fdxC Family assigned · medium auto-curated
H37Rv Rv1177 · MTBC0 mtbc0_001266 ·
108 aa · 1317446–1317772 (+) ·
RefSeq NP_215693.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ferredoxin FdxC |
|---|---|
| MTBC0 PGAP re-annotation | ferredoxin family protein |
| Revised (this work) | Ferredoxin family protein. Pfam: Fer4 (PF00037.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50433
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ferredoxin |
| Curated function | Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | fdxA |
| eggNOG description | ferredoxin |
| Orthologous group | COG1146 |
| KEGG orthology |
K05524
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
Fer4 | PF00037.33 | 2.1e-08 | 34–55 | 4Fe-4S binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dapC (aminotransferase), high confidence from genomic context alone (score 903 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1178 dapC |
aminotransferase | 950 | 903 ctx | neighborhood:833 fusion:405 textmining:510 |
Rv0824c desA1 |
acyl-ACP desaturase DesA | 896 | 798 | coexpression:798 textmining:511 |
Rv1094 desA2 |
acyl-ACP desaturase DesA | 883 | 770 | coexpression:770 textmining:516 |
Rv0823c dusB |
tRNA-dihydrouridine synthase | 767 | 767 | coexpression:767 |
Rv1176c hyp |
hypothetical protein | 731 | 732 ctx | neighborhood:731 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 805 | 726 | coexpression:687 |
Rv0066c icd2 |
isocitrate dehydrogenase | 714 | 695 | coexpression:683 |
Rv1240 mdh |
malate dehydrogenase | 709 | 692 | coexpression:680 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 793 | 681 ctx | neighborhood:522 |
Rv3106 fprA |
NADPH-ferredoxin reductase FprA | 869 | 486 | textmining:756 |
Rv2454c korB |
2-oxoglutarate oxidoreductase subunit KorB | 487 | 437 | coexpression:416 |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 492 | 427 | |
Rv3797 fadE35 |
acyl-CoA dehydrogenase FadE35 | 404 | 403 ctx | neighborhood:403 |
Rv3858c gltD |
glutamate synthase small subunit | 415 | 382 | |
Rv3110 moaB1 |
pterin-4-alpha-carbinolamine dehydratase | 474 | 150 | textmining:407 |
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: ferredoxin FdxC
- MTBC0 PGAP product: ferredoxin family protein
- Pfam (hmmscan --cut_ga): Fer4 PF00037.33 (E=2e-08)
- (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_215693.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fer4 (PF00037.33)
- 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
COG1146 - Curated reference: UniProt O50433 (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 —
22 functional partner(s); context anchor
dapC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001266|Rv1177|fdxC MTYTIAEPCVDIKDKACIEECPVDCIYEGARMLYIHPDECVDCGACEPVCPVEAIFYEDDVPEQWSHYTQINADFFAELGSPGGAAKVGMTENDPQAVKDLAPQSEDA