L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
116-251
4.81e-41
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.
Pssm-ID: 341130 [Multi-domain] Cd Length: 121 Bit Score: 139.37 E-value: 4.81e-41
L,D-transpeptidase C-terminal domain; This is the C-terminal domain found in d-transpeptidases ...
254-317
3.81e-25
L,D-transpeptidase C-terminal domain; This is the C-terminal domain found in d-transpeptidases (Ldt) homologs from E.coli. Three of these enzymes (YbiS, ErfK, YcfS) have been shown to cross-link Braun's lipoprotein to the peptidoglycan (PG), while the other two (YnhG, YcbB) form direct meso-diaminopimelate (DAP-DAP, or 3-3) cross-links within the PG. Family members include erfK (ldtA), ybiS (ldtB), ycfS (ldtC), and ynhG (ldtE).
Pssm-ID: 465596 [Multi-domain] Cd Length: 67 Bit Score: 96.05 E-value: 3.81e-25
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
116-251
4.81e-41
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.
Pssm-ID: 341130 [Multi-domain] Cd Length: 121 Bit Score: 139.37 E-value: 4.81e-41
L,D-transpeptidase C-terminal domain; This is the C-terminal domain found in d-transpeptidases ...
254-317
3.81e-25
L,D-transpeptidase C-terminal domain; This is the C-terminal domain found in d-transpeptidases (Ldt) homologs from E.coli. Three of these enzymes (YbiS, ErfK, YcfS) have been shown to cross-link Braun's lipoprotein to the peptidoglycan (PG), while the other two (YnhG, YcbB) form direct meso-diaminopimelate (DAP-DAP, or 3-3) cross-links within the PG. Family members include erfK (ldtA), ybiS (ldtB), ycfS (ldtC), and ynhG (ldtE).
Pssm-ID: 465596 [Multi-domain] Cd Length: 67 Bit Score: 96.05 E-value: 3.81e-25
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
113-250
2.86e-14
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.
Pssm-ID: 461031 [Multi-domain] Cd Length: 89 Bit Score: 67.37 E-value: 2.86e-14
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
58-102
5.90e-07
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes.
Pssm-ID: 212030 [Multi-domain] Cd Length: 45 Bit Score: 45.55 E-value: 5.90e-07
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
60-103
3.21e-05
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known.
Pssm-ID: 396179 [Multi-domain] Cd Length: 43 Bit Score: 40.46 E-value: 3.21e-05
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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of your query sequence and the protein sequences used to curate the domain model,
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The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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Domains are color coded according to superfamilies
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Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
mapped to the query sequence.
Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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