SUPERFAMILY 1.75 HMM library and genome assignments server


Clathrin adaptor appendage domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Immunoglobulin-like beta-sandwich [ 48725] (28)
Superfamily:   Clathrin adaptor appendage domain [ 49348] (3)
Families:   Alpha-adaptin ear subdomain-like [ 49349] (2)
  gamma-adaptin C-terminal appendage domain-like [ 74857] (3)
  Coatomer appendage domain [ 101536]


Superfamily statistics
Genomes (455) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,997 2,609 16
Proteins 2,994 2,603 16


Functional annotation
General category Processes_IC
Detailed category 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) localization 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 1.302e-09 Least Informative Direct
Biological Process (BP) developmental process 0.6996 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.3168 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.02033 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) system process 4.142e-07 Moderately Informative Direct
Biological Process (BP) macromolecule localization 1.898e-05 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.3281 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.5919 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2939 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.00756 Moderately Informative Inherited
Biological Process (BP) organ development 0.7333 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.6723 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1878 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) transmission of nerve impulse 2.102e-11 Informative Direct
Biological Process (BP) cell-cell signaling 5.779e-10 Informative Direct
Biological Process (BP) membrane organization 8.349e-10 Informative Direct
Biological Process (BP) secretion by cell 1.267e-05 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 6.513e-05 Informative Direct
Biological Process (BP) regulation of immune effector process 0.0001163 Informative Direct
Biological Process (BP) protein complex assembly 0.0004902 Informative Direct
Biological Process (BP) sensory organ development 0.0007056 Informative Direct
Biological Process (BP) regulation of defense response 0.003708 Informative Inherited
Biological Process (BP) organelle localization 0.1985 Informative Inherited
Biological Process (BP) vesicle organization 1.932e-15 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 8.115e-08 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 3.378e-06 Highly Informative Direct
Biological Process (BP) regulation of response to biotic stimulus 4.407e-06 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 5.336e-06 Highly Informative Direct
Biological Process (BP) neurotransmitter transport 1.428e-05 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 0.0002214 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.0005814 Highly Informative Direct
Biological Process (BP) establishment of vesicle localization 0.000742 Highly Informative Direct
Biological Process (BP) synaptic vesicle localization 0.01239 Highly Informative Inherited
Biological Process (BP) signal release 0.007282 Highly Informative Inherited
Molecular Function (MF) binding 7.516e-05 Least Informative Direct
Molecular Function (MF) transporter activity 7.495e-07 Moderately Informative Direct
Molecular Function (MF) protein transporter activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 5.435e-06 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0002247 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.1659 Least Informative Inherited
Cellular Component (CC) protein complex 0.005599 Least Informative Inherited
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.273e-10 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.575 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 4.353e-14 Informative Direct
Cellular Component (CC) coated vesicle 1.009e-07 Informative Direct
Cellular Component (CC) synapse part 8.285e-06 Informative Direct
Cellular Component (CC) endosome 0.01722 Informative Inherited
Cellular Component (CC) trans-Golgi network 0 Highly Informative Direct
Cellular Component (CC) coated pit 0 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 5.069e-11 Highly Informative Direct
Cellular Component (CC) Golgi membrane 1.446e-09 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 2.201e-07 Highly Informative Direct
Cellular Component (CC) recycling endosome 7.351e-05 Highly Informative Direct
Cellular Component (CC) endocytic vesicle 1 Highly Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 0.2253 Highly Informative Inherited
Cellular Component (CC) transport vesicle 0.007092 Highly Informative Inherited

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.3444Least InformativeInherited
Mammalian Phenotype (MP)abnormal circulating glucose level0.003381InformativeInherited
Mammalian Phenotype (MP)decreased birth weight2.128e-05Highly InformativeDirect
Mammalian Phenotype (MP)hypoglycemia2.823e-05Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.01832Least InformativeInherited
Worm Phenotype (WP)locomotion variant0.0009551Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00121Moderately InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentEndosome2.045e-10Moderately InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
DomainRepeat1.081e-14Least InformativeDirect
Molecular functionLipid-binding1.167e-09InformativeDirect
Post-translational modificationPhosphoprotein8.336e-06Least InformativeDirect
Post-translational modificationUbl conjugation0.0007166Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013041 SSF49348 Protein matches
Abstract

This entry represents a beta-sandwich structural motif found in the appendage (ear) domain of alpha-, beta- and gamma-adaptin from AP clathrin adaptor complexes, the GAE (gamma-adaptin ear) domain of GGA adaptor proteins, and the appendage domain of the gamma subunit of coatomer complexes. These domains have an immunoglobulin-like beta-sandwich fold containing 7 or 8 strands in 2 beta-sheets in a Greek key topology [PubMed12042876, PubMed12808037, PubMed14527408]. Although the appendage domains from AP / GGA adaptins and coatomers share a similar fold, there is little sequence identity between them. However, they also share similar motif-based cargo recognition and accessory factor recruitment mechanisms.

More information about these proteins can be found at Protein of the Month: Clathrin.


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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 8 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 Clathrin adaptor appendage domain 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 8 hidden Markov models representing the Clathrin adaptor appendage domain 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]