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 (1,246) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,772 11,987 41
Proteins 4,805 9,709 39


Functional annotation
General category Metabolism
Detailed category Polysaccharide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)multicellular organismal process00.4442Least InformativeInherited
Biological Process (BP)developmental process01Least InformativeInherited
Biological Process (BP)organ development00.4587Moderately InformativeInherited
Biological Process (BP)tissue development00.1195Moderately InformativeInherited
Biological Process (BP)muscle structure development00.0001309InformativeDirect
Biological Process (BP)muscle organ development00.000003301Highly InformativeDirect
Molecular Function (MF)hydrolase activity00.006313Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds00.007323Moderately InformativeInherited
Molecular Function (MF)phosphoric diester hydrolase activity00.0003443Highly InformativeDirect

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) multicellular organismal process 0.4442 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.0000007897 Moderately Informative Direct
Biological Process (BP) organ development 0.4587 Moderately Informative Inherited
Biological Process (BP) tissue development 0.1195 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.09287 Moderately Informative Inherited
Biological Process (BP) muscle structure development 0.0001309 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.000000004245 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.001042 Informative Inherited
Biological Process (BP) muscle organ development 0.000003301 Highly Informative Direct
Biological Process (BP) polysaccharide catabolic process 0.0002257 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.006313 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.007323 Moderately Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.0002348 Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.0003443 Highly Informative Direct
Cellular Component (CC) protein complex 0.8894 Least Informative Inherited
Cellular Component (CC) membrane 0.9461 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.7546 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4185 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.000003374 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.0001508 Moderately Informative Direct
Cellular Component (CC) membrane region 0.0002922 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.07702 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.0000002999 Informative Direct
Cellular Component (CC) integral component of membrane 0.05102 Informative Inherited
Cellular Component (CC) integral component of organelle membrane 0.0000006706 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)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)Hydrolases0.000001685Least InformativeDirect
Enzyme Commission (EC)Lyases0.02255Least InformativeInherited
Enzyme Commission (EC)Glycosylases2.432e-16Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.000000000001435Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.00007773Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.01473Moderately InformativeInherited
Enzyme Commission (EC)Hexosyltransferases0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.0001359InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.0009169InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine phosphatase0.0005994Highly 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 degradation0.00000002026InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0.0000001846Least InformativeDirect
Post-translational modificationTransferase0.2539Least InformativeInherited
Post-translational modificationLyase0.00000001097Moderately InformativeDirect
Post-translational modificationGlycosidase0InformativeDirect
Post-translational modificationGlycosyltransferase0.000000000000009164InformativeDirect

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