oppC Family assigned · medium auto-curated
H37Rv Rv1282c · MTBC0 mtbc0_001372 ·
291 aa · 1444251–1445126 (-) ·
RefSeq NP_215798.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oligopeptide ABC transporter permease OppC |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter permease |
| Revised (this work) | ABC transporter permease. Pfam: OppC_N (PF12911.13), BPD_transp_1 (PF00528.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFZ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Oligopeptide transport system permease protein OppC |
| Curated function | Part of the ABC transporter complex OppABCD involved in the uptake of oligopeptides. Responsible for the translocation of the substrate across the membrane. 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 promote Mn(2+) uptake. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismP Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | oppC |
| eggNOG description | transport |
| Orthologous group | COG1173 |
| KEGG orthology |
K02034
|
| KEGG pathways |
map02024
|
| KEGG modules |
M00239
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.123 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
OppC_N | PF12911.13 | 1.1e-10 | 10–58 | N-terminal TM domain of oligopeptide transport permease C |
BPD_transp_1 | PF00528.28 | 3.9e-25 | 101–283 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: oppD (oligopeptide ABC transporter ATP-binding protein OppD), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1281c oppD |
oligopeptide ABC transporter ATP-binding protein OppD | 999 | 999 ctx | neighborhood:806 fusion:796 cooccurence:774 database:900 |
Rv1283c oppB |
oligopeptide ABC transporter permease OppB | 999 | 999 ctx | neighborhood:882 cooccurence:774 coexpression:670 database:900 textmining:591 |
Rv3663c dppD |
dipeptide ABC transporter ATP-binding protein DppD | 998 | 998 ctx | fusion:847 cooccurence:768 coexpression:457 database:900 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 998 | 998 ctx | neighborhood:881 cooccurence:651 coexpression:428 database:900 textmining:405 |
Rv2585c |
lipoprotein | 962 | 957 | coexpression:438 database:900 |
Rv3665c dppB |
dipeptide ABC transporter permease DppB | 973 | 949 ctx | cooccurence:774 coexpression:668 textmining:498 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 810 | 801 | coexpression:801 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 799 | 799 | coexpression:799 |
Rv3143 |
response regulator | 782 | 774 | coexpression:774 |
Rv3666c dppA |
dipeptide ABC transporter substrate-binding lipoprotein DppA | 798 | 771 ctx | cooccurence:575 coexpression:416 |
Rv1284 canA |
beta-carbonic anhydrase | 767 | 757 ctx | neighborhood:756 |
Rv0178 |
Mce associated membrane protein | 734 | 735 | coexpression:735 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 636 | 613 | coexpression:449 |
Rv2326c |
ABC transporter ATP-binding protein | 723 | 572 | coexpression:455 |
Rv3231c hyp |
hypothetical protein | 449 | 449 | coexpression:449 |
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 permease OppC
- MTBC0 PGAP product: ABC transporter permease
- Pfam (hmmscan --cut_ga): OppC_N PF12911.13 (E=1e-10), BPD_transp_1 PF00528.28 (E=4e-25)
- (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_215798.1)
- Domains: Pfam-A via hmmscan --cut_ga — OppC_N (PF12911.13), BPD_transp_1 (PF00528.28)
- 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
COG1173 - Curated reference: UniProt P9WFZ9 (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 —
18 functional partner(s); context anchor
oppD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001372|Rv1282c|oppC MTEFASRRTLVVRRFLRNRAAVASLAALLLLFVSAYALPPLLPYSYDDLDFNALLQPPGTKHWLGTNALGQDLLAQTLRGMQKSMLIGVCVAVISTGIAATVGAISGYFGGWRDRTLMWVVDLLLVVPSFILIAIVTPRTKNSANIMFLVLLLAGFGWMISSRMVRGMTMSLREREFIRAARYMGVSSRRIIVGHVVPNVASILIIDAALNVAAAILAETGLSFLGFGIQPPDVSLGTLIADGTASATAFPWVFLFPASILVLILVCANLTGDGLRDALDPASRSLRRGVR