Rv1287 Family assigned · medium auto-curated
H37Rv Rv1287 · MTBC0 mtbc0_001377 ·
161 aa · 1449788–1450273 (+) ·
RefSeq NP_215803.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | RrF2 family transcriptional regulator |
| Revised (this work) | RrF2 family transcriptional regulator. Pfam: Rrf2 (PF02082.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WME3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative HTH-type transcriptional regulator Rv1287 |
UniProt still lists this protein as Putative HTH-type transcriptional regulator Rv1287; 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 | COG1959 |
| KEGG orthology |
K13643
|
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 |
|---|---|---|---|---|
Rrf2 | PF02082.27 | 2.9e-34 | 3–131 | Iron-dependent Transcriptional regulator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysC (adenylyl-sulfate kinase), high confidence from genomic context alone (score 853 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1286 cysC |
adenylyl-sulfate kinase | 867 | 853 ctx | neighborhood:807 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 861 | 852 ctx | neighborhood:807 |
Rv3025c iscS |
cysteine desulfurase | 854 | 830 | coexpression:790 |
Rv1465 |
nitrogen fixation related protein | 759 | 685 | coexpression:645 |
Rv1288 hyp |
hypothetical protein | 684 | 668 ctx | neighborhood:645 |
Rv1289 hyp |
hypothetical protein | 520 | 521 ctx | neighborhood:516 |
Rv1284 canA |
beta-carbonic anhydrase | 443 | 443 ctx | neighborhood:437 |
Rv2204c hyp |
hypothetical protein | 499 | 387 | |
Rv1674c |
transcriptional regulator | 426 | 301 | |
Rv0385 |
monooxygenase | 410 | 227 | |
Rv0479c |
membrane protein | 625 | 205 | textmining:548 |
Rv3554 fdxB |
electron transfer protein FdxB | 419 | 190 | |
Rv2776c |
oxidoreductase | 418 | 189 | |
Rv3571 kshB |
3-ketosteroid-9-alpha-hydroxylase reductase subunit | 416 | 186 | |
Rv3230c |
stearoyl-CoA 9-desaturase electron transfer protein | 415 | 184 |
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: RrF2 family transcriptional regulator
- Pfam (hmmscan --cut_ga): Rrf2 PF02082.27 (E=3e-34)
- (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_215803.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rrf2 (PF02082.27)
- 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
COG1959 - Curated reference: UniProt P9WME3 (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 —
19 functional partner(s); context anchor
cysC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001377|Rv1287| MRMSAKAEYAVRAMVQLATAASGTVVKTDDLAAAQGIPPQFLVDILTNLRTDRLVRSHRGREGGYELARPGTEISIADVLRCIDGPLASVRDIGLGDLPYSGPTTALTDVWRALRASMRSVLEETTLADVAGGALPEHVAQLADDYRAQESTRHGASRHGD