Rv3552 Family assigned · low auto-curated
H37Rv Rv3552 · MTBC0 mtbc0_003769 ·
250 aa · 4014448–4015200 (+) ·
RefSeq NP_218069.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | CoA-transferase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | CoA-transferase subunit beta |
| Revised (this work) | CoA-transferase subunit beta. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPV9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cholesterol ring-cleaving hydrolase IpdB subunit |
| EC (curated) |
EC 4.1.99.-
|
| Curated function | Involved in the final steps of cholesterol and steroid degradation. Opens the last steroid ring of cholesterol by catalyzing the hydrolysis of (3E)-2-(2-carboxylatoethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA) to 6-methyl-3,7-dioxodecanedioyl-CoA (MeDODA-CoA). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | catJ |
| eggNOG description | COG2057 Acyl CoA acetate 3-ketoacid CoA transferase, beta subunit |
| Orthologous group | COG2057 |
| Gene Ontology (8) |
GO:0008150, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044403, GO:0044419, GO:0051704
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3551 (CoA-transferase subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3551 |
CoA-transferase subunit alpha | 999 | 1000 ctx | neighborhood:882 cooccurence:774 coexpression:952 experimental:999 database:900 textmining:820 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 999 | 998 ctx | neighborhood:882 cooccurence:749 coexpression:869 database:500 textmining:564 |
Rv3549c |
short-chain type dehydrogenase/reductase | 984 | 983 ctx | neighborhood:787 cooccurence:593 coexpression:807 |
Rv3553 |
oxidoreductase | 980 | 981 ctx | neighborhood:773 cooccurence:446 coexpression:860 |
Rv3548c |
short-chain type dehydrogenase/reductase | 957 | 956 ctx | neighborhood:588 cooccurence:455 coexpression:800 |
Rv3559c |
oxidoreductase | 943 | 941 ctx | cooccurence:709 coexpression:783 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 964 | 922 ctx | cooccurence:668 coexpression:771 textmining:564 |
Rv2504c scoA |
succinyl-CoA:3-ketoacid-CoA transferase subunit A | 928 | 922 | coexpression:670 experimental:766 |
Rv3556c fadA6 |
acetyl-CoA acetyltransferase FadA | 966 | 904 | coexpression:780 database:500 textmining:667 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 904 | 901 ctx | cooccurence:736 coexpression:631 |
Rv3561 fadD3 |
fatty-acid--CoA ligase FadD3 | 881 | 877 | coexpression:810 |
Rv3522 ltp4 |
lipid transfer protein | 824 | 816 ctx | cooccurence:761 |
Rv3540c ltp2 |
lipid transfer protein | 813 | 805 ctx | cooccurence:750 |
Rv3523 ltp3 |
lipid carrier protein | 799 | 791 ctx | cooccurence:732 |
Rv3541c chsH1 hyp |
hypothetical protein | 791 | 784 ctx | cooccurence:769 |
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: CoA-transferase subunit beta
- MTBC0 PGAP product: CoA-transferase subunit beta
- (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_218069.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2057 - Curated reference: UniProt P9WPV9 (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 —
57 functional partner(s); context anchor
Rv3551 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003769|Rv3552| MSTRAEVCAVACAELFRDAGEIMISPMTNMASVGARLARLTFAPDILLTDGEAQLLADTPALGKTGAPNRIEGWMPFGRVFETLAWGRRHVVMGANQVDRYGNQNISAFGPLQRPTRQMFGVRGSPGNTINHATSYWVGNHCKRVFVEAVDVVSGIGYDKVDPDNPAFRFVNVYRVVSNLGVFDFGGPDHSMRAVSLHPGVTPGDVRDATSFEVHDLDAAEQTRLPTDDELHLIRAVIDPKSLRDREIRS