dppB Family assigned · medium auto-curated
H37Rv Rv3665c · MTBC0 mtbc0_003883 ·
308 aa · 4128361–4129287 (-) ·
RefSeq NP_218182.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dipeptide ABC transporter permease DppB |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter permease |
| Revised (this work) | ABC transporter permease. Pfam: BPD_transp_1_N (PF19300.5), 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 |
I6YGV9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable dipeptide-transport integral membrane protein ABC transporter DppB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | dppB |
| eggNOG description | ABC transporter |
| Orthologous group | COG0601 |
| KEGG orthology |
K02033, K15581
|
| 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 | 0.333 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 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_N | PF19300.5 | 6.1e-06 | 4–77 | Binding-prot-dependent transport system membrane comp, N-term |
BPD_transp_1 | PF00528.28 | 1.7e-34 | 113–306 | Binding-protein-dependent transport system inner membrane component |
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:807 cooccurence:774 coexpression:678 database:900 textmining:458 |
Rv3666c dppA |
dipeptide ABC transporter substrate-binding lipoprotein DppA | 998 | 998 ctx | neighborhood:882 cooccurence:772 coexpression:475 database:900 |
Rv3663c dppD |
dipeptide ABC transporter ATP-binding protein DppD | 999 | 997 ctx | neighborhood:807 cooccurence:771 coexpression:478 database:900 textmining:732 |
Rv1282c oppC |
oligopeptide ABC transporter permease OppC | 973 | 949 ctx | cooccurence:774 coexpression:668 textmining:498 |
Rv1281c oppD |
oligopeptide ABC transporter ATP-binding protein OppD | 877 | 864 ctx | cooccurence:761 |
Rv3662c hyp |
hypothetical protein | 886 | 808 ctx | neighborhood:807 textmining:433 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 793 | 627 | coexpression:459 textmining:469 |
Rv3667 acs |
acetyl-CoAsynthetase | 553 | 554 ctx | neighborhood:544 |
Rv2585c |
lipoprotein | 591 | 546 | coexpression:456 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 564 | 537 | coexpression:458 |
Rv2326c |
ABC transporter ATP-binding protein | 671 | 530 | coexpression:470 |
Rv3104c |
transmembrane protein | 504 | 77 | textmining:485 |
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 permease DppB
- MTBC0 PGAP product: ABC transporter permease
- Pfam (hmmscan --cut_ga): BPD_transp_1_N PF19300.5 (E=6e-06), BPD_transp_1 PF00528.28 (E=2e-34)
- (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_218182.1)
- Domains: Pfam-A via hmmscan --cut_ga — BPD_transp_1_N (PF19300.5), 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
COG0601 - Curated reference: UniProt I6YGV9 (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 —
12 functional partner(s); context anchor
dppC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003883|Rv3665c|dppB MGWYVARRVAVMVPVFLGATLLIYGMVFLLPGDPVAALAGDRPLTPAVAAQLRSHYHLDDPFLVQYLRYLGGILHGDLGRAYSGLPVSAVLAHAFPVTIRLALIALAVEAVLGIGFGVIAGLRQGGIFDSAVLVTGLVIIAIPIFVLGFLAQFLFGVQLEIAPVTVGERASVGRLLLPGIVLGAMSFAYVVRLTRSAVAANAHADYVRTATAKGLSRPRVVTVHILRNSLIPVVTFLGADLGALMGGAIVTEGIFNIHGVGGVLYQAVTRQETPTVVSIVTVLVLIYLITNLLVDLLYAALDPRIRYG