accD1 Family assigned · medium auto-curated
H37Rv Rv2502c · MTBC0 mtbc0_002664 ·
529 aa · 2839775–2841364 (-) ·
RefSeq NP_217018.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acetyl-/propionyl-CoA carboxylase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | acetyl-/propionyl-CoA carboxylase subunit beta |
| Revised (this work) | Acetyl-/propionyl-CoA carboxylase subunit beta. Pfam: Carboxyl_trans (PF01039.28), ACCA (PF03255.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YDK7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Biotin-dependent 3-methylcrotonyl-coenzyme A carboxylase beta1 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. When associated with the alpha1 subunit AccA1, is involved in branched amino-acid catabolism with methylcrotonyl coenzyme A as the substrate. Shows residual with propionyl-CoA and acetyl-CoA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | accD1 |
| eggNOG description | Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) |
| Orthologous group | COG4799 |
| EC number |
EC 6.4.1.4
|
| KEGG orthology |
K01969
|
| KEGG pathways |
map00280, map01100
|
| KEGG modules |
M00036
|
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 | 0.846 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 10 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 |
|---|---|---|---|---|
Carboxyl_trans | PF01039.28 | 1.1e-156 | 42–519 | Carboxyl transferase domain |
ACCA | PF03255.20 | 1.0e-05 | 83–199 | Acetyl co-enzyme A carboxylase carboxyltransferase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: accA1 (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) |
|---|---|---|---|---|
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 999 | 1000 ctx | neighborhood:882 coexpression:842 experimental:454 database:956 textmining:909 |
Rv2503c scoB |
succinyl-CoA:3-ketoacid-CoA transferase subunit B | 977 | 969 ctx | neighborhood:881 coexpression:750 |
Rv2499c |
oxidase regulatory-like protein | 950 | 933 ctx | neighborhood:881 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 | 982 | 930 ctx | neighborhood:881 coexpression:433 textmining:764 |
Rv2504c scoA |
succinyl-CoA:3-ketoacid-CoA transferase subunit A | 971 | 923 ctx | neighborhood:882 textmining:647 |
Rv0975c fadE13 |
acyl-CoA dehydrogenase FadE13 | 925 | 922 | database:900 |
Rv0131c fadE1 |
acyl-CoA dehydrogenase FadE1 | 925 | 922 | database:900 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 925 | 921 | database:900 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 924 | 921 | database:900 |
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 | 924 | 921 | database:900 |
Rv2498c citE |
citrate (pro-3S)-lyase subunit beta | 991 | 907 ctx | neighborhood:881 textmining:916 |
Rv3285 accA3 |
bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA | 982 | 883 | coexpression:437 experimental:454 database:578 textmining:861 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 977 | 874 | coexpression:443 experimental:454 database:578 textmining:829 |
Rv2497c bkdA |
3-methyl-2-oxobutanoate dehydrogenase subunit alpha | 877 | 817 ctx | neighborhood:724 |
Rv0971c echA7 |
enoyl-CoA hydratase EchA7 | 805 | 799 | database:650 |
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: acetyl-/propionyl-CoA carboxylase subunit beta
- Pfam (hmmscan --cut_ga): Carboxyl_trans PF01039.28 (E=1e-156), ACCA PF03255.20 (E=1e-05)
- (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_217018.1)
- Domains: Pfam-A via hmmscan --cut_ga — Carboxyl_trans (PF01039.28), ACCA (PF03255.20)
- 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 I6YDK7 (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 —
69 functional partner(s); context anchor
accA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002664|Rv2502c|accD1 MTTPSIAIAPSFADEHRRLVAELNNKLAAAALGGNERARKRHVSRGKLLPRERVDRLLDPGSPFLELAPLAAGGMYGDESPGAGIITGIGRVSGRQCVIVANDATVKGGTYYPMTVKKHLRAQEVALQNMLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFYNQATMSAKGIPQVAAVLGSCTAGGAYVPAMSDEAVIVREQGTIFLGGPPLVKAATGEIVSAEELGGGDLHSRTSGVTDHLADDDEDALRIVRAIADTFGPCEPAQWDVRRSVEPKYPQAELYDVVPPDPRVPYDVHEVVVRIVDGSEFSEFKAKYGKTLVTAFARVHGHPVGIVANNGVLFSESALKGAHFIELCDKRKIPLLFLQNIAGFMVGRDYEAGGIAKHGAKMVTAVACARVPKLTVVIGGSYGAGNYSMCGRAYSPRFLWMWPNARISVMGGEQAASVLATVRGEQLSAAGTPWSPDEEEAFKAPIRAQYEDQGNPYYSTARLWDDGIIDPADTRTVVGLALSLCAHAPLDQVGYGVFRM