fdxD Resolved · high auto-curated
H37Rv Rv3503c · MTBC0 mtbc0_003718 ·
63 aa · 3946647–3946838 (-) ·
RefSeq NP_218020.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ferredoxin FdxD |
|---|---|
| MTBC0 PGAP re-annotation | ferredoxin |
| Revised (this work) | Ferredoxin. Pfam: Fer4_15 (PF13459.12), Fer4_13 (PF13370.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X7H4
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 | fdxD |
| eggNOG description | ferredoxin |
| Orthologous group | COG1141 |
| KEGG orthology |
K05337
|
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 | 0.158 · 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 |
|---|---|---|---|---|
Fer4_15 | PF13459.12 | 5.1e-14 | 3–59 | 4Fe-4S single cluster domain |
Fer4_13 | PF13370.12 | 1.2e-12 | 5–59 | 4Fe-4S single cluster domain of Ferredoxin I |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3502c (3-oxoacyl-ACP reductase), high confidence from genomic context alone (score 726 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3502c |
3-oxoacyl-ACP reductase | 726 | 726 ctx | neighborhood:717 |
Rv0310c hyp |
hypothetical protein | 545 | 545 ctx | cooccurence:545 |
Rv3504 fadE26 |
acyl-CoA dehydrogenase FadE26 | 515 | 515 ctx | neighborhood:500 |
Rv3687c rsfB |
anti-anti-sigma factor RsfB | 489 | 490 ctx | cooccurence:487 |
Rv0311 hyp |
hypothetical protein | 481 | 482 ctx | cooccurence:459 |
Rv0926c hyp |
hypothetical protein | 480 | 481 ctx | cooccurence:479 |
Rv3505 fadE27 |
acyl-CoA dehydrogenase FadE27 | 464 | 464 ctx | neighborhood:457 |
Rv0763c |
ferredoxin | 886 | 443 ctx | cooccurence:439 textmining:805 |
Rv0762c hyp |
hypothetical protein | 434 | 434 ctx | cooccurence:408 |
Rv2600 |
integral membrane protein | 419 | 420 ctx | cooccurence:418 |
Rv3501c yrbE4A |
integral membrane protein | 413 | 413 ctx | neighborhood:410 |
Rv0764c cyp51 |
lanosterol 14-alpha demethylase | 675 | 357 | textmining:516 |
Rv1786 |
ferredoxin | 543 | 300 | |
Rv3059 cyp136 |
cytochrome P450 Cyp136 | 501 | 204 | textmining:400 |
Rv2266 cyp124 |
cytochrome P450 Cyp124 | 594 | 199 | textmining:515 |
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 FdxD
- MTBC0 PGAP product: ferredoxin
- Pfam (hmmscan --cut_ga): Fer4_15 PF13459.12 (E=5e-14), Fer4_13 PF13370.12 (E=1e-12)
- (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_218020.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fer4_15 (PF13459.12), Fer4_13 (PF13370.12)
- 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
COG1141 - Curated reference: UniProt I6X7H4 (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 —
26 functional partner(s); context anchor
Rv3502c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003718|Rv3503c|fdxD MRVIVDRDRCEGNAVCLGIAPDIFDLDDEDYAVVKTDPIPVDQEDLAEQAIAECPRAALSRGE