TABLE 2.
Contigs, coordinates, and terminal sequences corresponding to the OPR-13 primer of the RAPD fragments of strains G-1, F1-1, and F2-1
| Fragment and strain | Gene product(s) | Contig no. | Coordinates (nt) | Sequence corresponding to OPR-13a | Length (bp) | Band presenceb |
|---|---|---|---|---|---|---|
| A | Amido-phospho-ribosyl transferase PurF, phospho-ribosyl-formyl glycinamidine cyclo-ligase PurM | |||||
| Strain G-1 | 12 | 46579–48192 | 5′-GCACGACAAG-3′ | 1,614 | Y | |
| 5′-AGACGACAAG-3′ | ||||||
| Strain F1-1 | 30 | 88368–89980 | 5′-GCACGACGAG-3′ | 1,614 | N | |
| 5′-AGACGACGAG-3′ | ||||||
| Strain F2-1 | 29 | 76720–78332 | 5′-GCACGACGAG-3′ | 1,614 | N | |
| 5′-AGACGACGAG-3′ | ||||||
| B | Transmembrane protein YrbG, putative integral inner membrane protein YrzE | |||||
| Strain G-1 | 30 | 353213–354689 | 5′-TGCCGACAAG-3′ | 1,477 | Y | |
| 5′-AAACGACAAG-3′ | ||||||
| Strain F1-1 | 1 | 1223031–1224525 | 5′-TGCCGACAAG-3′ | 1,503 | Y | |
| 5′-AAACGACAAG-3′ | ||||||
| Strain F2-1 | 35 | 105908–107402 | 5′-TGCCGACAAG-3′ | 1,504 | Y | |
| 5′-AAACGACAAG-3′ | ||||||
| C | Arabinose metabolism transcriptional repressor protein | |||||
| Strain G-1 | 4 | 1276–1751 | 5′-CGACGACAAG-3′ | 476 | Y | |
| 5′-GGACGACAAG-3′ | ||||||
| Strain F1-1 | 15 | 1297–1773 | 5′-CGACGACCAA-3′ | 478 | N | |
| 5′-GGACGACAAG-3′ | ||||||
| Strain F2-1 | 13 | 1293–1769 | 5′-CGACGACCAA-3′ | 478 | N | |
| 5′-GGACGACAAG-3′ | ||||||
| D | Rod-shape-determining protein RodA | |||||
| Strain G-1 | 15 | 347230–348138 | 5′-ATACGACAAG-3′ | 910 | Y | |
| 5′-GCACGACAAG-3′ | ||||||
| Strain F1-1 | 5 | 27148–28056 | 5′-ATACGACAAG-3′ | 909 | Y | |
| 5′-GCACGACAAG-3′ | ||||||
| Strain F2-1 | 6 | 62068–62976 | 5′-GCACGACAAG-3′ | 909 | Y | |
| 5′-ATACGACAAG-3′ | ||||||
| E | Homologous, with a region encoding a hypothetical protein of B. licheniformis WX-02 that has homology to an ABC-type exporter (of probably bacteriocin/lantibiotic) and peptidase domains | |||||
| Strain G-1 | N | |||||
| Strain F1-1 | N | |||||
| Strain F2-1 | 35 | 237929–238561 | 5′-GGAAGACAAG-3′ | 633 | Y | |
| 5′-AGACGACAAG-3′ | ||||||
| F | Phospholipid biosynthesis protein PlsX, malonyl coenzyme A-acyl carrier protein transacylase | |||||
| Strain G-1 | 31 | 223684–224583 | 5′-GGACGCCAAG-3′ | 900 | Y | |
| 5′-AAACGACAAG-3′ | ||||||
| Strain F1-1 | 1 | 129878–130777 | 5′-GGACGCCAAG-3′ | 900 | Y | |
| 5′-AAACGACAAG-3′ | ||||||
| Strain F2-1 | 27 | 129870–130769 | 5′-GGACGCCAAG-3′ | 900 | Y | |
| 5′-AAACGACAAG-3′ |
a
Bases in boldface are the differences in the regions corresponding to the OPR-13 primer (5′-GGACGACAAG-3′) compared to the genome sequence. Note that although there are mismatches in the regions corresponding to the OPR-13 primer in most of the terminal ends of these sequences, there are additional mismatches in the fragments A and C at the 3′ end of one or both these regions in strains F1-1 and F2-1 compared to the sequence in strain G-1. This is probably the reason that these bands were seen in the RAPD gel only in the case of strain G-1.
b
Presence (Y) or absence (N) of the bands in the RAPD gel.