Table 3. PaLoc of isolates 103, 106 and 133 compared with other Clade 3 strains and a representative strain of each Clade 1, 2 and 5.
| Clade | Strain | tcdR | tcdB | tcdE | Tn6218 | tcdA | tcdC | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| int | xis | rep | xre | merR | oxidoreductase | flavodoxin | orf | σ70 | |||||||
| 1 | CD630 | 12 (6NS) | 92 (48NS) | 5 + 31nt del + 1nt in (7NS + 10 del) | — | — | — | — | — | — | — | — | — | 116 (44NS) | 5 + 318nt del (1NS + 106 del) |
| 2 | CD196 | 12 (6NS) | 446 (175NS) | 3 + 31nt del + 1nt in (6NS + 10 del) | — | — | — | — | — | — | — | — | — | 89 + 63nt del (34NS + 21 del) | 4 + 36nt del (12 del) |
| 5 | M120 | 18 (8NS) | 173 (87NS) | 4 + 42nt in (2NS + 14 in) | — | — | — | — | — | — | — | — | — | 89SNP + 63nt del (44NS + 21 del) | 3 + 15nt del (3NS + 5 del)a |
| 3 | ZJCDC-S82 | ID | 6 (3NS) | ID | ID | ID | 5 (3NS) | ID | ID | ID | ID | ID | 11 + 210nt in (5NS + 70 del) | 18 (11NS) | 36nt del (12 del) |
| CD69 | ID | 12 (7NS) | ID | 3 (4NS) | ID | 5 (3NS) | ID | ID | ID | ID | ID | ID | 153 (73NS) | ID | |
| VL-0391 | ID | 2 (2NS) | ID | 7 (4NS) | ID | 3 (3NS) | 1 (1NS) | ID | 1 (1NS) | 1 (1NS) | ID | 1 (0NS) | 11 + 36nt del (5NS + 12 del) | 36nt del (12 del) | |
| VL-0104 | ID | 2 (2NS) | ID | 8 (4NS) | ID | 3 (3NS) | 1 (1NS) | ID | 1 (1NS) | 1 (1NS) | ID | 1 (0NS) | 11 + 36nt del (5NS + 12 del) | 36nt del (12 del) | |
| L058 | 1 (1NS) | 5 (2NS) | ID | 5 (3NS) | ID | 3 (2NS) | ID | ID | 2 (2NS) | ID | ID | ID | 8 (4NS) | ID | |
| OX561 | 1 (1NS) | 6 (3NS) | ID | 9 (3NS) | 1 (1NS) | 2 (2NS) | ID | ID | 1 (1NS) | ID | ID | ID | 7 + 63nt del (5NS + 21 del) | ID | |
| OX1232 | 1 (1NS) | 6 (3NS) | ID | 8 (3NS) | ID | 2 (2NS) | ID | ID | 1 (1NS) | ID | ID | ID | 14 (10NS) | ID | |
| OX1485 | 1 (1NS) | 5 (3NS) | ID | 8 (3NS) | ID | 2 (2NS) | ID | ID | 1 (1NS) | ID | ID | ID | 37 (21NS) | ID | |
| OX2183 | ID | 3 (3NS) | ID | ID | 47nt in (9 in) | 5 (3NS) | ID | ID | ID | ID | ID | ID | 51 (23NS) | 36nt del (12 del) | |
| Q24 | ID | 8 (4NS) | ID | 7 (2NS) | 1 (1NS) | 2 + 108nt in (1NS + 36 in) | 2 (1NS) | 1 (1NS) | 1 (1NS) | 3 (0NS) | 2 (0NS) | ID | 62 (35NS) | 36nt del (12 del) | |
The results shown in the Table are that the PaLoc sequence of isolate 103, 106 and 133 queries those of strains listed in the Strain column. The number of SNP is shown in the column with the resulted amino acid substitutions and deletions being indicated in parentheses. ID, identical; in, insertion; del, deletion; -, absent; nt, nucleotide; NS, non-synonymous SNP. The nucleotide deletions and insertions are consecutive. atcdC of strain NAP08 has a nonsense mutation, resulting in 37 aa deletions of the C-terminal end compared to those of isolates 103, 106 and 133.