opcA Resolved · high auto-curated
H37Rv Rv1446c · MTBC0 mtbc0_001548 ·
303 aa · 1633822–1634733 (-) ·
RefSeq NP_215962.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | OXPP cycle protein OpcA |
|---|---|
| MTBC0 PGAP re-annotation | glucose-6-phosphate dehydrogenase assembly protein OpcA |
| Revised (this work) | Glucose-6-phosphate dehydrogenase assembly protein OpcA. Pfam: OpcA_G6PD_assem (PF10128.16), OpcA_G6PD_C (PF20171.4). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06813
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | OXPP cycle protein OpcA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | opcA |
| eggNOG description | OpcA protein |
| Orthologous group | COG3429 |
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) pseudogene candidate
| pN/pS | 1.08 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 12 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 2.27% of strains (3293) · clonal |
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 |
|---|---|---|---|---|
OpcA_G6PD_assem | PF10128.16 | 2.8e-34 | 52–161 | Glucose-6-phosphate dehydrogenase subunit N-terminal domain |
OpcA_G6PD_C | PF20171.4 | 3.3e-34 | 168–294 | Glucose-6-phosphate dehydrogenase subunit C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: devB (6-phosphogluconolactonase), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1445c devB |
6-phosphogluconolactonase | 996 | 996 ctx | neighborhood:882 fusion:892 coexpression:615 |
Rv1447c zwf2 |
glucose-6-phosphate 1-dehydrogenase | 955 | 927 ctx | neighborhood:811 coexpression:417 textmining:419 |
Rv1444c hyp |
hypothetical protein | 866 | 867 ctx | neighborhood:865 |
Rv1448c tal |
transaldolase | 924 | 853 ctx | neighborhood:811 textmining:509 |
Rv1449c tkt |
transketolase | 880 | 801 ctx | neighborhood:798 textmining:423 |
Rv2745c clgR |
transcriptional regulator ClgR | 541 | 541 ctx | cooccurence:540 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 518 | 519 ctx | cooccurence:517 |
Rv2146c |
transmembrane protein | 511 | 511 ctx | cooccurence:508 |
Rv3923c rnpA |
ribonuclease P protein component | 467 | 467 ctx | cooccurence:463 |
Rv1451 ctaB |
protoheme IX farnesyltransferase | 492 | 460 ctx | neighborhood:457 |
Rv2699c hyp |
hypothetical protein | 454 | 454 ctx | cooccurence:454 |
Rv2206 |
transmembrane protein | 453 | 454 ctx | cooccurence:451 |
Rv1423 whiA |
transcriptional regulator WhiA | 435 | 435 ctx | cooccurence:427 |
Rv2169c |
transmembrane protein | 422 | 422 ctx | cooccurence:422 |
Rv2413c hyp |
hypothetical protein | 401 | 402 |
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: OXPP cycle protein OpcA
- MTBC0 PGAP product: glucose-6-phosphate dehydrogenase assembly protein OpcA
- Pfam (hmmscan --cut_ga): OpcA_G6PD_assem PF10128.16 (E=3e-34), OpcA_G6PD_C PF20171.4 (E=3e-34)
- (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_215962.1)
- Domains: Pfam-A via hmmscan --cut_ga — OpcA_G6PD_assem (PF10128.16), OpcA_G6PD_C (PF20171.4)
- 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
COG3429 - Curated reference: UniProt O06813 (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
devB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001548|Rv1446c|opcA MIVDLPDTTTTAVNKKLDELREKIGAVAMGRVLTLIIAPDSEAMLEESIEAANDASHEHPSRIIVTMRGDPYADRPRLDAQLRVGADAGAGEFVVLRLSGPLAGHADSVVIPFLLPDIPVVAWWPDIAPAVPAQDALGKLAIRRITDATNAIDPLSAIKSRLAGYGAGDTDLAWSRITYWRALLTSAVDQPPHEPIESALVSGLKTEPALDVLAGWLASRIEGPVRRAVGELKVELVRNSETIVLSRPQEGITATLTRTGKPDALVPLARRVTGECLAEDLRRLDPDEIYCAALEGIKKVQYR