accD3 Family assigned · medium auto-curated
H37Rv Rv0904c · MTBC0 mtbc0_000958 ·
495 aa · 1009907–1011394 (-) ·
RefSeq NP_215419.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acetyl-CoAcarboxylase carboxyl transferase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | carboxyl transferase domain-containing protein |
| Revised (this work) | Carboxyl transferase domain-containing protein. 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 |
P9WQH9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable biotin-dependent acyl-coenzyme A carboxylase beta3 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 | accD3 |
| eggNOG description | carboxyl transferase |
| Orthologous group | COG0777 |
| EC number |
EC 2.1.3.15, EC 6.4.1.2
|
| KEGG orthology |
K01962, K01963
|
| KEGG pathways |
map00061, map00620, map00640, map00720, map01100, map01110, map01120, map01130, map01200, map01212
|
| KEGG modules |
M00082, M00376
|
| Gene Ontology (44) |
GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006629, GO:0006631, GO:0006633, GO:0008150, GO:0008152, GO:0008610, GO:0009058, GO:0009059 +32 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) pseudogene candidate
| pN/pS | 1.984 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.32% of strains (1919) · clonal |
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 | 1.2e-103 | 14–479 | Carboxyl transferase domain |
ACCA | PF03255.20 | 1.5e-37 | 242–491 | Acetyl co-enzyme A carboxylase carboxyltransferase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fas (fatty acid synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2524c fas |
fatty acid synthase | 999 | 1000 ctx | neighborhood:544 coexpression:999 textmining:788 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 999 | 997 ctx | cooccurence:508 coexpression:486 experimental:975 database:500 textmining:759 |
Rv3285 accA3 |
bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA | 998 | 996 ctx | cooccurence:461 coexpression:483 experimental:975 textmining:605 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 998 | 993 | coexpression:486 experimental:975 textmining:759 |
Rv1722 |
carboxylase | 995 | 986 | coexpression:843 experimental:874 textmining:688 |
Rv0533c fabH |
3-oxoacyl-ACP synthase III | 993 | 984 | coexpression:969 textmining:587 |
Rv2245 kasA |
3-oxoacyl-ACP synthase 1 | 983 | 976 | coexpression:961 |
Rv2246 kasB |
3-oxoacyl-ACP synthase 2 | 983 | 976 | coexpression:961 |
Rv1484 inhA |
NADH-dependent enoyl-[ACP | 986 | 974 | coexpression:959 textmining:511 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 977 | 951 | coexpression:932 textmining:560 |
Rv1023 eno |
enolase | 883 | 880 | experimental:863 |
Rv0905 echA6 |
enoyl-CoA hydratase EchA6 | 824 | 805 ctx | neighborhood:790 |
Rv0906 hyp |
hypothetical protein | 791 | 791 ctx | neighborhood:790 |
Rv1527c pks5 |
polyketide synthase | 902 | 765 ctx | neighborhood:544 coexpression:440 textmining:604 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 902 | 764 ctx | neighborhood:544 coexpression:437 textmining:604 |
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-CoAcarboxylase carboxyl transferase subunit beta
- MTBC0 PGAP product: carboxyl transferase domain-containing protein
- Pfam (hmmscan --cut_ga): Carboxyl_trans PF01039.28 (E=1e-103), ACCA PF03255.20 (E=1e-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_215419.1)
- 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
COG0777 - Curated reference: UniProt P9WQH9 (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 —
163 functional partner(s); context anchor
fas - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000958|Rv0904c|accD3 MSRITTDQLRHAVLDRGSFVSWDSEPLAVPVADSYARELAAARAATGADESVQTGEGRVFGRRVAVVACEFDFLGGSIGVAAAERITAAVERATAERLPLLASPSSGGTRMQEGTVAFLQMVKIAAAIQLHNQARLPYLVYLRHPTTGGVFASWGSLGHLTVAEPGALIGFLGPRVYELLYGDPFPSGVQTAENLRRHGIIDGVVALDRLRPMLDRALTVLIDAPEPLPAPQTPAPVPDVPTWDSVVASRRPDRPGVRQLLRHGATDRVLLSGTDQGEAATTLLALARFGGQPTVVLGQQRAVGGGGSTVGPAALREARRGMALAAELCLPLVLVIDAAGPALSAAAEQGGLAGQIAHCLAELVTLDTPTVSILLGQGSGGPALAMLPADRVLAALHGWLAPLPPEGASAIVFRDTAHAAELAAAQGIRSADLLKSGIVDTIVPEYPDAADEPIEFALRLSNAIAAEVHALRKIPAPERLATRLQRYRRIGLPRD