Rv1255c Family assigned · medium auto-curated
H37Rv Rv1255c · MTBC0 mtbc0_001344 ·
202 aa · 1411222–1411830 (-) ·
RefSeq NP_215771.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | helix-turn-helix domain-containing protein |
| Revised (this work) | Helix-turn-helix domain-containing protein. Pfam: TetR_N (PF00440.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMD5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv1255c |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv1255c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG1309 |
| Gene Ontology (41) |
GO:0000976, GO:0001067, GO:0003674, GO:0003676, GO:0003677, GO:0003690, GO:0003700, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737 +29 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.906 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
TetR_N | PF00440.30 | 1.6e-15 | 19–63 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cyp130 (cytochrome P450 Cyp130), high confidence from genomic context alone (score 925 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1256c cyp130 |
cytochrome P450 Cyp130 | 925 | 925 ctx | neighborhood:881 |
Rv1257c |
oxidoreductase | 743 | 743 ctx | neighborhood:732 |
Rv3060c |
GntR family transcriptional regulator | 740 | 733 | coexpression:732 |
Rv1258c tap |
multidrug-efflux transporter | 572 | 573 ctx | neighborhood:570 |
Rv3736 |
AraC/XylS family transcriptional regulator | 503 | 495 | coexpression:494 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 496 | 481 ctx | cooccurence:405 |
Rv3131 |
NAD(P)H nitroreductase | 466 | 465 ctx | cooccurence:463 |
Rv2032 acg |
NAD(P)H nitroreductase | 454 | 453 ctx | cooccurence:450 |
Rv3132c devS |
two component sensor histidine kinase DevS | 466 | 446 | |
Rv1275 lprC |
lipoprotein LprC | 431 | 432 ctx | cooccurence:430 |
Rv1259 udgB |
uracil DNA glycosylase | 427 | 427 ctx | neighborhood:425 |
Rv2027c dosT |
two component sensor histidine kinase DosT | 439 | 417 | |
Rv0227c |
membrane protein | 413 | 413 ctx | cooccurence:411 |
Rv1260 |
oxidoreductase | 414 | 409 ctx | neighborhood:407 |
Rv3127 hyp |
hypothetical protein | 409 | 407 ctx | cooccurence:406 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: HTH-type transcriptional regulator
- MTBC0 PGAP product: helix-turn-helix domain-containing protein
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=2e-15)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215771.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1309 - Curated reference: UniProt P9WMD5 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
26 functional partner(s); context anchor
cyp130 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001344|Rv1255c| MAGTDWLSARRTELAADRILDAAERLFTQRDPASIGMNEIAKAAGCSRATLYRYFDSREALRTAYVHRETRRLGREIMVKIADVVEPAERLLVSITTTLRMVRDNPALAAWFTTTRPPIGGEMAGRSEVIAALAAAFLNSLGPDDPTTVERRARWVVRMLTSLLMFPGRDEADERAMIAEFVVPIVTPASAAARKAGHPGPE