dppC Family assigned · medium auto-curated
H37Rv Rv3664c · MTBC0 - ·
266 aa · 4103675–4104475 (-) ·
RefSeq NP_218181.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dipeptide ABC transporter permease DppC |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Dipeptide ABC transporter permease DppC. Pfam: 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
L0TEV4
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable dipeptide-transport integral membrane protein ABC transporter DppC |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismP Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | dppC |
| eggNOG description | ABC transporter |
| Orthologous group | COG1173 |
| KEGG orthology |
K02034, K15582
|
| KEGG pathways |
map01501, map02010, map02024
|
| KEGG modules |
M00239, M00439
|
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 | 1.489 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 5.4e-32 | 79–261 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dppB (dipeptide ABC transporter permease DppB), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3665c dppB |
dipeptide ABC transporter permease DppB | 999 | 999 ctx | neighborhood:807 cooccurence:774 coexpression:678 database:900 textmining:458 |
Rv3663c dppD |
dipeptide ABC transporter ATP-binding protein DppD | 999 | 999 ctx | neighborhood:882 fusion:478 cooccurence:773 coexpression:560 database:900 textmining:596 |
Rv3666c dppA |
dipeptide ABC transporter substrate-binding lipoprotein DppA | 998 | 997 ctx | neighborhood:807 cooccurence:768 coexpression:425 database:900 textmining:665 |
Rv1281c oppD |
oligopeptide ABC transporter ATP-binding protein OppD | 978 | 971 ctx | fusion:822 cooccurence:769 |
Rv1283c oppB |
oligopeptide ABC transporter permease OppB | 981 | 937 ctx | cooccurence:774 coexpression:670 textmining:711 |
Rv3662c hyp |
hypothetical protein | 917 | 882 ctx | neighborhood:881 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 839 | 633 | coexpression:429 textmining:580 |
Rv3667 acs |
acetyl-CoAsynthetase | 552 | 553 ctx | neighborhood:544 |
Rv2326c |
ABC transporter ATP-binding protein | 590 | 552 | coexpression:453 |
Rv2585c |
lipoprotein | 586 | 525 | coexpression:429 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 544 | 516 | coexpression:432 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): dipeptide ABC transporter permease DppC
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=5e-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_218181.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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 L0TEV4 (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 —
11 functional partner(s); context anchor
dppB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3664c|dppC MIAAALILLILVVAAFPSLFTAADPTYADPSQSMLAPSAAHWFGTDLQGHDIYSRTVYGARASVTVGLGATLAVFVVGGALGALAGFYGSWIDAVVSRVTDVFLGLPLLLAAIVLMQVMHHRTVWTVIAILALFGWPQVARIARGAVLEVRASDYVLAAKALGLNRFQILLRHALPNAVGPVIAVATVALGIFIVTEATLSYLGVGLPTSVVSWGGDINVAQTRLRSGSPILFYPAGALAITVLAFMMMGDALRDALDPASRAWRA