fdxB Resolved · high auto-curated
H37Rv Rv3554 · MTBC0 mtbc0_003771 ·
685 aa · 4016362–4018419 (+) ·
RefSeq NP_218071.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | electron transfer protein FdxB |
|---|---|
| MTBC0 PGAP re-annotation | fatty acid desaturase |
| Revised (this work) | Fatty acid desaturase. Pfam: FA_desaturase (PF00487.31), FAD_binding_6 (PF00970.31), NAD_binding_1 (PF00175.27), Fer2 (PF00111.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71846
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible electron transfer protein FdxB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | paaE |
| eggNOG description | Oxidoreductase FAD-binding domain |
| Orthologous group | COG1018 |
| KEGG orthology |
K02613
|
| KEGG pathways |
map00360, map01120
|
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 | 0.497 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.42% of strains (611) · clonal |
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 |
|---|---|---|---|---|
FA_desaturase | PF00487.31 | 7.5e-38 | 67–299 | Fatty acid desaturase |
FAD_binding_6 | PF00970.31 | 4.5e-11 | 344–439 | Oxidoreductase FAD-binding domain |
NAD_binding_1 | PF00175.27 | 3.6e-15 | 456–562 | Oxidoreductase NAD-binding domain |
Fer2 | PF00111.33 | 4.4e-15 | 601–675 | 2Fe-2S iron-sulfur cluster binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3553 (oxidoreductase), high confidence from genomic context alone (score 780 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1465 |
nitrogen fixation related protein | 885 | 851 | database:621 |
Rv3025c iscS |
cysteine desulfurase | 867 | 848 | experimental:422 database:621 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 914 | 802 | experimental:759 textmining:586 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 914 | 802 | experimental:759 textmining:586 |
Rv1527c pks5 |
polyketide synthase | 914 | 802 | experimental:759 textmining:586 |
Rv2048c pks12 |
polyketide synthase | 914 | 802 | experimental:759 textmining:586 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 914 | 801 | experimental:759 textmining:586 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 901 | 786 | experimental:430 database:568 textmining:558 |
Rv1663 pks17 |
polyketide synthase | 841 | 781 | experimental:759 |
Rv3553 |
oxidoreductase | 798 | 780 ctx | neighborhood:779 |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 918 | 776 | experimental:430 database:568 textmining:651 |
Rv1666c cyp139 |
cytochrome P450 Cyp139 | 781 | 754 | |
Rv3106 fprA |
NADPH-ferredoxin reductase FprA | 821 | 753 | experimental:430 database:568 |
Rv3858c gltD |
glutamate synthase small subunit | 818 | 752 | experimental:430 database:568 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 787 | 752 | experimental:700 |
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: electron transfer protein FdxB
- MTBC0 PGAP product: fatty acid desaturase
- Pfam (hmmscan --cut_ga): FA_desaturase PF00487.31 (E=7e-38), FAD_binding_6 PF00970.31 (E=4e-11), NAD_binding_1 PF00175.27 (E=4e-15), Fer2 PF00111.33 (E=4e-15)
- (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_218071.1)
- Domains: Pfam-A via hmmscan --cut_ga — FA_desaturase (PF00487.31), FAD_binding_6 (PF00970.31), NAD_binding_1 (PF00175.27), Fer2 (PF00111.33)
- 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
COG1018 - Curated reference: UniProt P71846 (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 —
153 functional partner(s); context anchor
Rv3553 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003771|Rv3554|fdxB MTDACQAEYAIAAMSTVEMDQAAPESAAHHPLPDPGESVPRLALPTIGIFLATLTAFVGSTTAYISGWIPFWVTIPVNAAVTFVMFTVVHDASHYAISSIRWVNGLFGRLAWLFVGPVVAFPAFGYIHIQHHRHSNDDEQDPDTFASHGSLWVLPLRWSMVEYFYIKYYLPRGRSRPVIEVAETLVMMTLFLTGLIVAIVTGNFWTLAIVFLIPQRIGLTVLAWWFDWLPHHGLEDTQRSNRYRATRNRVGAEWLFTPVLLSQNYHLVHHLHPSVPFYRYLRTWRRNEEAYLERNAAISTVFGQQLNPDEYRQWKELNGRLARLLPVRMPARSSSPHAVLHRIPVASVDPITADATLVTFAVPEALRDAFRFEPGQHVTVRTDLGGQGIRRNYSICAPATRAQLRIAVKHIPGGAFSTFVANELKAGDVLELMTPTGRFGTPLDPLHRKHYVGLVAGSGITPVLSILATTLEIETESRFTLIYGNRTKESTMFRAELDRLESRYADRLEILHVLSSEPLHTPELRGRIDRDKLTRWLTSTLRPAGVDEWFICGPLAMATAVRETLIEHGVDSERIHLELFYGFDTPPATRPSYAGATVTFTLSGQRAIFDLVPGDSILEGALGLRSDAPYACMGGACGTCRAKLIEGNVEMDHNFALRKAELDAGYILTCQSHPTTPFVAVDYDA