fadE31 Family assigned · medium auto-curated
H37Rv Rv3562 · MTBC0 mtbc0_003779 ·
377 aa · 4026838–4027971 (+) ·
RefSeq NP_218079.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyl-CoA dehydrogenase FadE31 |
|---|---|
| MTBC0 PGAP re-annotation | acyl-CoA dehydrogenase family protein |
| Revised (this work) | Acyl-CoA dehydrogenase family protein. Pfam: Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_M (PF02770.25), Acyl-CoA_dh_1 (PF00441.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YGH7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable acyl-CoA dehydrogenase FadE31 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | fadE31 |
| eggNOG description | acyl-CoA dehydrogenase |
| Orthologous group | COG1960 |
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 | 0.125 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 3 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 |
|---|---|---|---|---|
Acyl-CoA_dh_N | PF02771.22 | 2.3e-17 | 7–120 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_M | PF02770.25 | 5.7e-19 | 124–218 | Acyl-CoA dehydrogenase, middle domain |
Acyl-CoA_dh_1 | PF00441.30 | 8.7e-18 | 230–370 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE33 (acyl-CoA dehydrogenase FadE33), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3564 fadE33 |
acyl-CoA dehydrogenase FadE33 | 999 | 996 ctx | neighborhood:881 cooccurence:768 coexpression:800 textmining:825 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 998 | 994 ctx | neighborhood:881 cooccurence:773 coexpression:804 textmining:820 |
Rv3559c |
oxidoreductase | 988 | 980 ctx | neighborhood:788 cooccurence:505 coexpression:736 textmining:478 |
Rv3561 fadD3 |
fatty-acid--CoA ligase FadD3 | 990 | 973 ctx | neighborhood:801 coexpression:838 textmining:676 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 966 | 964 ctx | neighborhood:788 coexpression:813 |
Rv3551 |
CoA-transferase subunit alpha | 931 | 929 ctx | cooccurence:730 coexpression:742 |
Rv3565 aspB |
aspartate aminotransferase AspB | 945 | 910 ctx | neighborhood:881 textmining:423 |
Rv3552 |
CoA-transferase subunit beta | 904 | 901 ctx | cooccurence:736 coexpression:631 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 962 | 892 ctx | cooccurence:641 coexpression:538 textmining:667 |
Rv3541c chsH1 hyp |
hypothetical protein | 853 | 849 ctx | cooccurence:713 |
Rv3553 |
oxidoreductase | 843 | 836 | coexpression:737 |
Rv3540c ltp2 |
lipid transfer protein | 843 | 834 ctx | cooccurence:716 |
Rv1933c fadE18 |
acyl-CoA dehydrogenase FadE18 | 859 | 816 ctx | cooccurence:738 |
Rv3522 ltp4 |
lipid transfer protein | 834 | 802 ctx | cooccurence:664 |
Rv0860 fadB |
fatty oxidation protein FadB | 803 | 788 | coexpression:647 |
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: acyl-CoA dehydrogenase FadE31
- MTBC0 PGAP product: acyl-CoA dehydrogenase family protein
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=2e-17), Acyl-CoA_dh_M PF02770.25 (E=6e-19), Acyl-CoA_dh_1 PF00441.30 (E=9e-18)
- (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_218079.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_M (PF02770.25), Acyl-CoA_dh_1 (PF00441.30)
- 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
COG1960 - Curated reference: UniProt I6YGH7 (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 —
135 functional partner(s); context anchor
fadE33 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003779|Rv3562|fadE31 MDLNFDDETLAFQAEVREFLAANAASIPTKSYDNAEGFAQHRYWDRVLFDAGLSVITWPAKYGGRDAPLLHWIVFEEEYFRAGAPGRASANGTSMLAPTLFAHGTAEQLDRILPKMASGEQIWAQAWSEPESGSDLASLRSTASKVDGGWLLNGQKIWSSRAPFADMGFGLFRSDPAVERHRGLTYFMFDLKAKGVTVRPIAQLGGDTGFGEIFLDDVFVPDRDVIGAPNDGWRAAMSTSSNERGMSLRSPARFLASAERLVQLWKDRGSPPEFADRVADAWIKAQAYRLQTFGTVTRLAAGGELGAESSVTKVFWSELDVHLHQTALDLRGADGELAGPWTEGLLFALGGPIYAGTNEIQRNIIAERLLGLPREKT