oppA Family assigned · medium auto-curated
H37Rv Rv1280c · MTBC0 mtbc0_001370 ·
591 aa · 1440648–1442423 (-) ·
RefSeq NP_215796.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oligopeptide ABC transporter substrate-binding lipoprotein OppA |
|---|---|
| MTBC0 PGAP re-annotation | oligopeptide ABC transporter substrate-binding protein OppA |
| Revised (this work) | Oligopeptide ABC transporter substrate-binding protein OppA. Pfam: SBP_bac_5 (PF00496.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGU5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Oligopeptide-binding protein OppA |
| Curated function | Part of the ABC transporter complex OppABCD involved in the uptake of oligopeptides. Peptide-binding protein that shows broad specificity but a moderate preference for hydrophobic oligopeptides and those that are 6-16 amino acids long. Can bind the tripeptide glutathione (GSH) and the nonapeptide bradykinin. Glutathione (GSH) uptake by mycobacteria through the OppABCD system contributes to the depletion of the GSH pool in infected macrophages, which impairs the ability of the macrophage to detoxify methylglyoxal (MG) and contributes to enhanced production of inflammatory cytokines. May also pr. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | oppA |
| eggNOG description | extracellular solute-binding |
| Orthologous group | COG0747 |
| KEGG orthology |
K02035
|
| KEGG pathways |
map02024
|
| KEGG modules |
M00239
|
| Gene Ontology (45) |
GO:0003674, GO:0005215, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0006810, GO:0008104, GO:0008150, GO:0015031, GO:0015833 +33 more
|
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 | 0.575 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 12 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 |
|---|---|---|---|---|
SBP_bac_5 | PF00496.28 | 2.3e-52 | 152–511 | Bacterial extracellular solute-binding proteins, family 5 Middle |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: oppB (oligopeptide ABC transporter permease OppB), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1283c oppB |
oligopeptide ABC transporter permease OppB | 999 | 998 ctx | neighborhood:881 cooccurence:693 coexpression:459 database:900 textmining:914 |
Rv1282c oppC |
oligopeptide ABC transporter permease OppC | 998 | 998 ctx | neighborhood:881 cooccurence:651 coexpression:428 database:900 textmining:405 |
Rv1281c oppD |
oligopeptide ABC transporter ATP-binding protein OppD | 993 | 993 ctx | neighborhood:802 cooccurence:617 database:900 |
Rv3663c dppD |
dipeptide ABC transporter ATP-binding protein DppD | 989 | 934 | database:900 textmining:851 |
Rv2585c |
lipoprotein | 913 | 913 | database:900 |
Rv1284 canA |
beta-carbonic anhydrase | 756 | 756 ctx | neighborhood:756 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 669 | 669 | coexpression:647 |
Rv3664c dppC |
dipeptide ABC transporter permease DppC | 839 | 633 | coexpression:429 textmining:580 |
Rv3665c dppB |
dipeptide ABC transporter permease DppB | 793 | 627 | coexpression:459 textmining:469 |
Rv2326c |
ABC transporter ATP-binding protein | 567 | 540 | |
Rv1286 cysC |
adenylyl-sulfate kinase | 526 | 526 | |
Rv2862c hyp |
hypothetical protein | 482 | 482 ctx | cooccurence:482 |
Rv3666c dppA |
dipeptide ABC transporter substrate-binding lipoprotein DppA | 742 | 445 | textmining:555 |
Rv0320 hyp |
hypothetical protein | 442 | 443 ctx | cooccurence:435 |
Rv2397c cysA1 |
sulfate ABC transporter ATP-binding protein CysA | 442 | 443 |
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: oligopeptide ABC transporter substrate-binding lipoprotein OppA
- MTBC0 PGAP product: oligopeptide ABC transporter substrate-binding protein OppA
- Pfam (hmmscan --cut_ga): SBP_bac_5 PF00496.28 (E=2e-52)
- (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_215796.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBP_bac_5 (PF00496.28)
- 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
COG0747 - Curated reference: UniProt P9WGU5 (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 —
35 functional partner(s); context anchor
oppB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001370|Rv1280c|oppA MADRGQRRGCAPGIASALRASFQGKSRPWTQTRYWAFALLTPLVVAMVLTGCSASGTQLELAPTADRRAAVGTTSDINQQDPATLQDGGNLRLSLTDFPPNFNILHIDGNNAEVAAMMKATLPRAFIIGPDGSTTVDTNYFTSIELTRTAPQVVTYTINPEAVWSDGTPITWRDIASQIHAISGADKAFEIASSSGAERVASVTRGVDDRQAVVTFAKPYAEWRGMFAGNGMLLPASMTATPEAFNKGQLDGPGPSAGPFVVSALDRTAQRIVLTRNPRWWGARPRLDSITYLVLDDAARLPALQNNTIDATGVGTLDQLTIAARTKGISIRRAPGPSWYHFTLNGAPGSILADKALRLAIAKGIDRYTIARVAQYGLTSDPVPLNNHVFVAGQDGYQDNSGVVAYNPEQAKRELDALGWRRSGAFREKDGRQLVIRDLFYDAQSTRQFAQIAQHTLAQIGVKLELQAKSGSGFFSDYVNVGAFDIAQFGWVGDAFPLSSLTQIYASDGESNFGKIGSPQIDAAIERTLAELDPGKARALANQVDELIWAEGFSLPLTQSPGTVAVRSTLANFGATGLADLDYTAIGFMRR