Rv0161 Resolved · high auto-curated
H37Rv Rv0161 · MTBC0 mtbc0_000174 ·
449 aa · 190953–192302 (+) ·
RefSeq NP_214675.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | FAD-binding oxidoreductase |
| Revised (this work) | FAD-binding oxidoreductase. Pfam: FAD_binding_4 (PF01565.29), FAD-oxidase_C (PF02913.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07406
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | FAD linked |
| Orthologous group | COG0277 |
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 | 0.257 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 19 synonymous, 13 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.34% of strains (499) · 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 |
|---|---|---|---|---|
FAD_binding_4 | PF01565.29 | 3.7e-35 | 37–173 | FAD binding domain |
FAD-oxidase_C | PF02913.25 | 4.9e-56 | 211–444 | FAD linked oxidases, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE4 (PE family protein PE4), medium confidence from genomic context alone (score 559 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1551 plsB1 |
acyltransferase PlsB | 622 | 606 | database:549 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 621 | 605 | database:549 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 609 | 590 | |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 599 | 580 | |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 590 | 570 | database:552 |
Rv0160c PE4 |
PE family protein PE4 | 559 | 559 ctx | neighborhood:559 |
Rv1310 atpD |
ATP synthase subunit beta | 573 | 557 | database:538 |
Rv1305 atpE |
ATP synthase subunit C | 538 | 539 | database:526 |
Rv3633 hyp |
hypothetical protein | 547 | 531 | database:463 |
Rv1501 hyp |
hypothetical protein | 543 | 526 | database:463 |
Rv0694 mftD |
mycofactocin system heme/flavin oxidoreductase MftD | 543 | 514 | |
Rv1872c lldD2 |
L-lactate dehydrogenase | 542 | 514 | |
Rv0440 groEL2 |
molecular chaperone GroEL | 470 | 450 | |
Rv3417c groEL1 |
chaperonin GroEL | 469 | 450 | |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 468 | 449 | database:434 |
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: FAD-binding oxidoreductase
- Pfam (hmmscan --cut_ga): FAD_binding_4 PF01565.29 (E=4e-35), FAD-oxidase_C PF02913.25 (E=5e-56)
- (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_214675.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_4 (PF01565.29), FAD-oxidase_C (PF02913.25)
- 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
COG0277 - Curated reference: UniProt O07406 (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 —
34 functional partner(s); context anchor
PE4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000174|Rv0161| MLTSLVSAVGSHHVTTDPDVLAGRSVDHTGRYRGRASALVRPGSAEEVAEVLRVCRDAGAYVTVQGGRTSLVAGTVPEHDDVLLSTERLCVVSDVDTVERRIEIGAGVTLAAVQHAASTAGLVFGVDLSARDTATVGGMASTNAGGLRTVRYGNMGEQVVGLDVALPDGTVLRRHSRVRRDNTGYDLPALFVGAEGTLGVITALDLRLHPTPSHRVTAVCGFAELAALVDAGRMFRDVEGIAALELIDGRAAALTREHLGVRPPVEADWLLLVELAADHDQTDRLADLLGGARMCGEPAVGVDAAAQQRLWRTRESLAEVLGVYGPPLKFDVSLPLSAISGFARDAVALVHRHVPDSPEALPLLFGHIGEGNLHLNVLRCPPDREPALYAKMMGLIAECGGNVSSEHGVGSRKRAYLGMSRQANDVAAMRRVKAALDPTGYLNAAVLFD