oplA Family assigned · medium auto-curated
H37Rv Rv0266c · MTBC0 mtbc0_000282 ·
1209 aa · 317907–321536 (-) ·
RefSeq NP_214780.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 5-oxoprolinase OplA |
|---|---|
| MTBC0 PGAP re-annotation | hydantoinase B/oxoprolinase family protein |
| Revised (this work) | Hydantoinase B/oxoprolinase family protein. Pfam: Hydant_A_N (PF05378.20), Hydantoinase_A (PF01968.25), Hydant_A_C (PF19278.5), Hydantoinase_B (PF02538.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95223
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable 5-oxoprolinase OplA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | oplA |
| eggNOG description | Hydantoinase/oxoprolinase |
| Orthologous group | COG0145 |
| EC number |
EC 3.5.2.14, EC 3.5.2.9
|
| KEGG orthology |
K01469, K01473
|
| KEGG pathways |
map00330, map00480, 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 | 0.24 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 15 synonymous, 10 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 |
|---|---|---|---|---|
Hydant_A_N | PF05378.20 | 2.7e-55 | 7–182 | Hydantoinase/oxoprolinase N-terminal region |
Hydantoinase_A | PF01968.25 | 2.7e-111 | 202–489 | Hydantoinase/oxoprolinase |
Hydant_A_C | PF19278.5 | 1.6e-08 | 504–663 | Hydantoinase/oxoprolinase C-terminal domain |
Hydantoinase_B | PF02538.20 | 3.2e-203 | 694–1200 | Hydantoinase B/oxoprolinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0265c (iron ABC transporter substrate-binding lipoprotein), high confidence from genomic context alone (score 855 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2394 ggtB |
gamma-glutamyltranspeptidase precursor GgtB | 928 | 924 | database:900 |
Rv0773c ggtA |
bifunctional cephalosporin acylase/gamma-glutamyltranspeptidase | 925 | 921 | database:900 |
Rv3704c gshA |
glutamate--cysteine ligase | 900 | 900 | database:900 |
Rv0433 |
carboxylate-amine ligase | 900 | 900 | database:900 |
Rv0265c |
iron ABC transporter substrate-binding lipoprotein | 979 | 855 ctx | neighborhood:855 textmining:861 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 830 | 831 | database:800 |
Rv3859c gltB |
glutamate synthase large subunit | 870 | 823 | database:800 |
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 819 | 813 | database:800 |
Rv3432c gadB |
glutamate decarboxylase GadB | 815 | 808 | database:800 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 807 | 807 | database:800 |
Rv3858c gltD |
glutamate synthase small subunit | 805 | 806 | database:800 |
Rv2220 glnA1 |
glutamine synthetase | 801 | 801 | database:800 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 801 | 801 | database:800 |
Rv2860c glnA4 |
glutamine synthetase | 800 | 800 | database:800 |
Rv2222c glnA2 |
glutamine synthetase | 800 | 800 | database:800 |
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: 5-oxoprolinase OplA
- MTBC0 PGAP product: hydantoinase B/oxoprolinase family protein
- Pfam (hmmscan --cut_ga): Hydant_A_N PF05378.20 (E=3e-55), Hydantoinase_A PF01968.25 (E=3e-111), Hydant_A_C PF19278.5 (E=2e-08), Hydantoinase_B PF02538.20 (E=3e-203)
- (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_214780.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydant_A_N (PF05378.20), Hydantoinase_A (PF01968.25), Hydant_A_C (PF19278.5), Hydantoinase_B (PF02538.20)
- 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
COG0145 - Curated reference: UniProt P95223 (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 —
26 functional partner(s); context anchor
Rv0265c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000282|Rv0266c|oplA MVGAGWHFWVDRGGTFTDVVARRPDGRLLTHKLLSDNPARYRDAAVAGIRALLANGEAGTRVDAVRMGTTVATNALLERTGERTLLVITRGFGDALRIAYQNRPRIFDRRIVLPEMLYERVVEVDERVTADGRVLRAPDLEALGEKMRQAHADGIRAVAVVCLHSYLYPGHEREIGTLAQRIGFAQISLSSEVSPLMKLVPRGDTTVVDAYLSPVLRRYINQVADQMRGVRLMFMQSNGGLAQAGHFRGKDAILSGPAGGIVGMVRMSALAGFDHVIGFDMGGTSTDVSHYAGEYERVFTTQVAGVRLRAPMLDIHTVAAGGGSILHFDGSRYRVGPDSAGADPGPACYRGGGPLCVTDANVMLGRIQPTHFPSVFGPSGDQPLDAGTVRRGFTDLAADIAARTGDDRSPEQVAEGYLRIAVANMANAVKKISVQKGHDVTRYALTTFGGAGGQHACAVADALGIRTVLIPPMAGVLSALGIGLADTTAMREQSVEIPLGPAAPQRLASVAESLERAARAELLDEGVPGERIRVVRRVHLRYEGTDTAIPVQLAEIETMATAFESSHRALYTFLLDRPLIAEAISVEATGLTDQPDLSQLGDQANDTTGSSETVRIYSNGLWRDAPLRRREAMRPGDVLTGPAIIAEANATTVVDDGWQATMTETGHLLAQRVVTPPRPDAATRAGFEAGFEADPVLLEIFNNLFMSIAEQMGFRLEATAQSVNIRERLDFSCALFDPDGNLVANAPHIPVHLGSMGTTVKEVIRRRLSGMKPGDVYAVNDPYHGGTHLPDITVITPVFNTGGEDVLFFVASRGHHAEIGGITPGSMPADSREIHEEGVLFDNWLLAENGRFREAETRRLLTEAPFGSRNPDTNLADLRAQIAANQKGVDEVGKMIDHFGRDVVAAYMRHVQDNAEEAVRRVIDRLDNGAYRYRMDSGATIAVRITVDRAARSATIDFTGTSAQLDTNFNAPTSVVNAAVLYVFRTLVADDIPLNDGCLRPLRIVVPEGSMLAPTHPAAVVAGNVETSQAITGALFAALGVQAEGSGTMNNVTFGNERHQYYETVGSGSGAGDGYHGASVVQTHMTNSRLTDPEVLEWRYPVLLREFAVRQGSGGAGRWRGGDGAVRRLEFTEPMTVSTLSGHRRVRPYGMAGGSPGELGRNRVERADGSTVELAGCGSTHVEPGDTLVIETPGGGGYGPASTSARRRR