fdhD Resolved · high auto-curated
H37Rv Rv2899c · MTBC0 mtbc0_003081 ·
276 aa · 3229405–3230235 (-) ·
RefSeq NP_217415.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | formate dehydrogenase accessory protein FdhD |
|---|---|
| MTBC0 PGAP re-annotation | formate dehydrogenase accessory sulfurtransferase FdhD |
| Revised (this work) | Formate dehydrogenase accessory sulfurtransferase FdhD. Pfam: FdhD-NarQ (PF02634.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNF1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Sulfur carrier protein FdhD |
| Curated function | Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | fdhD |
| eggNOG description | Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH |
| Orthologous group | COG1526 |
| KEGG orthology |
K02379
|
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 | 0.184 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 |
|---|---|---|---|---|
FdhD-NarQ | PF02634.22 | 4.0e-70 | 26–275 | FdhD/NarQ family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fdhF (formate dehydrogenase subunit alpha FdhF), high confidence from genomic context alone (score 972 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2900c fdhF |
formate dehydrogenase subunit alpha FdhF | 988 | 972 ctx | neighborhood:882 cooccurence:705 textmining:596 |
Rv2898c hyp |
hypothetical protein | 729 | 729 ctx | neighborhood:726 |
Rv2897c hyp |
hypothetical protein | 728 | 729 ctx | neighborhood:726 |
Rv2901c hyp |
hypothetical protein | 673 | 674 ctx | neighborhood:670 |
Rv0087 hycE |
formate hydrogenase HycE | 712 | 547 ctx | neighborhood:544 |
Rv2896c dprA hyp |
hypothetical protein | 533 | 533 ctx | neighborhood:531 |
Rv2902c rnhB |
ribonuclease HII | 518 | 519 ctx | neighborhood:512 |
Rv2903c lepB |
signal peptidase | 489 | 489 ctx | neighborhood:487 |
Rv0869c moaA2 |
molybdenum cofactor biosynthesis protein MoaA | 523 | 459 | coexpression:428 |
Rv2453c mobA |
molybdenum cofactor guanylyltransferase | 675 | 456 | textmining:428 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 582 | 455 | |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 516 | 451 | coexpression:420 |
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX | 574 | 401 | |
Rv3025c iscS |
cysteine desulfurase | 535 | 378 | |
Rv0197 |
oxidoreductase | 413 | 350 |
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 accessory protein FdhD
- MTBC0 PGAP product: formate dehydrogenase accessory sulfurtransferase FdhD
- Pfam (hmmscan --cut_ga): FdhD-NarQ PF02634.22 (E=4e-70)
- (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_217415.1)
- Domains: Pfam-A via hmmscan --cut_ga — FdhD-NarQ (PF02634.22)
- 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
COG1526 - Curated reference: UniProt P9WNF1 (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 —
16 functional partner(s); context anchor
fdhF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003081|Rv2899c|fdhD MGYATAHRRVRHLSADQVITRPETLAVEEPLEIRVNGTPVTVTMRTPGSDFELVQGFLLAEGVVAHREDVLTVSYCGRRVEGNATGASTYNVLDVALAPGVKPPDVDVTRTFYTTSSCGVCGKASLQAVSQVSRFAPGGDPATVAADTLKAMPDQLRRAQKVFARTGGLHAAALFGVDGAMLAVREDIGRHNAVDKVIGWAFERDRIPLGASVLLVSGRASFELTQKALMAGIPVLAAVSAPSSLAVSLADASGITLVAFLRGDSMNVYTRADRIT