TABLE 1.
ORFs in SCCmec’s of CA05 and 8/6-3P
| Strain (element) and ORFa | Location (position)b | Size (bp) of gene | Description of gene product |
|---|---|---|---|
| CA05 (JCSC1968) (type IV SCCmec subtype a) | |||
| CQ001 | Complement (1280-1900) | 621 | Hypothetical protein |
| Q001 | 2653-3657 | 1,005 | Hypothetical protein |
| CQ002 | Complement (4281-5771) | 1,491 | Hypothetical protein |
| CQ003 | Complement (6389-7438) | 1,050 | Conserved hypothetical protein |
| Q002 | 7577-7867 | 291 | Conserved hypothetical protein |
| Q003 | 7867-9654 | 1,788 | Conserved hypothetical protein |
| Q005 | 9888-11237 | 1,350 (ccrA2.1) | Cassette chromosome recombinase A |
| Q006 | 11259-12887 | 1,629 (ccrB2.1) | Cassette chromosome recombinase B |
| Q007 | 13409-13759 | 351 | Conserved hypothetical protein |
| Q008 | 13846-14157 | 312 | Conserved hypothetical protein |
| Q009 | 14169-14678 | 510 | Conserved hypothetical protein |
| Q010 | 14679-16337 | 1,659 | Putative transposase of IS 1272 |
| CQ004 | Complement (16560-17546) | 987 (ΔmecR1) | Truncated signal transducer protein MecR1 |
| Q011 | 17646-19652 | 2,007 (mecA) | PBP 2′ |
| CQ005 | Complement (19698-20126) | 429 | Conserved hypothetical protein |
| CQ007 | Complement (20223-20966) | 744 (ugpQ) | Glycerophosphoryldiester phosphodiesterase |
| Q012 | 22268-22942 | 675 tnp | Transposase for insertion sequence-like element IS431mec |
| CQ008 | Complement (22974-23213) | 240 | Conserved hypothetical protein |
| CQ009 | Complement (23628-24659) | 1,032 | Truncated conserved hypothetical protein |
| CQ010 | Complement (24509-24883) | 375 | Truncated conserved hypothetical protein |
| (CQ011) | Complement (25205-25684) | 480 | OrfX |
| 8/6-3P (JCSC1978) (type IV SCCmec subtype b) | |||
| CM001 | Complement (325-1446) | 1,122 | Hypothetical protein |
| CM002 | Complement (1424-2194) | 771 | Hypothetical protein |
| M001 | 2311-3741 | 1,431 | Hypothetical protein |
| M002 | 3861-5651 | 1,791 | Conserved hypothetical protein |
| M004 | 5885-7234 | 1,350 (ccrA2.2) | Cassette chromosome recombinase A |
| M005 | 7256-8884 | 1,629 (ccrB2.2) | Cassette chromosome recombinase B |
| M006 | 9406-9756 | 351 | Conserved hypothetical protein |
| M007 | 9843-10154 | 312 | Conserved hypothetical protein |
| M008 | 10166-10675 | 510 | Conserved hypothetical protein |
| M009 | 10676-12334 | 1,659 | Putative transposase of IS1272 |
| CM003 | Complement (12557-13543) | 987 (ΔmecR1) | Truncated signal transducer protein MecR1 |
| M010 | 13643-15649 | 2,007 (mecA) | PBP 2′ |
| CM004 | Complement (15695-16123) | 429 | Conserved hypothetical protein |
| CM006 | Complement (16220-16963) | 744 (ugpQ) | Glycerophosphoryldiester phosphodiesterase |
| M011 | 18265-18939 | 675 tnp | Transposase for insertion sequence-like element IS431mec |
| CM007 | Complement (18971-19210) | 240 | Conserved hypothetical protein |
| CM008 | Complement (19625-20656) | 1,032 | Truncated conserved hypothetical protein |
| CM009 | Complement (20506-20880) | 375 | Truncated conserved hypothetical protein |
