SUPERFAMILY 1.75 HMM library and genome assignments server

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Starch-binding domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Prealbumin-like [ 49451] (7)
Superfamily:   Starch-binding domain-like [ 49452] (3)
Families:   Rhamnogalacturonase B, RhgB, middle domain [ 110091]
  Starch-binding domain [ 49453] (3)
  PUD-like [ 158932]


Superfamily statistics
Genomes (1,253) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 5,802 37,354 41
Proteins 4,830 30,546 39


Functional annotation
General category Metabolism
Detailed category Polysaccharide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0.0163Least InformativeInherited
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.0000000000004855Moderately InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0InformativeDirect
Enzyme Commission (EC)Rhamnogalacturonan endolyase0Highly InformativeDirect
Enzyme Commission (EC)Cyclomaltodextrin glucanotransferase0Highly InformativeDirect
Enzyme Commission (EC)Pullulanase0.0000000000003917Highly InformativeDirect
Enzyme Commission (EC)Alpha-amylase0.0000001277Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.000008141Least InformativeDirect
Enzyme Commission (EC)Lyases0.00001371Least InformativeDirect
Enzyme Commission (EC)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.00000000006697Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.00000000008658Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.01108Moderately InformativeInherited
Enzyme Commission (EC)Hexosyltransferases0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.000115InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.0008655InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine phosphatase0.0006219Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR013784 SSF49452 Protein matches
Abstract

This entry represents domains with a carbohydrate-binding-like fold, which consists of a seven-stranded beta-sandwich with a Greek key topology, although some members may have 1-2 extra strands. These domains are present as carbohydrate-binding modules in a number of glycosyl hydrolases, often at the C-terminal end, as well as in rhamnogalacturonase B (RhgB), where it occurs as a central domain [PubMed12741813, PubMed15135077].


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) · Arabidopsis Plant Ontology (AP) · 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 15 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 Starch-binding domain-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 15 hidden Markov models representing the Starch-binding domain-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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]