TABLE 1.
Clonal complex association of six primary FarR clusters and associated variantsa
| FarR cluster | Primary sequence and variantsb | CC(s)c | Protein accessions (n)d |
|---|---|---|---|
| 1 | MKETDLRVIKTKKALSSSLLQLLEQQLFQTITVNQICDNALVHRTTFYKHFYDKYDLLEYLFNQLTKDYFARDISDRLNHPFQTMSDTINNKEDLREIAEFQEEDAEFNKVLKNVCIKIMHNDIKNNRDRIDIDSDIPDNLIFYIYDSLIEGFIHWIKDEKIDWPGEDIDNIFHKVINIKIK | 30, 239 | 2,649 |
| 1a | D134Y | 30 | 40 |
| 2 | MKETDLRVIKTKKALSSSLLQLLEQQLFQTITVNQICDNALVHRTTFYKHFYDKYDLLEYLFNQLTKDYFARDISDRLNHPFQTMSDTINNKEDLREIAEFQEEDAEFNKVLKNVCIKIMHNDIKNNRDRIDIDSDIPDNLIFYIYDSLIEGFIHWIKDEKIDWPGEDIDNIFHRLINIKIK | 5, 6, 7, 8, 9, 15, 25, 72, 80, 88, 97, 101, 772, 1,156 | 12,894 |
| 2a | E160G | 5 | 82 |
| 2b | G166D | 5, 8, 97 | 9 |
| 2c | E93EE | 5 | 61 |
| 2d | V115I | 5 | 3 |
| 2e | R96K | 5 | 4 |
| 2f | M85I | 395 | 11 |
| 2g | A14P | 5 (ST228) | 32 |
| 2h | S16L | 5 (ST228) | 2 |
| 2i | R77H | 97 | 11 |
| 2j | R130H | 8 | 6 |
| 2k | K110V | 8 | 2 |
| 2l | S75G | 45, 198 | 716 |
| 2m | L78I,N79T | 97 | 1 |
| 2n | S17T | 101 | 36 |
| 3 | MKETDLRVIKTKKALSSSLLQLLEQQLFQTITVNQICDNALVHRTTFYKHFYDKYDLLEYLFNQLTKDYFARDISDRLNHPFQTISDTINNKEDLREIAEFQEEDIEFNKVLKNVCIKIMHDDIKNNRDRIDIDSDVPDNLIFYIYDSLIEGFuHWIKDEKIDWPGEDIDNIFHRLINIKIK | 93 | 266 |
| 3a | I106S | Outgroup | 125 |
| 4 | MKETDLRVIKTKKALSSSLLQLLEQQLFQTITVNQICDNALVHRTTFYKHFYDKYDLLEYLFNQLTKDYFARDISDRLNHPFQTISDTINNKEDLRDIAEFQEEDAEFNKVLKNVCIKIMHNDIKNNRDRIDIDSDIPDNLIFYIYDSLIEGFMHWIKDEKIDWPGEDIDNIFHRLINIKIK | 12, 20 | 167 |
| 5 | MKETDLRVIKTKKALSSSLLQLLEQQLFQTITVNQICDNALVHRTTFYKHFYDKYDLLEYLFNQLTKDYFARDISDRLNHPFQTISDTINNKEDLRDIAEFQEEDAEFNKVLKNVCIKIMHNDIKNNRDRIDIDSDIPDNLIFYIYDSLIEGFMHWIKDEKIDWPGEEIDKIFHKVINIKIK | 1, 188, 1,148 | 1,128 |
| 5a | Q35L | 398, 2,272 | 1,530 |
| 5b | Q35L, V115F | 398 | 1 |
| 5c | D136H | 22 | 2,440 |
| 5d | D136H, I142T | 22 | 2 |
| 6 | MKETDLRVIKTKKALSSSLLQLLEQHLFQTITVNQICHNALVHRTTFYKHFYDKYDLLEYLFNQLTKAYFATDISDRLNHPFQTINDTINNKEDLQKVADFQQEDAEFNKVLKNVCIKIMNDDIKNNSDRIDVDGDIPNNLLFYIYDSLIEGFLHWIKDEKIDWPSEEIDKIFHKVINIKIK | 425 | 2 |
| 6a | D147G | 50, 130, 133, 121, 152, 350 | 841 |
| 6b | D147G, H80L | 133 | 2 |
| 6c | D147G, H155Y | 705 | 48 |
| 6d | D147G, S128C | 705, 707 | 89 |
| 6e | D147G, I154M | 59 | 481 |
CC, clonal complex.
The primary sequence of each cluster is shown. For clusters 2 to 6, amino acids which differ from those in cluster 1 are identified by bold underline. Variants are listed alphabetically and are defined by amino acid substitutions that differ from the primary cluster sequence.
Bold font designates clonal complexes that are phylogenetically separated from other strains in the same FarR cluster. For contextual purposes, the total number of genomes in the PATRIC database is 21,424, of which the numbers (n) corresponding to specific multilocus sequence types (MLSTs) are ST30 (562), ST239 (537), ST5 (3,484), ST8 (3135), ST97 (236), ST395 (3), ST228 (64), ST45 (636), ST101 (21), ST93 (56), ST12 (65), ST20 (54), ST1 (630), ST188 (201), ST1148 (1), ST398 (1,314), ST22 (2431), ST425 (20), ST50 (10), ST130 (28), ST133 (65), ST121 (250), ST152 (89), ST350 (2), ST705 (0), ST707 (8), and ST59 (481).
Number of protein accessions identical to the primary clade or intraclade variant sequences, as determined by BLASTP of each sequence versus S. aureus subsp. aureus nonredundant proteins.