Table 4. SNP/Indel locations in B. atrophaeus genomes1.
| Genome location | RAST Locus (NCBI Locus Tag #) | Types2 | Gene affected3 | B. subtilis Homolog (% Identity) | Mutation | AA change | Position in protein/total length |
| 246382 | BG236 (01550) | PS | yetF – hypothetical protein | BSU07140 (73.9) | C:T | * | 217/231 |
| 259001 | BG250 (12250) | SYN | yfnL – hypothetical protein | BSU07230 (91.5) | C:T | ||
| 419580 | BG405 (02000) | 1 bp INS | katA – vegetative catalase | BSU08820 (94.4) | +T | 197/483 | |
| 546358 | BG536 (02620) | NS | hpr/scoC – MarR family regulator(extracellular protease expression and sporulation) | BSU1000 (85.7) | C:G | A:P | 13/200 |
| 591250 | BG584 (02840) | NS | hemAT – heme-based aerotactic transducer | BSU10380 (87.7) | C:T | R:K | 215/432 |
| 686460 | BG685 (03350) | NS | Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein OppA | BSU11430 | T:G | W:G | 520/545 |
| 699955 | BG706 (03425) | PS | yjbL – truncated hemoglobin | BSU11590 (96.1) | +C | * | 89/132 |
| 771405 | BG795 (03855) | NS | rapA – response regulator (Dephosporylates Spo0F) | BSU12430 (91.2) | T:G | S:A | 261/378 |
| 859632 | BG904/905 (04400/04405) | IG | T:C | ||||
| 881336 | BG929 (04515) | NS | kinE – 2-component histidine kinase; regulates Spo0F activity | BSU13530 (84.6) | C:T | P:L | 577/739 |
| 889607 | BG939 (04560) | NS | Methylthioribulose-1-phosphate dehydratase (EC 4.2.1.109), mtnB | BSU13610 (87.6) | A:G | Y:C | 86/209 |
| 1162042 | BG1225 (05960) | INS | fliY – flagellar switch motor protein | BSU16320 (87.2) | +GTGGTC | V3:V5 | 355/379 |
| 1317617 | BG1320 (06415) | NS | pksR – Polyketide synthase | BSU17720 (71.0) | G:C | C:S | 1698/2574 |
| 1326096 | BG1327 (06450) | NS | ebrB – multidrug resistance family protein | BSU1729 (77.8) | A:G | S:P | 24/115 |
| 1414651 | BG1226 (07000) | NS | Chemotaxis regulator - transmits chemoreceptor signals to flagelllar motor components CheY | BSU17940 (86.0) | C:T | A:V | 97/120 |
| 14864084 | BG1487 (07220) | SYN | ppsA – Plipistatin synthase/non-ribosomal peptide synthetase. | BSU18340 | G:A | 1872/2560 | |
| 1668965 | BG1681 (08240) | 1 bp DEL | yozB – putative inner membrane protein | BSU19140 (93.8) | −T | 55/178 | |
| 1695248 | BG1706 (08360) | 5 bp INS | yojO – hypothetical protein, potential nitricoxide synthase activation protein | BSU19380 (87.5) | +GCTCT | 140/638 | |
| 1741391 | BG1764/1765 (08650/08655) | IG | A:G | ||||
| 1857762 | BG1903 (09335) | PS | ypfA – possible pilZ homolog | BSU22910 (60.1) | G:A | * | 197/218 |
| 19237675 | BG1978/1979 (09750/09755) | IG | C:T | ||||
| 1946572 | BG1997 (09870) | SYN | Putative phage protein | NA | T:C | 283/584 | |
| 2029530 | BG2096 (10375) | PS | 2-methylcitrate synthase | BSU24140 (78.3) | +GA | * | 197/218 |
| 2038809 | BG2105 (10420) | NS | spo0A – 2-component response regulator, controls initiation of sporulation | BSU24220 (96.6) | G:A | A:V | 225/265 |
| 2073239 | BG2144/2145 (10615/10610) | IG | Intergenic - possible promter region of sinI gene (repressor of SinR) | T:C | |||
