dacB1 Resolved · high auto-curated
H37Rv Rv3330 · MTBC0 mtbc0_003543 ·
405 aa · 3741762–3742979 (+) ·
RefSeq NP_217847.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | penicillin-binding protein DacB |
|---|---|
| MTBC0 PGAP re-annotation | D-alanyl-D-alanine carboxypeptidase DacB1 |
| Revised (this work) | D-alanyl-D-alanine carboxypeptidase DacB1. Pfam: Peptidase_S11 (PF00768.26), Beta-lactamase2 (PF13354.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53380
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | D-alanyl-D-alanine carboxypeptidase DacB1 |
| EC (curated) |
EC 3.4.16.-
|
| Curated function | Probably cleaves the terminal D-Ala-D-Ala dipeptide of the peptidoglycan stem peptide (Probable). Shows weak D,D-carboxypeptidase activity in vitro. Acts on the synthetic penta-peptide substrate Penta-DAP (L-Ala-gamma-D-Gln-DAP-D-Ala-D-Ala). The catalytic domain binds weakly to peptidoglycan in vitro. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | dacC |
| eggNOG description | Belongs to the peptidase S11 family |
| Orthologous group | COG1686 |
| EC number |
EC 3.4.16.4
|
| KEGG orthology |
K07258
|
| KEGG pathways |
map00550, map01100
|
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 | 0.299 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
Peptidase_S11 | PF00768.26 | 4.0e-36 | 88–310 | D-alanyl-D-alanine carboxypeptidase |
Beta-lactamase2 | PF13354.13 | 1.2e-08 | 97–216 | Beta-lactamase enzyme family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nagA (N-acetylglucosamine-6-phosphate deacetylase NagA), high confidence from genomic context alone (score 705 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2911 dacB2 |
penicillin-binding protein DacB2 | 921 | 911 | database:900 |
Rv3627c dacB hyp |
hypothetical protein | 995 | 900 | database:900 textmining:954 |
Rv3332 nagA |
N-acetylglucosamine-6-phosphate deacetylase NagA | 938 | 705 ctx | neighborhood:659 textmining:801 |
Rv3331 sugI |
sugar-transport integral membrane protein SugI | 840 | 656 ctx | neighborhood:654 textmining:556 |
Rv3329 |
aminotransferase | 909 | 654 ctx | neighborhood:628 textmining:750 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 886 | 643 | database:500 textmining:695 |
Rv0017c rodA |
cell division protein RodA | 661 | 630 | database:500 |
Rv2518c ldtB |
L,D-transpeptidase LdtB | 699 | 587 | database:500 |
Rv0192 hyp |
hypothetical protein | 598 | 576 | database:500 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 459 | 459 ctx | neighborhood:457 |
Rv2864c |
penicillin-binding lipoprotein | 820 | 450 | coexpression:432 textmining:687 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 708 | 391 | textmining:542 |
Rv2154c ftsW |
lipid II flippase FtsW | 442 | 389 | |
Rv0016c pbpA |
penicillin-binding protein PbpA | 607 | 328 | textmining:439 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 402 | 327 |
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: penicillin-binding protein DacB
- MTBC0 PGAP product: D-alanyl-D-alanine carboxypeptidase DacB1
- Pfam (hmmscan --cut_ga): Peptidase_S11 PF00768.26 (E=4e-36), Beta-lactamase2 PF13354.13 (E=1e-08)
- (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_217847.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_S11 (PF00768.26), Beta-lactamase2 (PF13354.13)
- 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
COG1686 - Curated reference: UniProt O53380 (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 —
33 functional partner(s); context anchor
nagA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003543|Rv3330|dacB1 MAFLRSVSCLAAAVFAVGTGIGLPTAAGEPNAAPAACPYKVSTPPAVDSSEVPAAGEPPLPLVVPPTPVGGNALGGCGIITAPGSAPAPGDVSAEAWLVADLDSGAVIAARDPHGRHRPASVIKVLVAMASINTLTLNKSVAGTADDAAVEGTKVGVNTGGTYTVNQLLHGLLMHSGNDAAYALARQLGGMPAALEKINLLAAKLGGRDTRVATPSGLDGPGMSTSAYDIGLFYRYAWQNPVFADIVATRTFDFPGHGDHPGYELENDNQLLYNYPGALGGKTGYTDDAGQTFVGAANRDGRRLMTVLLHGTRQPIPPWEQAAHLLDYGFNTPAGTQIGTLIEPDPSLMSTDRNPADRQRVDPQAAARISAADALPVRVGVAVIGALIVFGLIMVARAMNRRPQH