV SCCmecsHypothetical protein
26ZH2624493-24843100Various type IV SCCmecsHypothetical protein
27ccr2B25365-26993100ccrB SCCmec type IVd (JCSC4469)Cassette chromosome recombinase B
28ccr2A27015-28364100ccrA SCCmec type IVe (AR43)Cassette chromosome recombinase A
29ZH2928598-30391100R004 (MR108)aa 1-382: superfamily II helicase and inactivated derivatives (COG 5519)
30ZH3030391-30687100Different type IV SCCmecsHypothetical protein
31ZH3130880-31926100Different type IV SCCmecs (ATCC 12228)Hypothetical protein
32ZH3232381-33535100CR008 (MR108)aa 1-122: abi alpha protein, predicted transcriptional regulator (COG 2865)
33ZH3333565-34365100Different type IV SCCmecs and SE0042 (ATCC 12228)Hypothetical protein, abortive phage resistance protein
IR-R34423-34430Integration site sequence of SCCmec; right inverted repeat
DR-R34432-34449Integration site sequence of SCCmec; right direct repeat
  • a ORFs of known functions are named accordingly; putative and hypothetical ORFs have been assigned ZH numbers.

  • b Amino acid sequence identity.

  • c The name of the homologous gene is indicated, and the strain in which it was found is indicated in parentheses. If homologous ORFs were unnamed, the SCCmec type in which they were found is indicated.

  • d Information about the element, e.g., about the encoded protein. Positions and reference numbers of known protein domains are indicated. aa, amino acids; HMG, 3-hydroxy-3-methylglutaryl; COG, cluster of orthologous groups of proteins.