accD5 Family assigned · medium auto-curated
H37Rv Rv3280 · MTBC0 mtbc0_003488 ·
548 aa · 3684205–3685851 (+) ·
RefSeq NP_217797.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 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). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQH7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase beta5 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 propionyl-CoA. Is also required for the activity of the long-chain acyl-CoA carboxylase (LCC) complex. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | pccB |
| eggNOG description | Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) |
| Orthologous group | COG4799 |
| EC number |
EC 2.1.3.15, EC 6.4.1.3
|
| KEGG orthology |
K01966
|
| KEGG pathways |
map00280, map00630, map00640, map01100, map01120, map01130, map01200
|
| KEGG modules |
M00373, M00741
|
| Gene Ontology (50) |
GO:0003674, GO:0003824, GO:0003989, GO:0004658, GO:0005488, GO:0005515, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005886 +38 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 | 0.41 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 | 1.6e-206 | 51–545 | Carboxyl transferase domain |
ACCA | PF03255.20 | 1.5e-08 | 333–437 | Acetyl co-enzyme A carboxylase carboxyltransferase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: accA3 (bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3285 accA3 |
bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA | 999 | 995 ctx | neighborhood:591 coexpression:449 experimental:454 database:956 textmining:993 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 997 | 988 | coexpression:435 experimental:454 database:956 textmining:826 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 995 | 987 | coexpression:435 experimental:454 database:956 textmining:693 |
Rv3281 accE5 |
bifunctional protein acetyl-/propionyl-CoAcarboxylase subunit epsilon AccE | 996 | 970 ctx | neighborhood:881 database:720 textmining:901 |
Rv1322A hyp |
hypothetical protein | 969 | 968 ctx | cooccurence:636 database:900 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 959 | 936 ctx | neighborhood:788 database:622 |
Rv2790c ltp1 |
lipid-transfer protein | 931 | 928 | database:900 |
Rv3667 acs |
acetyl-CoAsynthetase | 924 | 918 | database:900 |
Rv2247 accD6 |
acetyl-/propionyl-CoA carboxylase subunit beta | 916 | 910 | database:900 |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase | 911 | 908 | database:900 |
Rv0408 pta |
phosphate acetyltransferase | 908 | 904 | database:900 |
Rv3282 hyp |
hypothetical protein | 951 | 898 ctx | neighborhood:881 textmining:539 |
Rv0860 fadB |
fatty oxidation protein FadB | 906 | 884 | coexpression:424 database:800 |
Rv3283 sseA |
thiosulfate sulfurtransferase SseA | 877 | 826 ctx | neighborhood:822 |
Rv3284 hyp |
hypothetical protein | 824 | 825 ctx | neighborhood:822 |
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: propionyl-CoA carboxylase subunit beta
- MTBC0 PGAP product: acyl-CoA carboxylase subunit beta
- Pfam (hmmscan --cut_ga): Carboxyl_trans PF01039.28 (E=2e-206), ACCA PF03255.20 (E=1e-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_217797.1)
- 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 P9WQH7 (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 —
65 functional partner(s); context anchor
accA3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003488|Rv3280|accD5 MTSVTDRSAHSAERSTEHTIDIHTTAGKLAELHKRREESLHPVGEDAVEKVHAKGKLTARERIYALLDEDSFVELDALAKHRSTNFNLGEKRPLGDGVVTGYGTIDGRDVCIFSQDATVFGGSLGEVYGEKIVKVQELAIKTGRPLIGINDGAGARIQEGVVSLGLYSRIFRNNILASGVIPQISLIMGAAAGGHVYSPALTDFVIMVDQTSQMFITGPDVIKTVTGEEVTMEELGGAHTHMAKSGTAHYAASGEQDAFDYVRELLSYLPPNNSTDAPRYQAAAPTGPIEENLTDEDLELDTLIPDSPNQPYDMHEVITRLLDDEFLEIQAGYAQNIVVGFGRIDGRPVGIVANQPTHFAGCLDINASEKAARFVRTCDCFNIPIVMLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVPKITVITRKAYGGAYCVMGSKDMGCDVNLAWPTAQIAVMGASGAVGFVYRQQLAEAAANGEDIDKLRLRLQQEYEDTLVNPYVAAERGYVDAVIPPSHTRGYIGTALRLLERKIAQLPPKKHGNVPL