Rv0940c Family assigned · medium auto-curated
H37Rv Rv0940c · MTBC0 mtbc0_000998 ·
288 aa · 1053810–1054676 (-) ·
RefSeq NP_215455.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | TIGR03619 family F420-dependent LLM class oxidoreductase |
| Revised (this work) | TIGR03619 family F420-dependent LLM class 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 |
P9WKP1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0940c |
UniProt still lists this protein as Uncharacterized protein Rv0940c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases |
| Orthologous group | COG2141 |
| 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 | 0.434 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (196) · clonal |
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 | 3.8e-43 | 11–226 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3520c (coenzyme F420-dependent oxidoreductase), high confidence from genomic context alone (score 870 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3520c |
coenzyme F420-dependent oxidoreductase | 870 | 870 ctx | neighborhood:544 cooccurence:726 |
Rv3521 hyp |
hypothetical protein | 799 | 792 ctx | neighborhood:544 cooccurence:559 |
Rv3522 ltp4 |
lipid transfer protein | 750 | 750 ctx | neighborhood:544 cooccurence:471 |
Rv3072c hyp |
hypothetical protein | 722 | 722 ctx | cooccurence:722 |
Rv3523 ltp3 |
lipid carrier protein | 668 | 668 ctx | neighborhood:544 |
Rv3178 |
nitroreductase | 685 | 665 ctx | cooccurence:663 |
Rv3531c hyp |
hypothetical protein | 630 | 631 ctx | cooccurence:627 |
Rv0941c hyp |
hypothetical protein | 622 | 622 ctx | neighborhood:601 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 635 | 616 ctx | cooccurence:615 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 634 | 611 ctx | cooccurence:611 |
Rv1261c hyp |
hypothetical protein | 610 | 610 ctx | cooccurence:608 |
Rv3529c hyp |
hypothetical protein | 602 | 600 ctx | cooccurence:593 |
Rv3570c hsaA |
flavin-dependent monooxygenase oxygenase subunit HsaA | 591 | 592 ctx | cooccurence:572 |
Rv3526 kshA |
3-ketosteroid-9-alpha-monooxygenase oxygenase subunit | 583 | 583 ctx | cooccurence:575 |
Rv1817 |
flavoprotein | 548 | 548 ctx | cooccurence:535 |
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: TIGR03619 family F420-dependent LLM class oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=4e-43)
- (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_215455.1)
- 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 P9WKP1 (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 —
33 functional partner(s); context anchor
Rv3520c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000998|Rv0940c| MRFSYAEAMTDFTFYIPLAKAAEAAGYSSMTIPDSIAYPFESDSKYPYTPDGNREFMDGKPFIETFVLTAALGAVTTRLRFNFFVLKLPIRPPALVAKQAGSLAALIGNRVGLGVGTSPWPEDYELMGVPFAKRGKRIDECIEIVRGLTTGDYFEFHGEFYDIPKTKMTPAPTQPIPILVGGHADAALRRAARADGWMHGGGDPDELDRLIARVKRLREEAGKTSPFEIHVISLDGFTVDGVKRLEDKGVTDVIVGFRVPYTMGPDTEPLQTKIRNLEMFAENVIAKV