fdhF Family assigned · medium auto-curated
H37Rv Rv2900c · MTBC0 mtbc0_003082 ·
779 aa · 3230235–3232574 (-) ·
RefSeq NP_217416.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | formate dehydrogenase subunit alpha FdhF |
|---|---|
| MTBC0 PGAP re-annotation | FdhF/YdeP family oxidoreductase |
| Revised (this work) | FdhF/YdeP family oxidoreductase. Pfam: Molybdopterin (PF00384.28), Molydop_binding (PF01568.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJP9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized oxidoreductase Rv2900c |
| EC (curated) |
EC 1.-.-.-
|
UniProt still lists this protein as Uncharacterized oxidoreductase Rv2900c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | fdhF |
| eggNOG description | Belongs to the prokaryotic molybdopterin-containing oxidoreductase family |
| Orthologous group | COG0243 |
| EC number |
EC 1.17.1.9
|
| KEGG orthology |
K00123
|
| KEGG pathways |
map00630, map00680, map01100, map01120, map01200
|
| 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 | 1.002 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 9 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 |
|---|---|---|---|---|
Molybdopterin | PF00384.28 | 6.8e-23 | 132–506 | Molybdopterin oxidoreductase |
Molydop_binding | PF01568.28 | 9.7e-07 | 660–716 | Molydopterin dinucleotide binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fdhD (formate dehydrogenase accessory protein FdhD), high confidence from genomic context alone (score 972 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2899c fdhD |
formate dehydrogenase accessory protein FdhD | 988 | 972 ctx | neighborhood:882 cooccurence:705 textmining:596 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 818 | 799 | experimental:774 |
Rv0685 tuf |
elongation factor Tu | 809 | 794 | experimental:783 |
Rv2901c hyp |
hypothetical protein | 674 | 675 ctx | neighborhood:670 |
Rv2898c hyp |
hypothetical protein | 577 | 576 ctx | neighborhood:570 |
Rv2897c hyp |
hypothetical protein | 577 | 576 ctx | neighborhood:570 |
Rv3859c gltB |
glutamate synthase large subunit | 769 | 575 | experimental:420 textmining:481 |
Rv2896c dprA hyp |
hypothetical protein | 575 | 574 ctx | neighborhood:570 |
Rv2902c rnhB |
ribonuclease HII | 532 | 533 ctx | neighborhood:512 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 564 | 518 | experimental:484 |
Rv2903c lepB |
signal peptidase | 496 | 497 ctx | neighborhood:487 |
Rv2895c viuB |
mycobactin utilization protein ViuB | 480 | 480 | |
Rv1162 narH |
nitrate reductase subunit beta | 653 | 457 | experimental:431 |
Rv3273 |
transmembrane carbonic anhydrase | 413 | 384 | |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 411 | 348 |
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: formate dehydrogenase subunit alpha FdhF
- MTBC0 PGAP product: FdhF/YdeP family oxidoreductase
- Pfam (hmmscan --cut_ga): Molybdopterin PF00384.28 (E=7e-23), Molydop_binding PF01568.28 (E=1e-06)
- (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_217416.1)
- Domains: Pfam-A via hmmscan --cut_ga — Molybdopterin (PF00384.28), Molydop_binding (PF01568.28)
- 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
COG0243 - Curated reference: UniProt P9WJP9 (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 —
29 functional partner(s); context anchor
fdhD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003082|Rv2900c|fdhF MYVEAVRWQRSAASRDVLADYDEQAVTVAPRKREAAGVRAVMVSLQRGMQQMGALRTAAALARLNQRNGFDCPGCAWPEEPGGRKLAEFCENGAKAVAEEATKRTVTAEFFARHSVAELSAKPEYWLSQQGRLAHPMVLRPGDDHYRPISWDAAYQLIAEQLNGLDSPDRAVFYTSGRTSNEAAFCYQLLVRSFGTNNLPDCSNMCHESSGAALTDSIGIGKGSVTIGDVEHADLIVIAGQNPGTNHPRMLSVLGKAKANGAKIIAVNPLPEAGLIRFKDPQKVNGVVGHGIPIADEFVQIRLGGDMALFAGLGRLLLEAEERVPGSVVDRSFVDNHCAGFDGYRRRTLQVGLDTVMDATGIELAQLQRVAAMLMASQRTVICWAMGLTQHAHAVATIGEVTNVLLLRGMIGKPGAGVCPVRGHSNVQGDRTMGIWEKMPEQFLAALDREFGITSPRAHGFDTVAAIRAMRDGRVSVFMGMGGNFASATPDTAVTEAALRRCALTVQVSTKLNRSHLVHGATALILPTLGRTDRDTRNGRKQLVSVEDSMSMVHLSRGSLHPPSDQVRSEVQIICQLARALFGPGHPVPWERFADDYDTIRDAIAAVVPGCDDYNHKVRVPDGFQLPHPPRDAREFRTSTGKANFAVNPLQWVPVPPGRLVLQTLRSHDQYNTTIYGLDDRYRGVKGGRRVVFINPADIETFGLTAGDRVDLVSEWTDGQGGLQERRAKDFLVVAYSTPVGNAAAYYPETNPLVPLDHTAAQSNTPVSKAIIVRLEPTA