SUPERFAMILY 1.75 HMM library and genome assignments server

  Home > SCOP hierarchy > Subdomain of clathrin and coatomer appendage domain superfamily


Subdomain of clathrin and coatomer appendage domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Subdomain of clathrin and coatomer appendage domain [ 55710]
Superfamily:   Subdomain of clathrin and coatomer appendage domain [ 55711] (2)
Families:   Clathrin adaptor appendage, alpha and beta chain-specific domain [ 55712] (2)
  Coatomer appendage domain [ 103159]

 Superfamily statistics
Genomes (439) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,540 1,330 7
Proteins 1,540 1,330 7

 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) single-organism cellular process 2.29e-05 Least Informative Direct
Biological Process (BP) localization 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.2525 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.03343 Least Informative Inherited
Biological Process (BP) system process 0.0001173 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0004757 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.03177 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.621 Moderately Informative Inherited
Biological Process (BP) synaptic transmission 1.158e-08 Informative Direct
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) cellular membrane organization 3.145e-05 Informative Direct
Biological Process (BP) vesicle-mediated transport 4.537e-11 Informative Direct
Biological Process (BP) vesicle organization 1.384e-11 Highly Informative Direct
Biological Process (BP) synaptic vesicle transport 0.000454 Highly Informative Direct
Molecular Function (MF) binding 0.03988 Least Informative Inherited
Molecular Function (MF) protein binding 0.000827 Moderately Informative Direct
Cellular Component (CC) membrane 6.689e-13 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1.24e-08 Least Informative Direct
Cellular Component (CC) protein complex 4.132e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.7289 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.001115 Least Informative Inherited
Cellular Component (CC) endomembrane system 5.691e-13 Moderately Informative Direct
Cellular Component (CC) organelle membrane 2.003e-05 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.009545 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 7.356e-05 Informative Direct
Cellular Component (CC) coated vesicle 0.001355 Informative Inherited
Cellular Component (CC) Golgi membrane 5.262e-05 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 2.129e-09 Highly Informative Direct
Cellular Component (CC) coated pit 0 Highly Informative Direct
Cellular Component (CC) vesicle membrane 3.129e-15 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 9.13e-15 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0.002583 Highly Informative Inherited
Cellular Component (CC) endocytic vesicle 0.6465 Highly Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 0.9827 Highly Informative Inherited

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least 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)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)lung0InformativeDirect
Xenopus ANatomical entity (XAN)spleen0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)plant cell0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0.0006465Moderately 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 componentCoated pit0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionLipid-binding2.07e-11InformativeDirect
Post-translational modificationPhosphoprotein0.0003019Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009028 SSF55711 Protein matches
Abstract

The alpha and beta2 adaptor subunits can each be divided into a trunk domain and the appendage domain (or ear domain), separated by a linker region. Clathrin polymerisation is promoted by its binding to the beta2 appendage and hinge domains. The alpha appendage domain interacts with a number of accessory proteins, including eps15, epsin, amphiphysin, AP180, auxilin, numb, and Dab2, thereby regulating the translocation of these proteins to the bud site.

This entry represents a subdomain of the appendage (ear) domain of alpha- and beta-adaptin from AP clathrin adaptor complexes, and the appendage domain of the gamma subunit of coatomer complexes. These domains have a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet [PubMed10430869, PubMed10944104, [PubMed14690497]. Although the appendage domains from AP 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) · Worm Phenotype (WP) · 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 3 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 Subdomain of clathrin and coatomer 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 3 hidden Markov models representing the Subdomain of clathrin and coatomer 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.