SUPERFAMILY 1.75 HMM library and genome assignments server

Chondroitin AC/alginate lyase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   alpha/alpha toroid [ 48207] (6)
Superfamily:   Chondroitin AC/alginate lyase [ 48230] (2)
Families:   Alginate lyase A1-III [ 48231]
  Hyaluronate lyase-like catalytic, N-terminal domain [ 48234] (4)


Superfamily statistics
Genomes (854) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,745 11,305 21
Proteins 1,741 11,288 21


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0.00002498 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.03 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.02315 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.02077 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0000000001338 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0000008665 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.005514 Moderately Informative Inherited
Biological Process (BP) glycosaminoglycan metabolic process 0.00000000000005424 Highly Informative Direct
Molecular Function (MF) lyase activity 0.0000004556 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0InformativeDirect
Enzyme Commission (EC)Hyaluronate lyase0.000002852Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.2647Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0.0008288InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives0.000009473Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0.00007186Moderately InformativeDirect
Cellular componentPeriplasm0InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionCalcium0.0001029Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)glycan metabolism0Moderately InformativeDirect
UniPathway (UP)glycosaminoglycan metabolism0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR008929 SSF48230 Protein matches
Abstract

Glycosaminoglycans (GAGs) are highly negatively charged polysaccharides, formed from disaccharide repeating units. For a number of bacterial species, including Flavobacterium heparinum synthesize GAG lyases, these enzymes are used to degrade and utilise glycosaminoglycans as a source of carbon in the bacterium's natural environment. In topological terms, the known structures of polysaccharide lyases fall within two protein fold families. Pectin and pectate lyases, as well as chondroitin lyase B belong to the right-handed parallel beta-helix family and have the substrate-binding site in roughly the same topological location. The second topological family, all of which contain a domain consisting of an incomplete (alpha/alpha)5 toroid, includes chondroitin AC lyase family, and alginate lyase A1-III family from Sphingomonas species A1 [PubMed11327856].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 7 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Chondroitin AC/alginate lyase domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 7 hidden Markov models representing the Chondroitin AC/alginate lyase superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]