accD6 Family assigned · medium auto-curated
H37Rv Rv2247 · MTBC0 mtbc0_002389 ·
473 aa · 2546901–2548322 (+) ·
RefSeq NP_216763.1
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: Carboxyl_trans (PF01039.28), ACCA (PF03255.20), MdcE (PF06833.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQH5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase beta6 subunit |
| EC (curated) |
EC 2.1.3.-, EC 2.1.3.15
|
| 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 alpha3 subunit AccA3, is involved in the carboxylation of acetyl-CoA and propionyl-CoA, with a preference for acetyl-CoA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | accD6 |
| eggNOG description | propionyl-CoA carboxylase |
| Orthologous group | COG4799 |
| EC number |
EC 2.1.3.15, EC 6.4.1.2, EC 6.4.1.3
|
| KEGG orthology |
K18472
|
| KEGG pathways |
map00061, map00280, map00620, map00630, map00640, map01100, map01110, map01120, map01130, map01200, map01212
|
| KEGG modules |
M00082, M00741
|
| Gene Ontology (55) |
GO:0003674, GO:0003824, GO:0003989, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0006082, GO:0006629, GO:0006631, GO:0006633 +43 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 | 0.603 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Carboxyl_trans | PF01039.28 | 1.3e-127 | 39–460 | Carboxyl transferase domain |
ACCA | PF03255.20 | 8.4e-08 | 286–459 | Acetyl co-enzyme A carboxylase carboxyltransferase-like |
MdcE | PF06833.17 | 8.6e-08 | 316–467 | Malonate decarboxylase gamma subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fabD (malonyl CoA-acyl carrier protein transacylase), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 998 | 994 ctx | neighborhood:732 coexpression:783 database:900 textmining:769 |
Rv3285 accA3 |
bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA | 998 | 991 | coexpression:464 experimental:454 database:956 textmining:868 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 996 | 988 | coexpression:436 experimental:454 database:956 textmining:706 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 995 | 988 | coexpression:435 experimental:454 database:956 textmining:634 |
Rv2246 kasB |
3-oxoacyl-ACP synthase 2 | 996 | 976 ctx | neighborhood:836 coexpression:860 textmining:841 |
Rv2245 kasA |
3-oxoacyl-ACP synthase 1 | 997 | 971 ctx | neighborhood:798 coexpression:860 textmining:914 |
Rv3221c TB7.3 |
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit | 972 | 971 | database:956 |
Rv2524c fas |
fatty acid synthase | 980 | 962 ctx | neighborhood:544 database:900 textmining:504 |
Rv1322A hyp |
hypothetical protein | 961 | 959 ctx | cooccurence:533 database:900 |
Rv3710 leuA |
2-isopropylmalate synthase | 944 | 942 | database:900 |
Rv2790c ltp1 |
lipid-transfer protein | 930 | 927 | database:900 |
Rv3667 acs |
acetyl-CoAsynthetase | 923 | 918 | database:900 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 919 | 916 | database:900 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 918 | 910 | database:900 |
Rv3280 accD5 |
propionyl-CoA carboxylase subunit beta | 916 | 910 | database:900 |
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): Carboxyl_trans PF01039.28 (E=1e-127), ACCA PF03255.20 (E=8e-08), MdcE PF06833.17 (E=9e-08)
- (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_216763.1)
- Domains: Pfam-A via hmmscan --cut_ga — Carboxyl_trans (PF01039.28), ACCA (PF03255.20), MdcE (PF06833.17)
- 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
COG4799 - Curated reference: UniProt P9WQH5 (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 —
82 functional partner(s); context anchor
fabD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002389|Rv2247|accD6 MTIMAPEAVGESLDPRDPLLRLSNFFDDGSVELLHERDRSGVLAAAGTVNGVRTIAFCTDGTVMGGAMGVEGCTHIVNAYDTAIEDQSPIVGIWHSGGARLAEGVRALHAVGQVFEAMIRASGYIPQISVVVGFAAGGAAYGPALTDVVVMAPESRVFVTGPDVVRSVTGEDVDMASLGGPETHHKKSGVCHIVADDELDAYDRGRRLVGLFCQQGHFDRSKAEAGDTDIHALLPESSRRAYDVRPIVTAILDADTPFDEFQANWAPSMVVGLGRLSGRTVGVLANNPLRLGGCLNSESAEKAARFVRLCDAFGIPLVVVVDVPGYLPGVDQEWGGVVRRGAKLLHAFGECTVPRVTLVTRKTYGGAYIAMNSRSLNATKVFAWPDAEVAVMGAKAAVGILHKKKLAAAPEHEREALHDQLAAEHERIAGGVDSALDIGVVDEKIDPAHTRSKLTEALAQAPARRGRHKNIPL