Table 2.
Preserved mutations happened in coding sequences
| Site | Locus_tag | Product and length | Base change* | Codon change |
|---|---|---|---|---|
| Indels | ||||
| 17391 | TRQ7_RS00090 | Flagellar biosynthesis protein FlhB | d11: AAAACAGGAAGT → A | Frame shift, truncation |
| 1006296 | TRQ7_RS05035 | Alpha-amylase | i1: T → TA | Frame shift, run-through |
| 1426409 | TRQ7_RS07315 | 2-hydroxyacid dehydrogenase | i1: AG → AGG | Frame shift, truncation |
| SNPs | ||||
| 205012 | TRQ7_RS01075 | Methylmalonyl-CoA carboxyltransferase | Transversion: G → T | Silent: V360 |
| 262000 | TRQ7_RS01400 | Hypothetical protein | Transition: G → A | Silent: L346 |
| 323128 | TRQ7_RS01715 | Queuosine precursor transporter | Transition: G → A | Silent: T204 |
| 459761 | TRQ7_RS02405 | Tyrosine-tRNA ligase | Transition: C → T | Silent: V15 |
| 1724427 | TRQ7_RS08830 | Alpha-glucuronidase Agu4A | Transition: T → C | Silent: H107 |
| ABC transporters | ||||
| 409,563 | TRQ7_RS02130 | ABC transporter substrate-binding protein | Transition: A → G | Missense: Q545R |
| 668132 | TRQ7_RS03395 | Sugar ABC transporter permease | Transition: C → T | Missense: A283V |
| 1046451 | TRQ7_RS05215 | Sugar ABC transporter ATP-binding protein | Transition: C → T | Missense: A406V |
| 1,049,370 | TRQ7_RS05225 | Sugar ABC transporter substrate-binding protein | Transition: C → T | Missense: P115S |
| 1542185 | TRQ7_RS07940 | ABC transporter ATP-binding protein | Transition: C → T | Missense: P290S |
| Stress response | ||||
| 442230 | TRQ7_RS02305 | PhoH family protein | Transversion: C → A | Missense: S123R |
| 789928 | TRQ7_RS04030 | Sodium-translocating pyrophosphatase | Transversion: C → A | Missense: A461E |
| 993287 | TRQ7_RS04975 | 5'/3'-nucleotidase SurE | Transition: C → T | Missense: P50L |
| 1105970 | TRQ7_RS05480 | Ribose-phosphate pyrophosphokinase | Transition: G → A | Missense: A83T |
| 1196396 | TRQ7_RS05995 | Phosphate signaling complex protein PhoU | Transition: G → A | Missense: G83S |
| Sensing and regulation | ||||
| 856804 | TRQ7_RS04355 | ROK family transcriptional regulator | Transversion: A → C | Missense: N12T |
| 998628 | TRQ7_RS05010 | Response regulator transcription factor | Transversion: C → A | Missense: L189M |
| 1242229 | TRQ7_RS06235 | Transcriptional repressor | Transition: C → T | Nonsense: Q9 |
| 1285475 | TRQ7_RS06565 | RNA polymerase sigma factor RpoD | Transition: C → T | Missense: L280F |
| 1618115 | TRQ7_RS08290 | Sensor domain-containing diguanylate cyclase | Transversion: T → A | Missense: V390E |
| Others | ||||
| 12579 | TRQ7_RS00060 | Ribonuclease HII | Transition: G → A | Missense: A237T |
| 26360 | TRQ7_RS00155 | Galactose-1-phosphate uridylyltransferase | Transition: C → T | Missense: P274L |
| 721511 | TRQ7_RS03655 | UDP-N-acetylmuramoyl-tripeptide–D-alanyl-D- alanine ligase | Transition: G → A | Missense: D148N |
| 731443 | TRQ7_RS03700 | NADH-quinone oxidoreductase subunit NuoE | Transition: C → T | Missense: S15L |
| 1021158 | TRQ7_RS05125 | Hypothetical protein | Transition: G → A | Missense: G148D |
| 1352603 | TRQ7_RS06890 | Hypothetical protein | Transition: G → A | Missense: V418I |
*d11: deletion of 11 bases; i1: insertion of 1 base