Rv0953c Resolved · high auto-curated
H37Rv Rv0953c · MTBC0 mtbc0_001017 ·
282 aa · 1071329–1072177 (-) ·
RefSeq NP_215468.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | LLM class F420-dependent oxidoreductase |
| Revised (this work) | LLM class F420-dependent oxidoreductase. Pfam: Bac_luciferase (PF00296.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKN5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0953c |
UniProt still lists this protein as Uncharacterized protein Rv0953c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | rutA_3 |
| eggNOG description | COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases |
| Orthologous group | COG2141 |
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 | 0.165 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 5.2e-47 | 18–233 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0954 (transmembrane protein), high confidence from genomic context alone (score 768 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0954 |
transmembrane protein | 767 | 768 ctx | neighborhood:768 |
Rv2893 |
oxidoreductase | 706 | 706 ctx | cooccurence:702 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 633 | 633 ctx | cooccurence:633 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 573 | 573 ctx | cooccurence:573 |
Rv3531c hyp |
hypothetical protein | 537 | 538 ctx | cooccurence:531 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 539 | 511 ctx | cooccurence:450 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 495 | 495 ctx | neighborhood:495 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 495 | 495 ctx | neighborhood:495 |
Rv3178 |
nitroreductase | 521 | 492 ctx | cooccurence:490 |
Rv3093c |
oxidoreductase | 475 | 476 ctx | cooccurence:474 |
Rv3529c hyp |
hypothetical protein | 477 | 474 ctx | cooccurence:465 |
Rv0121c hyp |
hypothetical protein | 489 | 469 ctx | cooccurence:466 |
Rv1261c hyp |
hypothetical protein | 460 | 461 ctx | cooccurence:459 |
Rv0955 |
integral membrane protein | 440 | 441 ctx | neighborhood:441 |
Rv2383c mbtB |
phenyloxazoline synthase | 462 | 433 |
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: oxidoreductase
- MTBC0 PGAP product: LLM class F420-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=5e-47)
- (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_215468.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_luciferase (PF00296.27)
- 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
COG2141 - Curated reference: UniProt P9WKN5 (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 —
18 functional partner(s); context anchor
Rv0954 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001017|Rv0953c| MHYGLVLFTSDRGITPAAAARLAESHGFRTFYVPEHTHIPVKRQAAHPTTGDASLPDDRYMRTLDPWVSLGAASAVTSRIRLATAVALPVEHDPITLAKSIATLDHLSHGRVSVGVGFGWNTDELVDHGVPPGRRRTMLREYLEAMRALWTQEEACYDGEFVKFGPSWAWPKPVQPHIPVLVGAAGTEKNFKWIARSADGWITTPRDVDIDEPVKLLQDIWAAAGRDGLPQIVALDVKPVPDKLARWAELGVTEVLFGMPDRSADDAAAYVERLAAKLACCV