Rv0959 Family assigned · medium auto-curated
H37Rv Rv0959 · MTBC0 mtbc0_001023 ·
672 aa · 1078470–1080488 (+) ·
RefSeq NP_215474.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | VWA domain-containing protein |
| Revised (this work) | VWA domain-containing protein. Pfam: Mb0984_helical (PF27532.1), Rv0959_3rd (PF27098.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKN1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0959 |
UniProt still lists this protein as Uncharacterized protein Rv0959; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | von Willebrand factor, type A |
| Orthologous group | COG4867 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 0.524 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 12 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 |
|---|---|---|---|---|
Mb0984_helical | PF27532.1 | 3.6e-30 | 99–169 | Mb0984 helical domain |
Rv0959_3rd | PF27098.1 | 3.4e-21 | 427–476 | Rv0959-like protein, third domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0958 (magnesium chelatase), high confidence from genomic context alone (score 984 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) |
|---|---|---|---|---|
Rv0958 |
magnesium chelatase | 984 | 984 ctx | neighborhood:881 cooccurence:774 coexpression:457 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 769 | 769 ctx | neighborhood:768 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 769 | 769 ctx | neighborhood:768 |
Rv0955 |
integral membrane protein | 696 | 696 ctx | neighborhood:694 |
Rv0954 |
transmembrane protein | 673 | 674 ctx | neighborhood:673 |
Rv0960 vapC9 |
ribonuclease VapC9 | 658 | 658 ctx | neighborhood:653 |
Rv0959A vapB9 |
antitoxin VapB9 | 653 | 653 ctx | neighborhood:653 |
Rv2133c hyp |
hypothetical protein | 579 | 579 ctx | cooccurence:451 |
Rv0961 |
integral membrane protein | 465 | 464 ctx | neighborhood:461 |
Rv2135c hyp |
hypothetical protein | 454 | 454 | |
Rv0443 hyp |
hypothetical protein | 423 | 423 ctx | cooccurence:422 |
Rv3592 mhuD |
heme-degrading monooxygenase | 415 | 416 ctx | cooccurence:414 |
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: VWA domain-containing protein
- Pfam (hmmscan --cut_ga): Mb0984_helical PF27532.1 (E=4e-30), Rv0959_3rd PF27098.1 (E=3e-21)
- (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_215474.1)
- Domains: Pfam-A via hmmscan --cut_ga — Mb0984_helical (PF27532.1), Rv0959_3rd (PF27098.1)
- 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
COG4867 - Curated reference: UniProt P9WKN1 (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 —
12 functional partner(s); context anchor
Rv0958 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001023|Rv0959| MAKSDGDDPLRPASPRLRSSRRHSLRYSAYTGGPDPLAPPVDLRDALEQIGQDVMAGASPRRALSELLRRGTRNLTGADRLAAEVNRRRRELLRRNNLDGTLQEIKKLLDEAVLAERKELARALDDDARFAELQLDALPASPAKAVQELAEYRWRSGQAREKYEQIKDLLGRELLDQRFAGMKQALAGATDDDRRRVTEMLDDLNDLLDKHARGEDTQRDFDEFMTKHGEFFPENPRNVEELLDSLAKRAAAAQRFRNSLSQEQRDELDALAQQAFGSPALMRALDRLDAHLQAARPGEDWTGSQQFSGDNPFGMGEGTQALADIAELEQLAEQLSQSYPGASMDDVDLDALARQLGDQAAVDARTLAELERALVNQGFLDRGSDGQWRLSPKAMRRLGETALRDVAQQLSGRHGERDHRRAGAAGELTGATRPWQFGDTEPWHVARTLTNAVLRQAAAVHDRIRITVEDVEVAETETRTQAAVALLVDTSFSMVMENRWLPMKRTALALHHLVCTRFRSDALQIIAFGRYARTVTAAELTGLAGVYEQGTNLHHALALAGRHLRRHAGAQPVVLVVTDGEPTAHLEDFDGDGTSVFFDYPPHPRTIAHTVRGFDDMARLGAQVTIFRLGSDPGLARFIDQVARRVQGRVVVPDLDGLGAAVVGDYLRFRRR