Rv1265 Family assigned · medium auto-curated
H37Rv Rv1265 · MTBC0 - ·
226 aa · 1413260–1413940 (+) ·
RefSeq NP_215781.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Rv1265_N (PF27105.1), Mb1296_C (PF27540.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WM49
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1265 |
UniProt still lists this protein as Uncharacterized protein Rv1265; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28M3Q |
|---|---|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.975 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
Rv1265_N | PF27105.1 | 6.7e-37 | 65–152 | Rv1265-like protein, N-terminal domain |
Mb1296_C | PF27540.1 | 3.2e-29 | 166–218 | Mb1296 C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsfB (anti-anti-sigma factor RsfB), medium confidence from genomic context alone (score 479 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3687c rsfB |
anti-anti-sigma factor RsfB | 479 | 479 ctx | cooccurence:476 |
Rv1362c |
membrane protein | 473 | 474 ctx | cooccurence:472 |
Rv0898c hyp |
hypothetical protein | 468 | 468 ctx | cooccurence:465 |
Rv1264 |
adenylyl cyclase | 650 | 467 ctx | neighborhood:461 |
Rv2390c hyp |
hypothetical protein | 461 | 461 ctx | cooccurence:461 |
Rv3492c |
Mce associated protein | 440 | 441 ctx | cooccurence:439 |
Rv2905 lppW |
lipoprotein LppW | 431 | 432 ctx | cooccurence:430 |
Rv1263 amiB2 |
amidase AmiB | 430 | 430 ctx | neighborhood:430 |
Rv1698 mctB |
copper transporter MctB | 427 | 428 ctx | cooccurence:427 |
Rv2226 hyp |
hypothetical protein | 416 | 416 ctx | cooccurence:416 |
Rv3495c lprN |
Mce family lipoprotein LprN | 413 | 413 ctx | cooccurence:412 |
Rv0685 tuf |
elongation factor Tu | 477 | 44 | textmining:476 |
Rv0440 groEL2 |
molecular chaperone GroEL | 438 | 44 | textmining:437 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 807 | 42 | textmining:807 |
Rv2971 |
oxidoreductase | 660 | 41 | textmining:660 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): Rv1265_N PF27105.1 (E=7e-37), Mb1296_C PF27540.1 (E=3e-29)
- (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_215781.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv1265_N (PF27105.1), Mb1296_C (PF27540.1)
- 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
28M3Q - Curated reference: UniProt P9WM49 (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 —
18 functional partner(s); context anchor
rsfB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1265| MVLARPDAVFAPARNRCHVSLPVNAMSLKMKVCNHVIMRHHHMHGRRYGRPGGWQQAQQPDASGAAEWFAGRLPEDWFDGDPTVIVDREEITVIGKLPGLESPEEESAARASGRVSRFRDETRPERMTIADEAQNRYGRKVSWGVEVGGERILFTHIAVPVMTRLKQPERQVLDTLVDAGVARSRSDALAWSVKLVGEHTEEWLAKLRTAMSAVDDLRAQGPDLPA