Rv1260 Family assigned · medium auto-curated
H37Rv Rv1260 · MTBC0 mtbc0_001349 ·
372 aa · 1416684–1417802 (+) ·
RefSeq NP_215776.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | FAD-binding protein |
| Revised (this work) | FAD-binding protein. Pfam: FAD_binding_3 (PF01494.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM51
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1260 |
UniProt still lists this protein as Uncharacterized protein Rv1260; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversionH Coenzyme transport and metabolism
|
|---|---|
| eggNOG description | oxidoreductase |
| Orthologous group | COG0654 |
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) pseudogene candidate
| pN/pS | 1.272 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 17.54% of strains (25465) · 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_3 | PF01494.26 | 1.8e-21 | 3–319 | FAD binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: udgB (uracil DNA glycosylase), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1259 udgB |
uracil DNA glycosylase | 882 | 883 ctx | neighborhood:881 |
Rv1258c tap |
multidrug-efflux transporter | 774 | 766 ctx | neighborhood:760 |
Rv1814 erg3 |
membrane-bound C-5 sterol desaturase | 639 | 611 | coexpression:401 |
Rv1257c |
oxidoreductase | 618 | 603 ctx | neighborhood:585 |
Rv1256c cyp130 |
cytochrome P450 Cyp130 | 583 | 567 ctx | neighborhood:407 |
Rv1879 hyp |
hypothetical protein | 497 | 472 | |
Rv1215c hyp |
hypothetical protein | 466 | 466 ctx | cooccurence:460 |
Rv1745c idi |
isopentenyl-diphosphate delta-isomerase | 481 | 440 | coexpression:440 |
Rv2946c pks1 |
polyketide synthase | 568 | 436 | |
Rv2048c pks12 |
polyketide synthase | 513 | 421 | |
Rv1255c |
HTH-type transcriptional regulator | 414 | 409 ctx | neighborhood:407 |
Rv3377c |
type B diterpene cyclase | 447 | 403 | coexpression:401 |
Rv3121 cyp141 |
cytochrome P450 Cyp141 | 409 | 387 | |
Rv1661 pks7 |
polyketide synthase | 434 | 369 | |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 456 | 352 |
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 protein
- Pfam (hmmscan --cut_ga): FAD_binding_3 PF01494.26 (E=2e-21)
- (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_215776.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_3 (PF01494.26)
- 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
COG0654 - Curated reference: UniProt P9WM51 (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 —
19 functional partner(s); context anchor
udgB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001349|Rv1260| MKTVVVSGASVAGTAAAYWLGRHGYSVTMVERHPGLRPGGQAIDVRGPALDVLERMGLLAAAQEHKTRIRGASFVDRDGNELFRDTESTPTGGPVNSPDIELLRDDLVELLYGATQPSVEYLFDDSISTLQDDGDSVRVTFERAAAREFDLVIGADGLHSNVRRLVFGPEEQFVKRLGTHAAIFTVPNFLELDYWQTWHYGDSTMAGVYSARNNTEARAALAFMDTELRIDYRDTEAQFAELQRRMAEDGWVRAQLLHYMRSAPDFYFDEMSQILMDRWSRGRVALVGDAGYCCSPLSGQGTSVALLGAYILAGELKAAGDDYQLGFANYHAEFHGFVERNQWLVSDNIPGGAPIPQEEFERIVHSITIKDY