Rv3295 Family assigned · medium auto-curated
H37Rv Rv3295 · MTBC0 mtbc0_003503 ·
221 aa · 3698146–3698811 (+) ·
RefSeq NP_217812.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | TetR family transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | TetR/AcrR family transcriptional regulator |
| Revised (this work) | TetR/AcrR family transcriptional regulator. 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 |
P96900
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 | 4.9e-15 | 17–63 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lhr (ATP-dependent helicase), high confidence from genomic context alone (score 820 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3296 lhr |
ATP-dependent helicase | 820 | 820 ctx | neighborhood:818 |
Rv3297 nei |
endonuclease VIII | 819 | 819 ctx | neighborhood:818 |
Rv3294c hyp |
hypothetical protein | 610 | 609 ctx | neighborhood:605 |
Rv0210 hyp |
hypothetical protein | 607 | 607 ctx | cooccurence:607 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 562 | 553 ctx | neighborhood:544 |
Rv1182 papA3 |
acyltransferase papA3 | 492 | 493 ctx | cooccurence:488 |
Rv3405c |
HTH-type transcriptional regulator | 482 | 483 ctx | cooccurence:478 |
Rv3291c lrpA |
transcriptional regulator LrpA | 492 | 477 ctx | neighborhood:469 |
Rv1978 hyp |
hypothetical protein | 476 | 477 ctx | cooccurence:415 |
Rv0169 mce1A |
Mce family protein Mce1A | 464 | 464 | |
Rv3824c papA1 |
acyltransferase | 452 | 453 ctx | cooccurence:451 |
Rv1006 hyp |
hypothetical protein | 433 | 433 | |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 422 | 423 | coexpression:423 |
Rv2035 hyp |
hypothetical protein | 417 | 417 ctx | cooccurence:417 |
Rv3033 hyp |
hypothetical protein | 410 | 411 ctx | cooccurence:407 |
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 family transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=5e-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_217812.1)
- 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 P96900 (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 —
22 functional partner(s); context anchor
lhr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003503|Rv3295| MATARRRLSPQDRRAELLALGAEVFGKRPYDEVRIDEIAERAGVSRALMYHYFPDKRAFFAAVVKDEADRLYAATNKAPAPGMTMFEEIRTGVLAYMAYHQQNPEAAWAAYVGLGRSDPVLLGIDDEAKNRQMEHIMSRIAEVVSGIDRDNTLDPEVERDLRVIIHGWLAFTFELCRQRIMDPSTDAERLADACAHALLDAISRLPQIPAELADAMATARM