Table 2. Genes in the variant SCCmec IVa element of the European CC1-MRSA-IV strain .
| Gene ID | Definition of gene product and comments (see also annotation of MH188467.1) | Orientation | Locus tag in MW2 (BA000033.2) | Nucleotide positions in GenBank RBVO | Nucleotide positions in GenBank MT380478 (Iasi-95037) |
|---|---|---|---|---|---|
| orfX | 23S rRNA methyltransferase | Forward | MW0024 |
RBVO01000005.1; nt 280,209–280,689 |
N/A |
| sRNA6 | Antisense RNA associated with orfX | Reverse | N/A |
RBVO01000005.1; nt 280,389–280,673 |
N/A |
| DR_SCC | Direct repeat of SCC, to 19 nt of the 3' end of the coding sequence of orfX | N/A | N/A |
RBVO01000005.1; nt 280,670–280,689 |
nt 1–19 |
| sccterm15 | SCC-terminal sequence adjacent to orfX, and alternate to dcs, see Discussion | N/A | Not present |
RBVO01000005.1; nt 280,689–280,912 |
nt 20–242 |
| E7MHX1 | Transcription regulator | Forward | Not present |
RBVO01000005.1; nt 280,912–281,239 |
nt 243–569 |
| ydiL2 | Hypothetical protein/putative membrane peptidase, associated with SCC elements | Forward | Not present |
RBVO01000005.1; nt 281,275–282,109 |
nt 606–1,439 |
| C5QAP8-M299 | Hypothetical protein | Forward | Not present |
RBVO01000005.1; nt 282,794–283,568 |
nt 2,125–2,898 |
| A8YYX4 | Hypothetical protein | Reverse | Not present |
RBVO01000005.1; nt 283,805–284,144 |
nt 3,136–3,474 |
| npd-SCC | Enoyl-[acyl-carrier-protein] reductase-like protein | Reverse | Not present |
RBVO01000005.1; nt 284,329–285,400 |
nt 3,660–4,730 |
| H4AYD7-trunc | Transcriptional regulator, LysR family | Truncated | Not present |
RBVO01000005.1; nt 285,412–286,024 |
nt 4,743–5,354 |
| Q7A213-trunc | Putative protein; it comprises the inverted repeat of IS431. In MW2 it is not truncated and comprises 240 nt | Truncated | MW0026 |
RBVO01000005.1; nt 286,024–286,052 |
nt 5,355–5,382 |
| IR_IS431 | Inverted repeat of IS431 | Truncated | N/A |
RBVO01000005.1; nt 286,024–286,040 |
nt 5,355–5,370 |
| tnpIS431 | Transposase for IS431 | Reverse | MW0027 |
RBVO01000005.1; nt 286,083–end of contig (nt 286,184) (partial) |
nt 5,414–6,088 |
| Teg143 | Trans-encoded RNA associated with tnpIS431 | Forward | N/A |
RBVO01000003.1; nt 203–237 |
nt 6,119–6,152 |
| IR_IS431 | Inverted repeat of IS431 | Truncated | N/A |
RBVO01000003.1; nt 213–229 |
nt 6,129–6,144 |
| mvaS-SCC | Truncated HMG-CoA synthase | Forward | MW0028 |
RBVO01000003.1; nt 245–598 |
nt 6,161–6,513 |
| Q5HJW6 | Hypothetical protein | Forward | N/A |
RBVO01000003.1; nt 695–1,046 |
nt 6,611–6,841 |
| dru | SCC direct repeat units | Truncated | N/A |
RBVO01000003.1; nt 835–1,273 |
nt 6,751–7,148 |
| ugpQ | Glycerophosphoryl diester phosphodiesterase-like protein | Forward | MW0029 |
RBVO01000003.1; nt 1,474–2,218 |
nt 7,350–8,093 |
| ydeM | Acyl dehydratase MaoC | Forward | MW0030 |
RBVO01000003.1; nt 2,314–2,743 |
nt 8,190–8,618 |
| mecA | Encodes penicillin binding protein 2 prime, defining MRSA | Reverse | MW0031 |
RBVO01000003.1; nt 2,812–4,795 |
nt 8,664–10,670 |
| mecR1-trunc | Meticillin resistance operon repressor 1, signal transducer protein, truncated in SCCmec IV | Truncated | MW0032 |
RBVO01000003.1; nt 4,894–5,862 |
nt 10,770–10,816 |
| hsdR2-IS1272 | Type I site-specific deoxyribonuclease restriction subunit | Truncated | MW0033 |
RBVO01000003.1; nt 5,869–6,103 |
nt 11,745–11,978 |
| tnpIS1272 | Transposase | Reverse | MW0034 |
RBVO01000003.1; nt 6,103–7,627 |
nt 11,979–13,502 |
| Q9KX75 | Hypothetical protein | Reverse | MW0035 |
RBVO01000003.1; nt 7,762–8,269 |
nt 13,638–14,144 |
| Q7A207 | Hypothetical protein | Reverse | MW0036 |
RBVO01000003.1; nt 8,283–8,595 |
nt 14,159–14,470 |
| Q7A206-trunc | Hypothetical protein, truncated | Truncated | N/A |
RBVO01000003.1; nt 8,596–8,683 |
nt 14,472–14,558 |
| Q7A206 | Hypothetical protein | Reverse | MW0037 |
RBVO01000003.1; nt 8,681–9,032 |
nt 14,557–14,907 |
| UTR_ccrB-2 | Highly conserved 3'-untranslated region of ccrB | N/A | N/A |
RBVO01000003.1; nt 9,032–9,553 |
nt 14,908–15,428 |
| ccrB-2 | Cassette chromosome recombinase B2 | Reverse | MW0038 |
RBVO01000003.1; nt 9,553–11,182 |
nt 15,429–17,057 |
| ccrA-2 | Cassette chromosome recombinase A2 | Reverse | MW0039 |
RBVO01000003.1; nt 11,203–12,553 |
nt 17,079–18,428 |
| cch-2 | Hypothetical protein/cassette chromosome helicase | Reverse | MW0040 |
RBVO01000003.1; nt 12,786–14,574 |
nt 18,662–20,449 |
| DUF1413 | Hypothetical protein, associated with cch | Reverse | MW0041 |
RBVO01000003.1; nt 14,573–14,864 |
nt 20,449–20,739 |
| Q2FKL7 | Putative membrane protein | Forward | MW0042 |
RBVO01000003.1; nt 15,002–16,052 |
nt 20,878–21,927 |
| Q8VUV8 | Putative transcriptional regulator | Forward | MW0043 |
RBVO01000003.1; nt 16,504–17,995 |
nt 22,380–23,870 |
| cstB-SCC2 | Includes a putative beta-lactamase; marker for SCCmec IVa | Truncated | MW0045 |
RBVO01000003.1; nt 18,367–19,685 |
nt 24,243–25,560 |
| Q2FKL3 | HNH endonuclease family protein | Forward | MW0046 |
RBVO01000003.1; nt 19,875–20,247 |
nt 25,751–26,122 |
| Q8VUW0 | Putative membrane protein | Forward | MW0047 |
RBVO01000003.1; nt 20,375–20,996 |
nt 26,251–26,871 |
| DR_SCC | Direct repeat of SCC | Truncated | N/A |
RBVO01000003.1; nt 21,300–21,319 |
nt 27,176–27,194 |
MRSA: meticillin-resistant Staphylococcus aureus; N/A: not available; nt: nucleotide position; SCC: staphylococcal cassette chromosome.