| 2073603 | BG2146 (10620) | NS | SinR, regulator of post-exponential-phase responses genes (competence and sporulation) | BSU26100 (98.0%) | A:G | K:E | |
| 2105290 | BG2186 (10820) | NS | yqgE – putative efflux transporter | BSU25010 (92.5) | G:C | H:D | 390/430 |
| 2827391 | BG2944 (14450) | NS | gerAB – spore germination protein | BSU33060 (67.7) | G:A | R:K | 35/365 |
| 2828580 | BG2945 (14455) | NS | gerAC – spore germination protein, governs germination in response to alanine | BSU33070 (61.8) | G:T | D:Y | 64/372 |
| 2843471 | BG2960 (14530) | NS | yvrG – sensor histidine kinase involved in cell wall processes | BSU33210 (75.4) | T:G | I:L | 18/580 |
| 2895934 | BG3014/3015 (14785/14790) | IG | A:G | ||||
| 3052929 | BG3176 (15575) | NS | Flagellin | NA | A:G | I:T | 279/320 |
| 3053059 | BG3176 (15575) | NS | Flagellin | NA | C:T | A:T | 236/320 |
| 3188439 | BG3318/3319 (16270/16275) | IG | Intergenic | 10 bp deletion | |||
| 3188440 | BG3318/3319 (16270/16275) | IG | Intergenic | NA | T:G | ||
| 3231470 | BG3372 (16525) | NS | Spo0F – 2-component response regulator. Integrates signals from sensor kinases to trigger entry into sporulation | BSU37130 (98.4) | T:C | H:R | 101/124 |
| 3231480 | C:G | A:P | 98/124 | ||||
| 34373505 | BG3610 (17625) | NS | Short chain dehydrogenase/reductase | NA | T:C | T:A | 149/247 |
| 3625727 | BG3807 (18590) | NS | trmE – GTPase and tRNA-U34 5-formylation enzyme TrmE | BSU41020 (93.3) | C:A | D:Y | 2/459 |
| 3728882 | BG3897/38996 (19040/19045) | IG | AA:TT | ||||
| 3739882 | BG3911 (19100) | NS | sigH (spo0H) RNA polymerase sigma factor | BSU00980 (98.6) | C:T | P:L | 197/218 |
| 3857860 | BG4037 (19695) | NS | Glycosyltransferase | NA | T:C | G:R | 374/402 |
| 4048456 | BG4209 (20515) | NS | yclF/dtpT – putative di-tripeptide-proton ABC transporter | BSU3670 (87.0) | A:G | W:R | 397/4927 |
| 4108902 | BG4273/4274 (20825/20830) | IG | C:A | ||||
| 41175585 | BG4285 (20875) | NS | ydaL – uncharacterized membrane protein | BSU04290 (76.5) | C:T | P::L | 9/574 |
1
In addition to the above mutations, putative SNPs at positions 39912, 45501, 61413, 611822, 1170114, 1251549, 2174033, 2771980, 3128882, 3269962, 3354410, 3528224, and 3880949 were common to all reference mapping experiments against the finished genome using 454 data, including the 1942 dataset. The commonality to all datasets suggest that these were errors in the finished sequence that are being verified.
2
PS = Premature stop; SYN = Synonomous; INS = Insertion; NS = Non-synonomous; IG = Intergenic; DEL = Deletion.
3
Annotations are a combination of RAST and directed tBLASTn and BLASTp searches vs Bacillus databases.
4
Forms part of a large polypeptide synthase containing highly homologous regions.
5
Also shared with strain ATCC 49822.
6
The conserved start codon of the radA gene (BG3899) of B. atrophaeus and B. subtilis falls within the BG3898 ORF. Therefore BG3898 as called by RAST is not deemed likely to be a protein-coding gene.
7
In putative transmembrane region.