Rv1786 Resolved · high auto-curated
H37Rv Rv1786 · MTBC0 mtbc0_001899 ·
67 aa · 2042839–2043042 (+) ·
RefSeq NP_216302.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ferredoxin |
|---|---|
| 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 |
O53937
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ferredoxin FdxE |
| Curated function | Ferredoxin that is the redox partner of cytochrome CYP143, a cytochrome P450 encoded by an adjacent gene. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | 4Fe-4S single cluster domain of Ferredoxin I |
| Orthologous group | COG1141 |
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 | 0.299 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 | 1.4e-14 | 3–60 | 4Fe-4S single cluster domain |
Fer4_13 | PF13370.12 | 6.8e-08 | 6–58 | 4Fe-4S single cluster domain of Ferredoxin I |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cyp143 (cytochrome P450 Cyp143), high confidence from genomic context alone (score 743 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1785c cyp143 |
cytochrome P450 Cyp143 | 884 | 743 ctx | neighborhood:707 textmining:569 |
Rv3060c |
GntR family transcriptional regulator | 623 | 623 ctx | cooccurence:622 |
Rv0138 hyp |
hypothetical protein | 583 | 584 ctx | cooccurence:580 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 599 | 539 ctx | cooccurence:539 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 580 | 518 ctx | cooccurence:518 |
Rv3519 hyp |
hypothetical protein | 495 | 495 ctx | cooccurence:479 |
Rv3061c fadE22 |
acyl-CoA dehydrogenase FadE22 | 483 | 483 ctx | cooccurence:480 |
Rv0771 |
4-carboxymuconolactone decarboxylase | 479 | 479 ctx | cooccurence:476 |
Rv1874 hyp |
hypothetical protein | 462 | 462 ctx | cooccurence:462 |
Rv1787 PPE25 |
PPE family protein PPE25 | 453 | 453 ctx | neighborhood:452 |
Rv1006 hyp |
hypothetical protein | 450 | 450 ctx | cooccurence:447 |
Rv1868 hyp |
hypothetical protein | 448 | 449 ctx | cooccurence:443 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 651 | 411 ctx | cooccurence:411 textmining:433 |
Rv3503c fdxD |
ferredoxin FdxD | 543 | 300 | |
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 577 | 277 | textmining:439 |
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
- MTBC0 PGAP product: ferredoxin
- Pfam (hmmscan --cut_ga): Fer4_15 PF13459.12 (E=1e-14), Fer4_13 PF13370.12 (E=7e-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_216302.1)
- 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 O53937 (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 —
22 functional partner(s); context anchor
cyp143 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001899|Rv1786| MKVRLDPSRCVGHAQCYAVDPDLFPIDDSGNSILAEHEVRPEDMQLTRDGVAACPEMALILEEDDAD