Rv3094c Family assigned · medium auto-curated
H37Rv Rv3094c · MTBC0 mtbc0_003288 ·
376 aa · 3484125–3485255 (-) ·
RefSeq NP_217610.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| 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_1 (PF00441.30), Acyl-CoA_dh_2 (PF08028.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05773
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Hydroxylase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | Acyl-CoA dehydrogenase, C-terminal domain |
| Orthologous group | COG1960 |
| EC number |
EC 1.14.13.235
|
| KEGG orthology |
K22027
|
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 | 0.727 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 | 1.3e-05 | 12–86 | Acyl-CoA dehydrogenase, N-terminal domain |
Acyl-CoA_dh_1 | PF00441.30 | 3.1e-08 | 222–347 | Acyl-CoA dehydrogenase, C-terminal domain |
Acyl-CoA_dh_2 | PF08028.17 | 8.3e-37 | 224–355 | Acyl-CoA dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3093c (oxidoreductase), high confidence from genomic context alone (score 983 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3093c |
oxidoreductase | 983 | 983 ctx | neighborhood:881 coexpression:865 |
Rv3095 |
HTH-type transcriptional regulator | 984 | 886 ctx | neighborhood:783 coexpression:494 textmining:870 |
Rv0860 fadB |
fatty oxidation protein FadB | 802 | 787 | coexpression:646 |
Rv3092c |
integral membrane protein | 711 | 711 ctx | neighborhood:697 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 666 | 652 | coexpression:409 experimental:419 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 664 | 650 | coexpression:406 experimental:418 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 649 | 634 | |
Rv0675 echA5 |
enoyl-CoA hydratase EchA5 | 647 | 634 | |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 645 | 632 | |
Rv1935c echA13 |
enoyl-CoA hydratase EchA13 | 640 | 627 | |
Rv2679 echA15 |
enoyl-CoA hydratase EchA15 | 636 | 623 | |
Rv2048c pks12 |
polyketide synthase | 623 | 593 | database:459 |
Rv1527c pks5 |
polyketide synthase | 619 | 588 | database:459 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 617 | 587 | database:459 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 617 | 587 | database:459 |
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: hypothetical protein
- MTBC0 PGAP product: acyl-CoA dehydrogenase family protein
- Pfam (hmmscan --cut_ga): Acyl-CoA_dh_N PF02771.22 (E=1e-05), Acyl-CoA_dh_1 PF00441.30 (E=3e-08), Acyl-CoA_dh_2 PF08028.17 (E=8e-37)
- (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_217610.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl-CoA_dh_N (PF02771.22), Acyl-CoA_dh_1 (PF00441.30), Acyl-CoA_dh_2 (PF08028.17)
- 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 O05773 (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 —
111 functional partner(s); context anchor
Rv3093c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003288|Rv3094c| MNQSETEIEILAEKIARWARARSAEIERDRRLPDELVTRLREAGLLRATMPREVAAPELAPGRALRCAEAVARGDASAGWCVSIAITSALLVAYLPARSREEMFGGGRGVAAGVWAPRGTARSVDGGVVVSGRWPFCSGINHADIMFAGCFVDDRQVPSVVALNKDELQVLDTWHTLGLRGTGSHDCVADDVFVPADRVFSVFDGPIVDRPLYRFPVFGFFALSIGAAALGNARAAIDDLVELAGGKKGLGSTRTLAERSATQAAAATAESALGAARALFYEVIEAAWQVSHDAEAVPVTMRNRLRLAATHAVRTSADVVRSMYDLAGGTAIYDNAPLQRRFRDAFTATAHFQVNEASRELPGRVLLDQPADVSML