SUPERFAMILY 1.75 HMM library and genome assignments server

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CBD9-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Immunoglobulin-like beta-sandwich [ 48725] (28)
Superfamily:   CBD9-like [ 49344] (3)
Families:   Cytochrome domain of cellobiose dehydrogenase [ 49345]
  Family 9 carbohydrate-binding module, CBD9 [ 63677]
  Glucodextranase, domain C [ 101533]


Superfamily statistics
Genomes (589) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 1,664 14,444 5
Proteins 1,570 13,959 5


Functional annotation
General category Other
Detailed category Unknown function

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0.0000000000005162Moderately InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.00002076Least InformativeDirect
Enzyme Commission (EC)Glycosylases0.000000000005544Moderately InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR008960 SSF49344 Protein matches
Abstract

This entry represents an immunoglobulin-like beta-sandwich domain found in a variety of protein families, including family 9 carbohydrate-binding (CDB9) enzymes like endo-1,4-beta-xylanase , as the C-terminal domain of glucodextranase enzymes , and as the cytochrome domain of cellobiose dehydrogenase enzymes . In general, these domains consist of 7 beta-strands in 2 sheets with a Greek key topology, but with an additional beta-strand at the N-terminus [PubMed11371186, PubMed12796496].

Bacterial extracellular cellulases and hemicellulases are involved in the hydrolysis of the major structural polysaccharides of plant cell walls. These are usually modular enzymes that contain catalytic and non-catalytic domains. The CBD9 domain binds to cellulose, xylan, as well as to a range of soluble di- and mono-saccharides, and is found in cellulose- and xylan-degrading enzymes [PubMed9752722].

Cellobiose dehydrogenases (CDHs) are extracellular hemoflavoenzymes produced by various wood-degrading fungi that are involved in the degradation of cellulose and lignin [PubMed10725534]. These enzymes consist of a cytochrome domain and a flavin domain, which are believed to have evolved in parallel as fused genes, because the two domains can be cleaved proteolytically to make a functional cytochrome and flavodehydrogenase [PubMed10673428]. The b-type cytochrome domain contains a 6-coordinate low spin b-type haem with unusual iron ligands and coordination geometry.

Glucodextranase hydrolyzes alpha-1,6-glucosidic linkages of dextran from the non-reducing end to produce beta-D-glucose via an inverting reaction mechanism and classified into the glycoside hydrolase family 15 (GH15) [PubMed14660574].


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

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Worm Phenotype (WP) · Enzyme Commission (EC) ]

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 4 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 CBD9-like 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 4 hidden Markov models representing the CBD9-like 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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Enzyme Commission (EC) · Internal database links ]