scoA Family assigned · medium auto-curated
H37Rv Rv2504c · MTBC0 mtbc0_002666 ·
248 aa · 2842014–2842760 (-) ·
RefSeq NP_217020.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | succinyl-CoA:3-ketoacid-CoA transferase subunit A |
|---|---|
| MTBC0 PGAP re-annotation | succinyl-CoA--3-ketoacid CoA transferase subunit A |
| Revised (this work) | Succinyl-CoA--3-ketoacid CoA transferase subunit A. Pfam: CoA_trans (PF01144.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPW5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit A |
| EC (curated) |
EC 2.8.3.5
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | scoA |
| eggNOG description | transferase |
| Orthologous group | COG1788 |
| EC number |
EC 2.8.3.5
|
| KEGG orthology |
K01028
|
| KEGG pathways |
map00072, map00280, map00650
|
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 | 1.045 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
CoA_trans | PF01144.30 | 4.2e-79 | 6–233 | Coenzyme A transferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: scoB (succinyl-CoA:3-ketoacid-CoA transferase subunit B), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2503c scoB |
succinyl-CoA:3-ketoacid-CoA transferase subunit B | 999 | 1000 ctx | neighborhood:881 fusion:900 cooccurence:774 coexpression:943 experimental:766 database:900 textmining:958 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 969 | 936 ctx | neighborhood:882 coexpression:483 textmining:543 |
Rv0860 fadB |
fatty oxidation protein FadB | 936 | 928 | database:900 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 971 | 923 ctx | neighborhood:882 textmining:647 |
Rv3556c fadA6 |
acetyl-CoA acetyltransferase FadA | 926 | 923 | database:900 |
Rv1323 fadA4 |
acetyl-CoA acetyltransferase | 962 | 922 | database:900 textmining:537 |
Rv3552 |
CoA-transferase subunit beta | 928 | 922 | coexpression:670 experimental:766 |
Rv1074c fadA3 |
beta-ketoacyl CoA thiolase FadA | 926 | 922 | database:900 |
Rv0859 fadA |
acyltransferase | 926 | 922 | database:900 |
Rv0914c |
lipid carrier protein or keto acyl-CoA thiolase | 924 | 921 | database:900 |
Rv3546 fadA5 |
acetyl-CoA acetyltransferase FadA | 924 | 921 | database:900 |
Rv0243 fadA2 |
acetyl-CoA acetyltransferase FadA | 924 | 920 | database:900 |
Rv3523 ltp3 |
lipid carrier protein | 924 | 920 | database:900 |
Rv1867 hyp |
hypothetical protein | 923 | 920 | database:900 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 917 | 912 | 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: succinyl-CoA:3-ketoacid-CoA transferase subunit A
- MTBC0 PGAP product: succinyl-CoA--3-ketoacid CoA transferase subunit A
- Pfam (hmmscan --cut_ga): CoA_trans PF01144.30 (E=4e-79)
- (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_217020.1)
- Domains: Pfam-A via hmmscan --cut_ga — CoA_trans (PF01144.30)
- 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
COG1788 - Curated reference: UniProt P9WPW5 (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 —
36 functional partner(s); context anchor
scoB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002666|Rv2504c|scoA MDKVVATAAEAVADIANGSSLAVGGFGLCGIPEALIAALVDSGVTDLETVSNNCGIDGVGLGLLLQHKRIRRTVSSYVGENKEFARQFLAGELEVELTPQGTLAERLRAGGMGIPAFYTPAGVGTQVADGGLPWRYDASGGVAVVSPAKETREFDGVTYVLERGIRTDFALVHAWQGDRHGNLMYRHAAANFNPECASAGRITIAEVEHLVEPGEIDPATVHTPGVFVHRVVHVPNPAKKIERETVRQ