SUPERFAMILY 1.75 HMM library and genome assignments server


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 (1,244) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,710 11,987 41
Proteins 4,750 9,709 39


Functional annotation
General category Metabolism
Detailed category Polysaccharide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) carbohydrate metabolic process 2.046e-07 Moderately Informative Direct
Biological Process (BP) polysaccharide metabolic process 1.474e-09 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.00108 Informative Inherited
Biological Process (BP) polysaccharide catabolic process 0.0002402 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.0001221 Informative Direct
Cellular Component (CC) protein complex 0.7836 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.6202 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2341 Least Informative Inherited
Cellular Component (CC) membrane 0.6923 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 1.195e-06 Moderately Informative Direct
Cellular Component (CC) endomembrane system 6.96e-05 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.00102 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.08503 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 1.407e-07 Informative Direct
Cellular Component (CC) integral to membrane 0.01849 Informative Inherited
Cellular Component (CC) intrinsic to organelle membrane 5.587e-07 Highly Informative Direct

Document: GO annotation of SCOP domains

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)Glycosyltransferases4.855e-13Moderately InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0InformativeDirect
Enzyme Commission (EC)Rhamnogalacturonan endolyase0Highly InformativeDirect
Enzyme Commission (EC)Cyclomaltodextrin glucanotransferase0Highly InformativeDirect
Enzyme Commission (EC)Pullulanase3.917e-13Highly InformativeDirect
Enzyme Commission (EC)Alpha-amylase1.277e-07Highly 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)Hydrolases1.55e-06Least InformativeDirect
Enzyme Commission (EC)Lyases0.02206Least InformativeInherited
Enzyme Commission (EC)Glycosylases2.422e-16Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases1.328e-12Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases7.863e-05Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.01475Moderately InformativeInherited
Enzyme Commission (EC)Hexosyltransferases0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.0001366InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.0009212InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine phosphatase0.0006026Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processPolysaccharide degradation1.974e-08InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase1.727e-07Least InformativeDirect
Post-translational modificationTransferase0.2541Least InformativeInherited
Post-translational modificationLyase1.029e-08Moderately InformativeDirect
Post-translational modificationGlycosidase0InformativeDirect
Post-translational modificationGlycosyltransferase9.158e-15InformativeDirect

Document: KW 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]