| CM010 | Complement (21204-21683) | 480 | OrfX |
| Homology to ORFs of type I SCCmec
|
Homology to ORFs of type II SCCmec
|
Homology to ORFs of type III SCCmec
|
Homology to ORFs of type IV SCCmec subtype b
|
||||
|---|---|---|---|---|---|---|---|
| % Identityc | Corresponding ORF(s) (size [bp]) | % Identityc | Corresponding ORF(s) (size [bp]) | % Identityc | Corresponding ORF(s) (size [bp]) | % Identityc | Corresponding ORF(s) (size [bp]) |
| 96.4 | E024 (1329) | 72.4 | N053d (861) | 72.4 | Z025d (861) | ||
| 77.8 | CZ002 (1,068) | ||||||
| 46.2 | E025 (297) | 46 | N030 (297) | 45.7 | Z003 (288) | ||
| 77.3 | E026 (1,770) | 85.3 | N031 (1,794) | 66.3 | Z004 (1,569) | 82.4 | M002 (1791) |
| 75 | ccrA1 (1,350) | 97.6 | ccrA2 (1,350) | 72.4 | ccrA3 (1,350) | 98.2 | M004 (1350) |
| 72.4 | ∗ccrB1 (1,152) | 97.4 | ccrB2 (1,629) | 87.5 | ccrB3 (1,629) | 99.3 | M005 (1629) |
| 85.3 | E031 (351) | 88.8 | N041 (351) | 51.3 | Z011 (351) | 100 | M006 (351) |
| 85.4 | E032 (327) | 89.2 | N042 (312) | 47.2 | Z013 (396) | 100 | M007 (312) |
| 97.6 | E033 (510) | 92.7 | N043 (318) | 61.3 | Z014 (522) | 100 | M008 (510) |
| 100 | E034 (1,659) | 100 | M009 (1659) | ||||
| 100 | ΔmecR1NCTC10442 (987) | 100 | mecR1N315 (1,758) | 100 | ΔmecR185/2082 (114) | 100 | |
| 99.9 | mecANCTC10442 (2,007) | 100 | mecAN315 (2,007) | 99.7 | mecA85/2082 (2007) | 100 | |
| 99.3 | CE025 (429) | 100 | CN038 (429) | 100 | CZ029 (429) | 100 | CM004 (429) |
| 100 | CE026 (744) | 100 | CN039 (744) | 100 | CZ030 (744) | 100 | |
| 100 | E040 (675) | 100 | N062 and N070 (675) | 100, 99.6, 99.1, 99.1 | Z035, Z041, Z046, and Z058 (675) | 100 | |
| 100 | CE029 (240) | 100 | CM007 (240) | ||||
| 100 | CE030 (1,296) | 100 | CN050 (1,296) | 100 | CM008 (1032) | ||
| 98.4 | CE030 (1,296) | 98.4 | CN050 (1,296) | 100 | CM009 (375) | ||
| 100 | orfX (480) | 100 | orfX (480) | 100 | orfX (480) | 100 | CM010 (480) |
| 70.3 | E026 (1,770) | 80.7 | N031 (1,794) | 72.1 | Z004 (1,569) | ||
| 75.2 | ccrA1 (1,350) | 96.2 | ccrA2 (1,350) | 73.5 | ccrA3 (1,350) | ||
| 80.6 | ccrB1 (1,152) | 98.2 | ccrB2 (1,629) | 87.1 | ccrB3 (1,629) | ||
| 85.3 | E031 (351) | 88.8 | N041 (351) | 5.3 | Z011 (351) | ||
| 85.4 | E032 (327) | 89.2 | N042 (312) | 4.2 | Z013 (396) | ||
| 97.6 | E033 (510) | 92.3 | N043 (318) | 61.3 | Z014 (522) | ||
| 100 | E034 (1,659) | ||||||
| 100 | ΔmecR1NCTC10442 (987) | 100 | mecR1N315 (1,758) | 100 | ΔmecR185/2082 (114) | ||
| 99.9 | mecANCTC10442 (2,007) | 100 | mecAN315 (2,007) | 99.7 | mecA85/2082 (2,007) | ||
| 99.3 | CE025 (429) | 100 | CN038 (429) | 100 | CZ029 (429) | ||
| 100 | CE026 (744) | 100 | CN039 (744) | 100 | CZ030 (744) | ||
| 100 | E040 (675) | 100 | N062 and N070 (675) | 100, 99.6, 99.1, 99.1 | Z035, Z041, Z046, and Z058 (675) | ||
| 100 | CE029 (240) | ||||||
| 100 | CE030 (1,296) | 100 | CN050 (1,296) | ||||
| 98.4 | CE030 (1,296) | 98.4 | CN050 (1,296) | ||||
| 100 | orfX (480) | 100 | orfX (480) | 100 | orfX (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.