accD2 Family assigned · medium auto-curated
H37Rv Rv0974c · MTBC0 mtbc0_001040 ·
529 aa · 1092971–1094560 (-) ·
RefSeq NP_215489.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acetyl-/propionyl-CoA carboxylase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | acyl-CoA carboxylase subunit beta |
| Revised (this work) | Acyl-CoA carboxylase subunit beta. Pfam: ACCA (PF03255.20), Carboxyl_trans (PF01039.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86318
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable biotin-dependent acyl-coenzyme A carboxylase beta2 subunit |
| EC (curated) |
EC 2.1.3.-
|
| Curated function | Component of a biotin-dependent acyl-CoA carboxylase complex. This subunit transfers the CO2 from carboxybiotin to the CoA ester substrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | accD2 |
| eggNOG description | Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) |
| Orthologous group | COG4799 |
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 | 0.479 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 7 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 |
|---|---|---|---|---|
ACCA | PF03255.20 | 4.5e-09 | 20–199 | Acetyl co-enzyme A carboxylase carboxyltransferase-like |
Carboxyl_trans | PF01039.28 | 9.0e-154 | 46–519 | Carboxyl transferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: accA2 (acetyl/propionyl-CoA carboxylase subuit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 999 | 1000 ctx | neighborhood:881 coexpression:918 experimental:454 database:956 textmining:898 |
Rv0976c hyp |
hypothetical protein | 992 | 992 ctx | neighborhood:881 coexpression:907 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 989 | 988 ctx | neighborhood:881 coexpression:888 |
Rv0972c fadE12 |
acyl-CoA dehydrogenase fadE12 | 992 | 986 ctx | neighborhood:881 coexpression:876 textmining:491 |
Rv0971c echA7 |
enoyl-CoA hydratase EchA7 | 976 | 934 ctx | neighborhood:881 textmining:656 |
Rv3285 accA3 |
bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA | 943 | 878 | coexpression:437 experimental:454 database:578 textmining:556 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 956 | 875 | coexpression:442 experimental:454 database:578 textmining:663 |
Rv2967c pca |
pyruvate carboxylase | 702 | 685 | database:576 |
Rv3221c TB7.3 |
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit | 701 | 684 | database:576 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 713 | 657 | database:622 |
Rv2524c fas |
fatty acid synthase | 797 | 618 ctx | neighborhood:544 textmining:493 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 586 | 570 | database:540 |
Rv0979A rpmF |
50S ribosomal protein L32 | 549 | 550 ctx | neighborhood:531 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 495 | 495 ctx | neighborhood:495 |
Rv0860 fadB |
fatty oxidation protein FadB | 519 | 468 | coexpression:450 |
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: acetyl-/propionyl-CoA carboxylase subunit beta
- MTBC0 PGAP product: acyl-CoA carboxylase subunit beta
- Pfam (hmmscan --cut_ga): ACCA PF03255.20 (E=4e-09), Carboxyl_trans PF01039.28 (E=9e-154)
- (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_215489.1)
- Domains: Pfam-A via hmmscan --cut_ga — ACCA (PF03255.20), Carboxyl_trans (PF01039.28)
- 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
COG4799 - Curated reference: UniProt O86318 (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 —
38 functional partner(s); context anchor
accA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001040|Rv0974c|accD2 MLQSTLDPNASAYDEAAATMSGKLDEINAELAKALAGGGPKYVDRHHARGKLTPRERIELLVDPDSPFLELSPLAAYGSNFQIGASLVTGIGAVCGVECMIVANDPTVKGGTSNPWTLRKILRANQIAFENRLPVISLVESGGADLPTQKEIFIPGGQMFRDLTRLSAAGIPTIALVFGNSTAGGAYVPGMSDHVVMIKERSKVFLAGPPLVKMATGEESDDESLGGAEMHARISGLADYFALDELDAIRIGRRIVARLNWIKQGPAPAPVTEPLFDAEELIGIVPPDLRIPFDPREVIARIVDGSEFDEFKPLYGSSLVTGWARLHGYPLGILANARGVLFSEESQKATQFIQLANRADTPLLFLHNTTGYMVGKDYEEGGMIKHGSMMINAVSNSTVPHISLLIGASYGAGHYGMCGRAYDPRFLFAWPSAKSAVMGGAQLSGVLSIVARAAAEARGQQVDEAADAAMRAAVEGQIEAESLPLVLSGMLYDDGVIDPRDTRTVLGMCLSAIANGPIKGTSNFGVFRM