Rv0492c Family assigned · medium auto-curated
H37Rv Rv0492c · MTBC0 mtbc0_000517 ·
629 aa · 584830–586719 (-) ·
RefSeq NP_215006.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GMC-type oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | GMC family oxidoreductase |
| Revised (this work) | GMC family oxidoreductase. Pfam: FAD_binding_3 (PF01494.26), FAD_binding_2 (PF00890.31), NAD_binding_8 (PF13450.13), GMC_oxred_N (PF00732.26), GMC_oxred_C (PF05199.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMV7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized GMC-type oxidoreductase Rv0492c |
| EC (curated) |
EC 1.1.-.-
|
UniProt still lists this protein as Uncharacterized GMC-type oxidoreductase Rv0492c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | oxidoreductase |
| Orthologous group | COG2303 |
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | 1.952 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 10 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 |
|---|---|---|---|---|
FAD_binding_3 | PF01494.26 | 1.1e-05 | 147–216 | FAD binding domain |
FAD_binding_2 | PF00890.31 | 1.5e-04 | 148–179 | FAD binding domain |
NAD_binding_8 | PF13450.13 | 1.1e-04 | 151–180 | NAD(P)-binding Rossmann-like domain |
GMC_oxred_N | PF00732.26 | 1.6e-62 | 196–408 | GMC oxidoreductase |
GMC_oxred_C | PF05199.20 | 9.2e-18 | 496–614 | GMC oxidoreductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0494 (HTH-type transcriptional regulator), high confidence from genomic context alone (score 741 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0493c hyp |
hypothetical protein | 976 | 976 ctx | neighborhood:881 cooccurence:770 |
Rv0492A hyp |
hypothetical protein | 932 | 933 ctx | neighborhood:881 coexpression:458 |
Rv1691 hyp |
hypothetical protein | 799 | 791 | experimental:411 database:583 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 784 | 773 | experimental:762 |
Rv1973 |
Mce associated membrane protein | 770 | 761 | database:536 |
Rv1972 |
Mce associated membrane protein | 765 | 756 | database:536 |
Rv3529c hyp |
hypothetical protein | 756 | 745 | experimental:411 database:583 |
Rv2267c stf3 hyp |
hypothetical protein | 755 | 745 | experimental:411 database:583 |
Rv0494 |
HTH-type transcriptional regulator | 741 | 741 ctx | neighborhood:622 |
Rv2328 PE23 |
PE family protein PE23 | 739 | 729 | database:573 |
Rv3812 PE_PGRS62 |
PE-PGRS family protein PE_PGRS62 | 739 | 729 | database:573 |
Rv3036c TB22.2 hyp |
hypothetical protein | 739 | 729 | database:573 |
Rv0832 PE_PGRS12 |
PE-PGRS family protein PE_PGRS12 | 739 | 729 | database:573 |
Rv3492c |
Mce associated protein | 692 | 680 | database:536 |
Rv0200 |
transmembrane protein | 692 | 680 | database:536 |
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: GMC-type oxidoreductase
- MTBC0 PGAP product: GMC family oxidoreductase
- Pfam (hmmscan --cut_ga): FAD_binding_3 PF01494.26 (E=1e-05), FAD_binding_2 PF00890.31 (E=1e-04), NAD_binding_8 PF13450.13 (E=1e-04), GMC_oxred_N PF00732.26 (E=2e-62), GMC_oxred_C PF05199.20 (E=9e-18)
- (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_215006.2)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_3 (PF01494.26), FAD_binding_2 (PF00890.31), NAD_binding_8 (PF13450.13), GMC_oxred_N (PF00732.26), GMC_oxred_C (PF05199.20)
- 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
COG2303 - Curated reference: UniProt P9WMV7 (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 —
31 functional partner(s); context anchor
Rv0494 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000517|Rv0492c| MSRLADRAKSYPLASFGAALLPPELGGPLPAQFVQRVDRYVTRLPATSRFAVRAGLASLAAASYLTTGRSLPRLHPDERARVLHRIAALSPEVAAAVEGLKAIVLLANGADTYAHELLARAQEHDAARPDAELTVILSADSPSVTRADAVVVGSGAGGAMVARTLARAGLDVVVLEEGRRWTVEEFRSTHPVDRYAGLYRGAGATVALGRPAVVLPMGRAVGGTTVVNSGTCFRPSLAVQRRWRDEFGLGLADPDQLGRRLDDAEQTLRVAPVPLEIMGRNGRLLLQAAKSLGWRAAPIPRNAPGCRGCCQCAIGCPSNAKFGVHLNALPQACAAGARIISWARVERILHRAGRAYGVRARRPDGTTLDVLADAVVVAAGATETPGLLRRSGLGGHPRLGHNLALHPATMLAGLFDDDVFAWRGVLQSAAVHEFHESDGVLIEATSTPPGMGSMVFPGYGAELLRWLDRAPQIATFGAMVADRGVGTVRSVRGETVVRYDIAPGEIAKLRVALQAIGRLLFAAGAVEVLTGIPGAPPMRSLPELQDVLRRANPRSLHLAAFHPTGTAAAGADEQLCPVDATGRLRGVEGVWVADASILPSCPEVNPQLSIMAMALAVADQTVAKVVGVR