oxcA Resolved · high auto-curated
H37Rv Rv0118c · MTBC0 mtbc0_000129 ·
582 aa · 142294–144042 (-) ·
RefSeq NP_214632.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxalyl-CoA decarboxylase OxcA |
|---|---|
| MTBC0 PGAP re-annotation | oxalyl-CoA decarboxylase |
| Revised (this work) | Oxalyl-CoA decarboxylase. Pfam: TPP_enzyme_N (PF02776.24), TPP_enzyme_M (PF00205.29), TPP_enzyme_C (PF02775.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53639
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable oxalyl-CoA decarboxylase OxcA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismH Coenzyme transport and metabolism
|
|---|---|
| Preferred name | oxc |
| eggNOG description | Belongs to the TPP enzyme family |
| Orthologous group | COG0028 |
| EC number |
EC 4.1.1.8
|
| KEGG orthology |
K01577
|
| KEGG pathways |
map00630, map01100
|
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 | 0.179 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 12 synonymous, 6 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 |
|---|---|---|---|---|
TPP_enzyme_N | PF02776.24 | 5.0e-32 | 15–129 | Thiamine pyrophosphate enzyme, N-terminal TPP binding domain |
TPP_enzyme_M | PF00205.29 | 4.3e-34 | 206–335 | Thiamine pyrophosphate enzyme, central domain |
TPP_enzyme_C | PF02775.27 | 3.2e-27 | 408–552 | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ilvN (acetolactate synthase small subunit), high confidence from genomic context alone (score 943 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3002c ilvN |
acetolactate synthase small subunit | 958 | 943 ctx | cooccurence:464 coexpression:650 experimental:704 |
Rv0119 fadD7 |
fatty-acid--CoA ligase FadD7 | 895 | 893 ctx | neighborhood:720 coexpression:454 |
Rv3001c ilvC |
ketol-acid reductoisomerase | 775 | 691 | coexpression:538 |
Rv0189c ilvD |
dihydroxy-acid dehydratase | 733 | 651 | coexpression:501 |
Rv1223 htrA |
serine protease HtrA | 619 | 620 | database:529 |
Rv3710 leuA |
2-isopropylmalate synthase | 713 | 611 | |
Rv0983 pepD |
serine protease PepD | 608 | 608 | database:529 |
Rv3534c hsaF |
4-hydroxy-2-oxovalerate aldolase | 624 | 604 | |
Rv3469c mhpE |
4-hydroxy-2-oxovalerate aldolase MhpE | 623 | 604 | |
Rv3672c hyp |
hypothetical protein | 602 | 601 | database:520 |
Rv1905c aao |
D-amino acid oxidase | 606 | 589 | database:518 |
Rv3339c icd1 |
isocitrate dehydrogenase | 606 | 588 | database:570 |
Rv2995c leuB |
3-isopropylmalate dehydrogenase | 679 | 580 | coexpression:402 |
Rv2210c ilvE |
branched-chain amino acid aminotransferase | 647 | 575 | coexpression:404 |
Rv3538 |
dehydrogenase | 589 | 574 | database:415 |
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: oxalyl-CoA decarboxylase OxcA
- MTBC0 PGAP product: oxalyl-CoA decarboxylase
- Pfam (hmmscan --cut_ga): TPP_enzyme_N PF02776.24 (E=5e-32), TPP_enzyme_M PF00205.29 (E=4e-34), TPP_enzyme_C PF02775.27 (E=3e-27)
- (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_214632.1)
- Domains: Pfam-A via hmmscan --cut_ga — TPP_enzyme_N (PF02776.24), TPP_enzyme_M (PF00205.29), TPP_enzyme_C (PF02775.27)
- 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
COG0028 - Curated reference: UniProt O53639 (TrEMBL, unreviewed; 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 —
158 functional partner(s); context anchor
ilvN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000129|Rv0118c|oxcA MTTRSASPCTVLTDGCHLVVDALKANDVDTIYGVVGIPITDLARAAQASGIRYIGFRHEASAGNAAAAAGFLTARPGVCLTTSGPGFLNGLPALANATTNCFPMIQISGSSSRPMVDLQRGDYQDLDQLNAARPFVKAAYRIGQVQDIGRGVARAIRTATSGRPGGVYLDIPGDVLGQAVEASAASGAIWRPVDPAPRLLPAPEAIDRALDVLAQAQRPLLVLGKGAAYAQADNVIREFVEHTGIPFLPMSMAKGLLPDSHPQSAAAARSLAMARADVVLLVGARLNWLLGNGESPQWSADAKFIQVDIEASEFDSNRPIVAPLTGDIGSVMSALLEAAADRSSVASAAWTGELADRKARNSAKMRRRLADDHHPMRFYNALGAIRSVLQRNPDVYVVNEGANALDLARNIIDMHLPRHRLDSGTWGVMGIGMGYAIAAAVETGRPVVAIEGDSAFGFSGMEFETICRYRLPVTVVILNNGGVYRGDEATIFRSAAPVWRHDPAPTVLNAHARHELIAEAFGGKGYHVSTPTELESALTDALASNGPSLIDCELDPADGVESGHLAKLNTTSAATPAISGDG