oppD Family assigned · medium auto-curated
H37Rv Rv1281c · MTBC0 mtbc0_001371 ·
612 aa · 1442416–1444254 (-) ·
RefSeq NP_215797.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oligopeptide ABC transporter ATP-binding protein OppD |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter ATP-binding protein |
| Revised (this work) | ABC transporter ATP-binding protein. Pfam: oligo_HPY (PF08352.18), ABC_tran (PF00005.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQJ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Oligopeptide transport ATP-binding protein OppD |
| EC (curated) |
EC 7.4.2.6
|
| Curated function | Part of the ABC transporter complex OppABCD involved in the uptake of oligopeptides. Responsible for energy coupling to the transport system. 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 |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | oppD |
| eggNOG description | Belongs to the ABC transporter superfamily |
| Orthologous group | COG1123 |
| KEGG orthology |
K02031, K02032
|
| KEGG pathways |
map02024
|
| KEGG modules |
M00239
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, 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 | 0.68 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 11 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 |
|---|---|---|---|---|
oligo_HPY | PF08352.18 | 3.8e-16 | 234–299 | Oligopeptide/dipeptide transporter, C-terminal region |
ABC_tran | PF00005.34 | 6.8e-32 | 378–527 | ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: oppC (oligopeptide ABC transporter permease OppC), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1282c oppC |
oligopeptide ABC transporter permease OppC | 999 | 999 ctx | neighborhood:806 fusion:796 cooccurence:774 database:900 |
Rv1283c oppB |
oligopeptide ABC transporter permease OppB | 998 | 997 ctx | neighborhood:816 cooccurence:773 coexpression:404 database:900 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 993 | 993 ctx | neighborhood:802 cooccurence:617 database:900 |
Rv3664c dppC |
dipeptide ABC transporter permease DppC | 978 | 971 ctx | fusion:822 cooccurence:769 |
Rv2585c |
lipoprotein | 916 | 916 | database:900 |
Rv3663c dppD |
dipeptide ABC transporter ATP-binding protein DppD | 917 | 915 | database:900 |
Rv3665c dppB |
dipeptide ABC transporter permease DppB | 877 | 864 ctx | cooccurence:761 |
Rv1284 canA |
beta-carbonic anhydrase | 506 | 506 ctx | neighborhood:505 |
Rv3666c dppA |
dipeptide ABC transporter substrate-binding lipoprotein DppA | 621 | 465 |
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 ATP-binding protein OppD
- MTBC0 PGAP product: ABC transporter ATP-binding protein
- Pfam (hmmscan --cut_ga): oligo_HPY PF08352.18 (E=4e-16), ABC_tran PF00005.34 (E=7e-32)
- (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_215797.1)
- Domains: Pfam-A via hmmscan --cut_ga — oligo_HPY (PF08352.18), ABC_tran (PF00005.34)
- 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
COG1123 - Curated reference: UniProt P9WQJ5 (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 —
9 functional partner(s); context anchor
oppC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001371|Rv1281c|oppD MSPLLEVTDLAVTFRTDGDPVTAVRGISYRVEPGEVVAMVGESGSGKSAAAMAVVGLLPEYAQVRGSVRLQGTELLGLADNAMSRFRGKAIGTVFQDPMSALTPVYTVGDQIAEAIEVHQPRVGKKAARRRAVELLDLVGISQPQRRSRAFPHELSGGERQRVVIAIAIANDPDLLICDEPTTALDVTVQAQILDVLKAARDVTGAGVLIITHDLGVVAEFADRALVMYAGRVVESAGVNDLYRDRRMPYTVGLLGSVPRLDAAQGTRLVPIPGAPPSLAGLAPGCPFAPRCPLVIDECLTAEPELLDVATDHRAACIRTELVTGRSAADIYRVKTEARPAALGDASVVVRVRHLVKTYRLAKGVVLRRAIGEVRAVDGISLELRQGRTLGIVGESGSGKSTTLHEILELAAPQSGSIEVLGTDVATLGTAERRSLRRDIQVVFQDPVASLDPRLPVFDLIAEPLQANGFGKNETHARVAELLDIVGLRHGDASRYPAEFSGGQKQRIGIARALALQPKILALDEPVSALDVSIQAGIINLLLDLQEQFGLSYLFVSHDLSVVKHLAHQVAVMLAGTVVEQGDSEEVFGNPKHEYTRRLLGAVPQPDPARRG