dppA Family assigned · medium auto-curated
H37Rv Rv3666c · MTBC0 mtbc0_003884 ·
541 aa · 4129289–4130914 (-) ·
RefSeq NP_218183.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dipeptide ABC transporter substrate-binding lipoprotein DppA |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter substrate-binding protein |
| Revised (this work) | ABC transporter substrate-binding protein. Pfam: SBP_bac_5 (PF00496.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X811
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable periplasmic dipeptide-binding lipoprotein DppA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | dppA |
| eggNOG description | Bacterial extracellular solute-binding proteins, family 5 Middle |
| Orthologous group | COG4166 |
| KEGG orthology |
K02035, K15580
|
| 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 | 0.666 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (241) · clonal |
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 |
|---|---|---|---|---|
SBP_bac_5 | PF00496.28 | 5.6e-52 | 77–462 | Bacterial extracellular solute-binding proteins, family 5 Middle |
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 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3665c dppB |
dipeptide ABC transporter permease DppB | 998 | 998 ctx | neighborhood:882 cooccurence:772 coexpression:475 database:900 |
Rv3664c dppC |
dipeptide ABC transporter permease DppC | 998 | 997 ctx | neighborhood:807 cooccurence:768 coexpression:425 database:900 textmining:665 |
Rv3663c dppD |
dipeptide ABC transporter ATP-binding protein DppD | 998 | 996 ctx | neighborhood:807 cooccurence:677 database:900 textmining:562 |
Rv3662c hyp |
hypothetical protein | 864 | 808 ctx | neighborhood:807 |
Rv1283c oppB |
oligopeptide ABC transporter permease OppB | 881 | 778 ctx | cooccurence:550 coexpression:470 textmining:487 |
Rv1282c oppC |
oligopeptide ABC transporter permease OppC | 798 | 771 ctx | cooccurence:575 coexpression:416 |
Rv0783c emrB |
multidrug resistance protein EmrB | 751 | 751 | coexpression:751 |
Rv2326c |
ABC transporter ATP-binding protein | 705 | 666 | |
Rv3667 acs |
acetyl-CoAsynthetase | 563 | 563 ctx | neighborhood:544 |
Rv1281c oppD |
oligopeptide ABC transporter ATP-binding protein OppD | 621 | 465 | |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 742 | 445 | textmining:555 |
Rv0928 pstS3 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 425 | 388 | |
Rv1244 lpqZ |
lipoprotein LpqZ | 524 | 365 | |
Rv0934 pstS1 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 453 | 364 | |
Rv3759c proX |
glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding lipoprotein ProX | 401 | 364 |
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 substrate-binding lipoprotein DppA
- MTBC0 PGAP product: ABC transporter substrate-binding protein
- Pfam (hmmscan --cut_ga): SBP_bac_5 PF00496.28 (E=6e-52)
- (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_218183.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBP_bac_5 (PF00496.28)
- 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
COG4166 - Curated reference: UniProt I6X811 (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 —
17 functional partner(s); context anchor
dppB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003884|Rv3666c|dppA MVRRMRAALAALATGLLVLAPVAGCGGGVLSPDVVLVNGGEPPNPLIPTGTNDSNGGRIIDRLFAGLMSYDAVGKPSLEVAQSIESADNVNYRITVKPGWKFTDGSPVTAHSFVDAWNYGALSTNAQLQQHFFSPIEGFDDVAGAPGDKSRTTMSGLRVVNDLEFTVRLKAPTIDFTLRLGHSSFYPLPDSAFRDMAAFGRNPIGNGPYKLADGPAGPAWEHNVRIDLVPNPDYHGNRKPRNKGLRFEFYANLDTAYADLLSGNLDVLDTIPPSALTVYQRDLGDHATSGPAAINQTLDTPLRLPHFGGEEGRLRRLALSAAINRPQICQQIFAGTRSPARDFTARSLPGFDPNLPGNEVLDYDPQRARRLWAQADAISPWSGRYAIAYNADAGHRDWVDAVANSIKNVLGIDAVAAPQPTFAGFRTQITNRAIDSAFRAGWQGDYPSMIEFLAPLFTAGAGSNDVGYINPEFDAALAAAEAAPTLTESHELVNDAQRILFHDMPVVPLWDYISVVGWSSQVSNVTVTWNGLPDYENIVKA