Rv1257c Family assigned · medium auto-curated
H37Rv Rv1257c · MTBC0 mtbc0_001346 ·
455 aa · 1413161–1414528 (-) ·
RefSeq NP_215773.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | FAD-linked oxidase C-terminal domain-containing protein |
| Revised (this work) | FAD-linked oxidase C-terminal domain-containing protein. 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 |
Q11061
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | FAD linked |
| Orthologous group | COG0277 |
| EC number |
EC 1.1.2.4, EC 1.1.3.15
|
| KEGG orthology |
K00102, K00104
|
| KEGG pathways |
map00620, map00630, map01100, map01110, map01120, map01130
|
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 | 0.365 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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_4 | PF01565.29 | 1.4e-42 | 41–179 | FAD binding domain |
FAD-oxidase_C | PF02913.25 | 6.8e-69 | 218–452 | FAD linked oxidases, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tap (multidrug-efflux transporter), high confidence from genomic context alone (score 912 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2280 |
Rv2280, (MTCY339.30c), len: 459 aa. Probable dehydrogenase. Similar to D-lactate dehydrogenase (cytochrome) precursor e.g. G1061264 (587 aa) | 920 | 920 | database:900 |
Rv1837c glcB |
malate synthase | 918 | 914 | database:900 |
Rv1258c tap |
multidrug-efflux transporter | 911 | 912 ctx | neighborhood:881 |
Rv0467 icl1 |
isocitrate lyase | 904 | 901 | database:900 |
Rv1916 aceAb |
isocitrate lyase AceAb | 903 | 900 | database:900 |
Rv1915 aceAa |
isocitrate lyase AceAa | 903 | 900 | database:900 |
Rv2725c hflX |
GTP-binding protein HflX | 862 | 862 | coexpression:860 |
Rv0337c aspC |
aspartate aminotransferase | 829 | 823 | coexpression:821 |
Rv1905c aao |
D-amino acid oxidase | 809 | 803 | database:800 |
Rv1256c cyp130 |
cytochrome P450 Cyp130 | 778 | 777 ctx | neighborhood:736 |
Rv1473 |
macrolide ABC transporter ATP-binding protein | 751 | 751 | coexpression:751 |
Rv1255c |
HTH-type transcriptional regulator | 743 | 743 ctx | neighborhood:732 |
Rv2415c hyp |
hypothetical protein | 732 | 733 | coexpression:732 |
Rv1551 plsB1 |
acyltransferase PlsB | 622 | 606 | database:549 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 622 | 606 | database:549 |
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-linked oxidase C-terminal domain-containing protein
- Pfam (hmmscan --cut_ga): FAD_binding_4 PF01565.29 (E=1e-42), FAD-oxidase_C PF02913.25 (E=7e-69)
- (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_215773.1)
- 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 Q11061 (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 —
45 functional partner(s); context anchor
tap - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001346|Rv1257c| MNTDVLAGLMAELPEGMVVTDPAVTDGYRQDRAFDPSAGKPLAIIRPRRTEEVQTVLRWASANQVPVVTRGAGSGLSGGATALDGGIVLSTEKMRDITVDPVTRTAVCQPGLYNAEVKEAAAEHGLWYPPDPSSFEICSIGGNIATNAGGLCCVKYGVTGDYVLGMQVVLANGTAVRLGGPRLKDVAGLSLTKLFVGSEGTLGVITEVTLRLLPAQNASSIVVASFGSVQAAVDAVLGVTGRLRPAMLEFMDSVAINAVEDTLRMDLDRDAAAMLVAGSDERGRAATEDAAVMAAVFAENGAIDVFSTDDPDEGEAFIAARRFAIPAVESKGALLLEDVGVPLPALGELVTGIARIAEERNLMISVIAHAGDGNTHPLLVYDPADAAMLERAHLAYGEIMDLAVGLGGTITGEHGVGRLKRPWLAGYLGPDVLALNQRIKQALDPQGILNPGSAI