Polysaccharide Lyase Family 6; Polysaccharide Lyase Family 6 is a family of beta-helical ...
33-400
3.84e-128
Polysaccharide Lyase Family 6; Polysaccharide Lyase Family 6 is a family of beta-helical polysaccharide lyases. Members include alginate lyase (EC 4.2.2.3) and chondroitinase B (EC 4.2.2.19). Chondroitinase B is an enzyme that only cleaves the beta-(1,4)-linkage of dermatan sulfate (DS), leading to 4,5-unsaturated dermatan sulfate disaccharides as the product. DS is a highly sulfated, unbranched polysaccharide belonging to a family of glycosaminoglycans (GAGs) composed of alternating hexosamine (gluco- or galactosamine) and uronic acid (D-glucuronic or L-iduronic acid) moieties. DS contains alternating 1,4-beta-D-galactosamine (GalNac) and 1,3-alpha-L-iduronic acid units. The related chondroitin sulfate (CS) contains alternating GalNac and 1,3-beta-D-glucuronic acid units. Alginate lyases (known as either mannuronate (EC 4.2.2.3) or guluronate lyases (EC 4.2.2.11) catalyze the degradation of alginate, a copolymer of alpha-L-guluronate and its C5 epimer beta-D-mannuronate.
The actual alignment was detected with superfamily member PLN02188:
Pssm-ID: 450265 [Multi-domain] Cd Length: 404 Bit Score: 374.95 E-value: 3.84e-128
Glycosyl hydrolases family 28; Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2. ...
64-387
9.09e-65
Glycosyl hydrolases family 28; Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2.1.15 as well as rhamnogalacturonase A(RGase A), EC:3.2.1.-. These enzymes is important in cell wall metabolism.
Pssm-ID: 425588 [Multi-domain] Cd Length: 319 Bit Score: 209.55 E-value: 9.09e-65
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family ...
31-77
9.29e-04
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes fungal glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Trichoderma harzianum BGN13.1 and T. viride LamA1 in this family have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A and Chaetomium thermophilum CtLam55 are exo-acting enzymes. The CtLam55 substrate binding cleft exhibits restricted access on one side, thus rendering the enzyme as an exo-beta-1,3-glucanase; this has been confirmed by thin layer chromatography experiments. Also, a binding pocket was identified that could explain binding of branched laminarin and accumulation of laminaritriose. A similar binding pocket has been observed in T. chrysosporium Lam55A through structural studies and site-directed mutagenesis; both support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base.
Pssm-ID: 467840 [Multi-domain] Cd Length: 623 Bit Score: 41.35 E-value: 9.29e-04
Glycosyl hydrolases family 28; Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2. ...
64-387
9.09e-65
Glycosyl hydrolases family 28; Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2.1.15 as well as rhamnogalacturonase A(RGase A), EC:3.2.1.-. These enzymes is important in cell wall metabolism.
Pssm-ID: 425588 [Multi-domain] Cd Length: 319 Bit Score: 209.55 E-value: 9.09e-65
Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure ...
33-281
1.30e-05
Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28.
Pssm-ID: 403800 [Multi-domain] Cd Length: 213 Bit Score: 45.77 E-value: 1.30e-05
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family ...
31-77
9.29e-04
fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins; This family includes fungal glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Trichoderma harzianum BGN13.1 and T. viride LamA1 in this family have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A and Chaetomium thermophilum CtLam55 are exo-acting enzymes. The CtLam55 substrate binding cleft exhibits restricted access on one side, thus rendering the enzyme as an exo-beta-1,3-glucanase; this has been confirmed by thin layer chromatography experiments. Also, a binding pocket was identified that could explain binding of branched laminarin and accumulation of laminaritriose. A similar binding pocket has been observed in T. chrysosporium Lam55A through structural studies and site-directed mutagenesis; both support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base.
Pssm-ID: 467840 [Multi-domain] Cd Length: 623 Bit Score: 41.35 E-value: 9.29e-04
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.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
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.
Click here to see more details.
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
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
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
(CDART).
Modify your query to search against a different database and/or use advanced search options
