Rv1117 Family assigned · medium auto-curated
H37Rv Rv1117 · MTBC0 mtbc0_001200 ·
107 aa · 1250073–1250396 (+) ·
RefSeq NP_215633.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | putative quinol monooxygenase |
| Revised (this work) | Putative quinol monooxygenase. Pfam: ABM (PF03992.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06569
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Antibiotic biosynthesis monooxygenase |
| Orthologous group | COG1359 |
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 | 0.585 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
ABM | PF03992.23 | 7.8e-20 | 1–76 | Antibiotic biosynthesis monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1116A (Rv1116A, len: 91 aa. Conserved hypothetical protein (possibly gene fragment), similar to C-terminal part of Rv1646|Z85982_9 from Mycobacteri), medium confidence from genomic context alone (score 499 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) |
|---|---|---|---|---|
Rv2260 hyp |
hypothetical protein | 519 | 520 ctx | cooccurence:509 |
Rv1116A |
Rv1116A, len: 91 aa. Conserved hypothetical protein (possibly gene fragment), similar to C-terminal part of Rv1646|Z85982_9 from Mycobacteri | 500 | 499 ctx | neighborhood:489 |
Rv0360c hyp |
hypothetical protein | 491 | 492 ctx | cooccurence:436 |
Rv1629 polA |
DNA polymerase I | 415 | 416 | coexpression:416 |
Rv1929c hyp |
hypothetical protein | 409 | 409 ctx | cooccurence:406 |
Rv0088 |
polyketide cyclase/dehydrase | 406 | 406 ctx | cooccurence:406 |
Rv1879 hyp |
hypothetical protein | 403 | 404 |
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: putative quinol monooxygenase
- Pfam (hmmscan --cut_ga): ABM PF03992.23 (E=8e-20)
- (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_215633.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABM (PF03992.23)
- 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
COG1359 - Curated reference: UniProt O06569 (TrEMBL, unreviewed; 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 —
7 functional partner(s); context anchor
Rv1116A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001200|Rv1117| MIFIVVKFETKPEWTERWPDLVASFTAATRAEEGNLWFEWSRSLDDPAEYVLVESFRDGEAGGVHVNSDHFRQAMRELPKALASTPKIISQTIDATGWSAMGEMTVG