fixA Family assigned · medium auto-curated
H37Rv Rv3029c · MTBC0 mtbc0_003220 ·
266 aa · 3409380–3410180 (-) ·
RefSeq NP_217545.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | electron transfer flavoprotein subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | electron transfer flavoprotein subunit beta/FixA family protein |
| Revised (this work) | Electron transfer flavoprotein subunit beta/FixA family protein. Pfam: ETF (PF01012.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNG7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Electron transfer flavoprotein subunit beta |
| Curated function | The electron transfer flavoprotein serves as a specific electron acceptor for other dehydrogenases. It transfers the electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase (ETF dehydrogenase) (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | etfB |
| eggNOG description | Electron transfer flavoprotein |
| Orthologous group | COG2086 |
| KEGG orthology |
K03521
|
| Gene Ontology (25) |
GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006091, GO:0008150, GO:0008152 +13 more
|
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 | 0.169 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 2 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 |
|---|---|---|---|---|
ETF | PF01012.28 | 6.2e-36 | 25–214 | Electron transfer flavoprotein domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fixB (electron transfer flavoprotein subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 999 | 1000 ctx | neighborhood:827 fusion:807 cooccurence:774 coexpression:957 experimental:928 database:844 textmining:639 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 996 | 995 | experimental:994 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 | 905 | 901 ctx | cooccurence:729 coexpression:406 experimental:418 |
Rv3274c fadE25 |
acyl-CoA dehydrogenase | 897 | 893 ctx | cooccurence:694 coexpression:432 experimental:418 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 865 | 860 ctx | cooccurence:615 coexpression:408 experimental:418 |
Rv2789c fadE21 |
acyl-CoA dehydrogenase FadE21 | 851 | 845 ctx | cooccurence:573 coexpression:410 experimental:418 |
Rv1933c fadE18 |
acyl-CoA dehydrogenase FadE18 | 846 | 840 ctx | cooccurence:563 coexpression:406 experimental:418 |
Rv0215c fadE3 |
Rv0215c, (MTCY08D5.10c), len: 357 aa. Probable fadE3, acyl- dehydrogenase, similar to many e.g. ACDB_BACSU|P45857 acyl-CoA dehydrogenase fro | 839 | 833 ctx | cooccurence:542 coexpression:406 experimental:418 |
Rv3139 fadE24 |
acyl-CoA dehydrogenase | 834 | 827 ctx | cooccurence:523 coexpression:410 experimental:418 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 848 | 819 ctx | cooccurence:499 coexpression:413 experimental:418 |
Rv2724c fadE20 |
acyl-CoA dehydrogenase FadE20 | 819 | 812 ctx | cooccurence:483 coexpression:408 experimental:418 |
Rv0972c fadE12 |
acyl-CoA dehydrogenase fadE12 | 815 | 808 ctx | cooccurence:470 coexpression:410 experimental:418 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 833 | 800 | coexpression:410 experimental:652 |
Rv3505 fadE27 |
acyl-CoA dehydrogenase FadE27 | 806 | 798 ctx | cooccurence:450 coexpression:404 experimental:418 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 793 | 785 ctx | cooccurence:407 coexpression:410 experimental:418 |
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 flavoprotein subunit beta
- MTBC0 PGAP product: electron transfer flavoprotein subunit beta/FixA family protein
- Pfam (hmmscan --cut_ga): ETF PF01012.28 (E=6e-36)
- (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_217545.1)
- Domains: Pfam-A via hmmscan --cut_ga — ETF (PF01012.28)
- 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
COG2086 - Curated reference: UniProt P9WNG7 (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 —
138 functional partner(s); context anchor
fixB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003220|Rv3029c|fixA MTNIVVLIKQVPDTWSERKLTDGDFTLDREAADAVLDEINERAVEEALQIREKEAADGIEGSVTVLTAGPERATEAIRKALSMGADKAVHLKDDGMHGSDVIQTGWALARALGTIEGTELVIAGNESTDGVGGAVPAIIAEYLGLPQLTHLRKVSIEGGKITGERETDEGVFTLEATLPAVISVNEKINEPRFPSFKGIMAAKKKEVTVLTLAEIGVESDEVGLANAGSTVLASTPKPAKTAGEKVTDEGEGGNQIVQYLVAQKII