Rv1289 Family assigned · medium auto-curated
H37Rv Rv1289 · MTBC0 mtbc0_001379 ·
210 aa · 1451750–1452382 (+) ·
RefSeq NP_215805.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains Rv1289 (PF27329.1) 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.
Curated reference (UniProt)
| UniProt |
P9WM37
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1289 |
UniProt still lists this protein as Uncharacterized protein Rv1289; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EP2R |
|---|---|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, 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 | 0.783 · 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 |
|---|---|---|---|---|
Rv1289 | PF27329.1 | 1.9e-86 | 4–203 | Rv1289 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1287 (HTH-type transcriptional regulator), medium confidence from genomic context alone (score 521 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) |
|---|---|---|---|---|
Rv0265c |
iron ABC transporter substrate-binding lipoprotein | 732 | 732 | coexpression:732 |
Rv1288 hyp |
hypothetical protein | 667 | 667 ctx | neighborhood:665 |
Rv1287 |
HTH-type transcriptional regulator | 520 | 521 ctx | neighborhood:516 |
Rv1286 cysC |
adenylyl-sulfate kinase | 445 | 445 ctx | neighborhood:445 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 412 | 412 ctx | neighborhood:412 |
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: hypothetical protein
- MTBC0 PGAP product: hypothetical protein
- Pfam (hmmscan --cut_ga): Rv1289 PF27329.1 (E=2e-86)
- (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_215805.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv1289 (PF27329.1)
- 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
2EP2R - Curated reference: UniProt P9WM37 (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 —
5 functional partner(s); context anchor
Rv1287 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001379|Rv1289| MCVSVGESVAQSLQQWDRKLWDVAMLHACNAVDETGRKRYPTLGVGTRFRTALRDSLDIYGVMATPGVDLEKTRFPVGVRSDLLPDKRPDIADVLYGIHRWLHGHADESSVEFEVSPYVNASAALRIANDGKIQLPKSAILGLLAVAVFAPENKGEVIPPDYQLSWYDHVFFISVWWGWQDHFREIVNVDRASLVALDFGDLWNGWTPVG