Rv0955 Family assigned · medium auto-curated
H37Rv Rv0955 · MTBC0 mtbc0_001019 ·
455 aa · 1073293–1074660 (+) ·
RefSeq NP_215470.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF6350 family protein |
| Revised (this work) | DUF6350 family protein. Pfam: PerM (PF19877.5). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKN3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0955 |
UniProt still lists this protein as Uncharacterized protein Rv0955; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EKVE |
|---|---|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.581 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
PerM | PF19877.5 | 1.4e-31 | 50–374 | Cell division protein PerM |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0954 (transmembrane protein), high confidence from genomic context alone (score 828 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0954 |
transmembrane protein | 828 | 828 ctx | neighborhood:823 |
Rv3604c |
transmembrane protein | 776 | 776 ctx | cooccurence:773 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 767 | 767 ctx | cooccurence:767 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 766 | 766 ctx | neighborhood:764 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 765 | 765 ctx | neighborhood:764 |
Rv1159 pimE |
polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase | 762 | 762 ctx | cooccurence:760 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 745 | 745 ctx | cooccurence:745 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 762 | 741 ctx | cooccurence:735 |
Rv0256c PPE2 |
PPE family protein PPE2 | 738 | 738 ctx | cooccurence:737 |
Rv2633c hyp |
hypothetical protein | 723 | 724 ctx | cooccurence:721 |
Rv0051 |
transmembrane protein | 722 | 722 ctx | cooccurence:718 |
Rv0804 hyp |
hypothetical protein | 720 | 720 ctx | cooccurence:707 |
Rv1978 hyp |
hypothetical protein | 718 | 718 ctx | cooccurence:718 |
Rv2687c |
antibiotic ABC transporter permease | 700 | 700 ctx | cooccurence:697 |
Rv0959 hyp |
hypothetical protein | 696 | 696 ctx | neighborhood:694 |
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: integral membrane protein
- MTBC0 PGAP product: DUF6350 family protein
- Pfam (hmmscan --cut_ga): PerM PF19877.5 (E=1e-31)
- (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_215470.1)
- Domains: Pfam-A via hmmscan --cut_ga — PerM (PF19877.5)
- 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
2EKVE - Curated reference: UniProt P9WKN3 (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 —
61 functional partner(s); context anchor
Rv0954 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001019|Rv0955| MNRVSASADDRAAGARPARDLVRVAFGPGVVALGIIAAVTLLQLLIANSDMTGAWGAIASMWLGVHLVPISIGGRALGVMPLLPVLLMVWATARSTARATSPQSSGLVVRWVVASALGGPLLMAAIALAVIHDASSVVTELQTPSALRAFTSVLVVHSVGAATGVWSRVGRRALAATALPDWLHDSMRAAAAGVLALLGLSGVVTAGSLVVHWATMQELYGITDSIFGQFSLTVLSVLYAPNVIVGTSAIAVGSSAHIGFATFSSFAVLGGDIPALPILAAAPTPPLGPAWVALLIVGASSGVAVGQQCARRALPFVAAMAKLLVAAVAGALVMAVLGYGGGGRLGNFGDVGVDEGALVLGVLFWFTFVGWVTVVIAGGISRRPKRLRPAPPVELDADESSPPVDMFDGAASEQPPASVAEDVPPSHDDIANGLKAPTADDEALPLSDEPPPRAD