Rv0102 Resolved · high auto-curated
H37Rv Rv0102 · MTBC0 mtbc0_000111 ·
661 aa · 117877–119862 (+) ·
RefSeq NP_214616.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | cytochrome c oxidase assembly protein |
| Revised (this work) | Cytochrome c oxidase assembly protein. Pfam: Caa3_CtaG (PF09678.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM63
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0102 |
UniProt still lists this protein as Uncharacterized protein Rv0102; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | CytoChrome c oxidase Caa3 assembly factor |
| Orthologous group | COG3336 |
| KEGG orthology |
K02351, K07245
|
| 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 | 0.476 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 9 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 |
|---|---|---|---|---|
Caa3_CtaG | PF09678.16 | 1.7e-88 | 381–625 | Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: qcrC (ubiquinol-cytochrome C reductase cytochrome subunit C), high confidence from genomic context alone (score 797 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 811 | 797 ctx | cooccurence:740 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 772 | 761 ctx | cooccurence:661 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 742 | 742 ctx | cooccurence:686 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 715 | 715 ctx | cooccurence:712 |
Rv0528 |
transmembrane protein | 714 | 714 ctx | cooccurence:709 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 669 | 650 | coexpression:418 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 658 | 636 | coexpression:412 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 638 | 615 | coexpression:449 |
Rv1456c |
antibiotic ABC transporter permease | 585 | 559 ctx | cooccurence:528 |
Rv2219A |
membrane protein | 558 | 559 ctx | cooccurence:552 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 532 | 533 ctx | cooccurence:526 |
Rv3201c adnB |
ATP-dependent DNA helicase | 528 | 528 ctx | cooccurence:528 |
Rv0097 |
oxidoreductase | 572 | 522 ctx | neighborhood:458 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 494 | 494 ctx | cooccurence:491 |
Rv3876 espI |
ESX-1 secretion-associated protein EspI | 467 | 468 ctx | cooccurence:460 |
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: cytochrome c oxidase assembly protein
- Pfam (hmmscan --cut_ga): Caa3_CtaG PF09678.16 (E=2e-88)
- (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_214616.1)
- Domains: Pfam-A via hmmscan --cut_ga — Caa3_CtaG (PF09678.16)
- 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
COG3336 - Curated reference: UniProt P9WM63 (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 —
35 functional partner(s); context anchor
qcrC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000111|Rv0102| MGTHGATKSATSAVPTPRSNSMAMVRLAIGLLGVCAVVAAFGLVSGARRYAEAGNPYPGAFVSVAEPVGFFAASLAGALCLGALIHVVMTAKPEPDGLIDAAAFRIHLLAERVSGLWLGLAATMVVIQAAHDTGVGPARLLASGALSDSVAASEMARGWIVAAICALVVATALRLYTRWLGHVVLLVPTVLAVVATAVTGNPGQGPDHDYATSAAIVFAVAFATLTGLKIAAALAGTTPSRAVLVTQVTCGALALAYGAMLLYLFIPGWAVDSDFARLGLLAGVILTSVWLFDCWRLLVRPPHAGRRRGGGSGAALAMMAAMASIAAMAVMTAPRFLTHAFTAWDVFLGYELPQPPTIARVLTVWRFDSLIGAAGVVLAIGYAAGFAALRRRGNSWPVGRLIAWLTGCAALVFTSGSGVRAYGSAMFSVHMAEHMTLNMFIPVLLVLGGPVTLALRVLPVTGDGRPPGAREWLTWLLHSRVTTFLSHPITAFVLFVASPYIVYFTPLFDTFVRYHWGHEFMAIHFLVVGYLFYWAIIGIDPGPRRLPYPGRIGLLFAVMPFHAFFGIALMTMSSTVGATFYRSVNLPWLSSIIADQHLGGGIAWSLTELPVIMVIVALVTQWARQDRRVASREDRHADSDYADDELEAYNAMLRELSRMRR