dppD Family assigned · medium auto-curated
H37Rv Rv3663c · MTBC0 mtbc0_003881 ·
548 aa · 4125862–4127508 (-) ·
RefSeq NP_218180.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dipeptide ABC transporter ATP-binding protein DppD |
|---|---|
| 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 |
I6Y482
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable dipeptide-transport ATP-binding protein ABC transporter DppD |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | dppD |
| eggNOG description | Belongs to the ABC transporter superfamily |
| Orthologous group | COG1123 |
| KEGG orthology |
K02031, K02032
|
| KEGG pathways |
map02024
|
| KEGG modules |
M00239
|
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 | 0.292 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 | 7.7e-05 | 233–267 | Oligopeptide/dipeptide transporter, C-terminal region |
ABC_tran | PF00005.34 | 6.5e-31 | 308–459 | ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dppC (dipeptide ABC transporter permease DppC), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3664c dppC |
dipeptide ABC transporter permease DppC | 999 | 999 ctx | neighborhood:882 fusion:478 cooccurence:773 coexpression:560 database:900 textmining:596 |
Rv1282c oppC |
oligopeptide ABC transporter permease OppC | 998 | 998 ctx | fusion:847 cooccurence:768 coexpression:457 database:900 |
Rv3665c dppB |
dipeptide ABC transporter permease DppB | 999 | 997 ctx | neighborhood:807 cooccurence:771 coexpression:478 database:900 textmining:732 |
Rv3666c dppA |
dipeptide ABC transporter substrate-binding lipoprotein DppA | 998 | 996 ctx | neighborhood:807 cooccurence:677 database:900 textmining:562 |
Rv1283c oppB |
oligopeptide ABC transporter permease OppB | 997 | 989 ctx | cooccurence:765 coexpression:473 database:900 textmining:791 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 989 | 934 | database:900 textmining:851 |
Rv2585c |
lipoprotein | 944 | 922 | database:900 |
Rv1281c oppD |
oligopeptide ABC transporter ATP-binding protein OppD | 917 | 915 | database:900 |
Rv3662c hyp |
hypothetical protein | 928 | 883 ctx | neighborhood:881 textmining:412 |
Rv2325c hyp |
hypothetical protein | 815 | 792 | experimental:652 |
Rv0408 pta |
phosphate acetyltransferase | 706 | 706 | coexpression:703 |
Rv3667 acs |
acetyl-CoAsynthetase | 560 | 549 ctx | neighborhood:544 |
Rv1286 cysC |
adenylyl-sulfate kinase | 490 | 472 | coexpression:454 |
Rv1735c |
membrane protein | 415 | 416 | coexpression:416 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 494 | 70 | textmining:479 |
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: dipeptide ABC transporter ATP-binding protein DppD
- MTBC0 PGAP product: ABC transporter ATP-binding protein
- Pfam (hmmscan --cut_ga): oligo_HPY PF08352.18 (E=8e-05), ABC_tran PF00005.34 (E=6e-31)
- (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_218180.1)
- 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 I6Y482 (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 —
16 functional partner(s); context anchor
dppC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003881|Rv3663c|dppD MSVPAAPLLSVEGLEVTFGTDAPAVCGVDLAVRSGQTVAVVGESGSGKSTTAAAILGLLPAGGRITAGRVVFDGRDITGADAKRLRSIRGREIGYVPQDPMTNLNPVWKVGFQVTEALRANTDGRAARRRAVELLAEAGLPDPAKQAGRYPHQLSGGMCQRALIAIGLAGRPRLLIADEPTSALDVTVQRQVLDHLQGLTDELGTALLLITHDLALAAQRAEAVVVVRRGVVVESGAAQSILQSPQHEYTRRLVAAAPSLTARSRRPPESRSRATTQAGDILVVSELTKIYRESRGAPWRRVESRAVDGVSFRLPRASTLAIVGESGSGKSTLARMVLGLLQPTSGTVVFDGTYDVGALARDQVLAFRRRVQPVFQNPYSSLDPMYSVFRAIEEPLRVHHVGDRRQRQRAVRELVDQVALPSSILGRRPRELSGGQRQRVAIARALALRPEVLVCDEAVSALDVLVQAQILDLLADLQADLGLTYLFISHDLAVIRQIADDVLVMRAGRVVEHASTEEVFSRPRHEYTRQLLQAIPGAPSAPRKVGNL