SUPERFAMILY 1.75 HMM library and genome assignments server


alpha-catenin/vinculin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Four-helical up-and-down bundle [ 47161] (28)
Superfamily:   alpha-catenin/vinculin-like [ 47220] (2)
Families:   alpha-catenin/vinculin [ 47221] (2)
  VBS domain [ 140408]


Superfamily statistics
Genomes (142) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,952 3,586 19
Proteins 1,127 1,069 11


Functional annotation
General category Processes_EC
Detailed category Cell adhesion

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) developmental process 0.0003648 Least Informative Direct
Biological Process (BP) single-organism cellular process 1.133e-05 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 9.403e-13 Least Informative Direct
Biological Process (BP) localization 0.009469 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.9167 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.008941 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.0008812 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0002964 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0008516 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0001379 Moderately Informative Direct
Biological Process (BP) cellular localization 0.01934 Moderately Informative Inherited
Biological Process (BP) system process 0.004714 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.0177 Moderately Informative Inherited
Biological Process (BP) organ development 0.9205 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.006422 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.006052 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.008164 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.05527 Moderately Informative Inherited
Biological Process (BP) cytoskeleton organization 2.86e-11 Informative Direct
Biological Process (BP) synaptic transmission 2.536e-05 Informative Direct
Biological Process (BP) biological adhesion 0 Informative Direct
Biological Process (BP) cell projection organization 3.089e-08 Informative Direct
Biological Process (BP) regulation of locomotion 1.755e-07 Informative Direct
Biological Process (BP) generation of neurons 1.43e-06 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0002829 Informative Direct
Biological Process (BP) central nervous system development 0.008281 Informative Inherited
Biological Process (BP) organ morphogenesis 0.005375 Informative Inherited
Biological Process (BP) actin filament-based process 0.001866 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.003776 Informative Inherited
Biological Process (BP) cell adhesion 0 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.0006724 Highly Informative Direct
Biological Process (BP) maintenance of location 1.36e-11 Highly Informative Direct
Biological Process (BP) cell projection assembly 0.01588 Highly Informative Inherited
Molecular Function (MF) binding 3.425e-07 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.0002832 Moderately Informative Direct
Molecular Function (MF) protein binding 1.45e-11 Moderately Informative Direct
Molecular Function (MF) cytoskeletal protein binding 2.773e-09 Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 3.131e-05 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.01054 Least Informative Inherited
Cellular Component (CC) cell projection 6.541e-13 Moderately Informative Direct
Cellular Component (CC) cell junction 0 Informative Direct
Cellular Component (CC) cell leading edge 0 Informative Direct
Cellular Component (CC) contractile fiber part 0 Informative Direct
Cellular Component (CC) synapse 9.498e-07 Informative Direct
Cellular Component (CC) neuron part 0.00233 Informative Inherited
Cellular Component (CC) adherens junction 0 Highly Informative Direct
Cellular Component (CC) lamellipodium 2.739e-06 Highly Informative Direct
Cellular Component (CC) cell-substrate junction 0.01314 Highly Informative Inherited
Cellular Component (CC) cell-cell junction 0.9407 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)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect
Mammalian Phenotype (MP)muscle phenotype0.02578Moderately InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organ system development variant0.0005268Moderately InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect

Document: FA 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least 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)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation2.667e-10Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Cellular componentMembrane1.227e-12Least InformativeDirect
Cellular componentCytoplasm2.128e-09Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentCell junction0Moderately InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentCell projection6.395e-16Moderately InformativeDirect
Molecular functionActin-binding0InformativeDirect
Post-translational modificationDevelopmental protein1.122e-09Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation2.671e-07Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006077 SSF47220 Protein matches
Abstract

Vinculin is a eukaryotic protein that seems to be involved in the attachment of the actin-based microfilaments to the plasma membrane. Vinculin is located at the cytoplasmic side of focal contacts or adhesion plaques [PubMed2112986]. In addition to actin, vinculin interacts with other structural proteins such as talin and alpha-actinins.

Vinculin is a large protein of 116 kDa (about a 1000 residues). Structurally the protein consists of an acidic N-terminal domain of about 90 kDa separated from a basic C-terminal domain of about 25 kDa by a proline-rich region of about 50 residues. The central part of the N-terminal domain consists of a variable number (3 in vertebrates, 2 in Caenorhabditis elegans) of repeats of a 110 amino acids domain.

Alpha-catenins are evolutionary related to vinculin [PubMed1924379]. Catenins are proteins that associate with the cytoplasmic domain of a variety of cadherins. The association of catenins to cadherins produces a complex which is linked to the actin filament network, and which seems to be of primary importance for cadherins cell-adhesion properties. Three different types of catenins seem to exist: alpha, beta, and gamma. Alpha-catenins are proteins of about 100 kDa which are evolutionary related to vinculin. In terms of their structure the most significant differences are the absence, in alpha-catenin, of the repeated domain and of the proline-rich segment.


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) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 12 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 alpha-catenin/vinculin-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 12 hidden Markov models representing the alpha-catenin/vinculin-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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]