Rv3173c Family assigned · medium auto-curated
H37Rv Rv3173c · MTBC0 mtbc0_003372 ·
200 aa · 3566291–3566893 (-) ·
RefSeq NP_217689.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | TetR/Acr family 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 |
O53323
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Bacterial regulatory proteins, tetR family |
| Orthologous group | COG1309 |
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 | 0.355 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 | 8.0e-17 | 22–67 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3174 (short-chain dehydrogenase/reductase), medium confidence from genomic context alone (score 672 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3174 |
short-chain dehydrogenase/reductase | 672 | 672 ctx | neighborhood:598 |
Rv3172c hyp |
hypothetical protein | 588 | 588 ctx | neighborhood:583 |
Rv3175 |
amidase | 538 | 539 ctx | neighborhood:532 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 400 | 401 | |
Rv0377 |
HTH-type transcriptional regulator | 518 | 350 | |
Rv0067c |
transcriptional regulator | 519 | 336 | |
Rv3833 |
AraC family transcriptional regulator | 475 | 293 | |
Rv2034 |
ArsR family HTH-type transcriptional repressor | 438 | 275 | |
Rv2640c |
ArsR family transcriptional regulator | 569 | 227 | textmining:466 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 461 | 85 | textmining:436 |
Rv2711 ideR |
iron-dependent repressor and activator IdeR | 472 | 81 | textmining:450 |
Rv1657 argR |
arginine repressor | 436 | 63 | textmining:423 |
Rv0465c ramB |
HTH-type transcriptional regulator | 491 | 52 | textmining:486 |
Rv0712 hyp |
hypothetical protein | 523 | 50 | textmining:519 |
Rv3096 hyp |
hypothetical protein | 440 | 47 | textmining:437 |
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: TetR/Acr family transcriptional regulator
- MTBC0 PGAP product: helix-turn-helix domain-containing protein
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=8e-17)
- (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_217689.1)
- 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 O53323 (TrEMBL, unreviewed; 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 —
18 functional partner(s); context anchor
Rv3174 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003372|Rv3173c| MPPVTRTTEPPRRGGRGARQRILKAAAELFYCEGINATGVELIANKASVSKRTLYQHFPSKSALVEEYLRGLRQAAGEADKMPKASNATPRERLLALFDRPNRGDGRMRGCPFHNAAVEAAGEMPGVERIVHSHKRDYIKGLARLAREAGAAHPRSLGNQLAVLFEGAAALSTSLDDAGPWAHARAAAEVLIDQATARPV