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 (144) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 4,034 3,586 19
Proteins 1,153 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 0.0002552 Least Informative Direct
Biological Process (BP) single-organism cellular process 6.42e-06 Least Informative Direct
Biological Process (BP) localization 0.0004411 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 2.696e-13 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.9125 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.006225 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.000665 Moderately Informative Direct
Biological Process (BP) cell differentiation 2.321e-05 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0008375 Moderately Informative Direct
Biological Process (BP) macromolecule localization 5.634e-05 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0005312 Moderately Informative Direct
Biological Process (BP) cellular localization 0.001021 Moderately Informative Inherited
Biological Process (BP) system process 0.004889 Moderately Informative Inherited
Biological Process (BP) organ development 0.9199 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.06399 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.005879 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.007239 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.006698 Moderately Informative Inherited
Biological Process (BP) cytoskeleton organization 1.247e-11 Informative Direct
Biological Process (BP) cell-cell signaling 0.0002631 Informative Direct
Biological Process (BP) transmission of nerve impulse 5.747e-05 Informative Direct
Biological Process (BP) biological adhesion 0 Informative Direct
Biological Process (BP) cell projection organization 3.45e-08 Informative Direct
Biological Process (BP) locomotion 0.0001893 Informative Direct
Biological Process (BP) regulation of locomotion 2.365e-10 Informative Direct
Biological Process (BP) generation of neurons 1.175e-06 Informative Direct
Biological Process (BP) regulation of cellular component movement 8.241e-07 Informative Direct
Biological Process (BP) localization of cell 0.0005575 Informative Direct
Biological Process (BP) central nervous system development 0.007864 Informative Inherited
Biological Process (BP) organ morphogenesis 0.003756 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.01079 Informative Inherited
Biological Process (BP) actin filament-based process 0.001473 Informative Inherited
Biological Process (BP) cell adhesion 0 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.0006312 Highly Informative Direct
Biological Process (BP) cell junction organization 0 Highly Informative Direct
Biological Process (BP) maintenance of location 6.227e-11 Highly Informative Direct
Biological Process (BP) neuron projection development 0.6542 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.0226 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.06158 Highly Informative Inherited
Biological Process (BP) cell projection assembly 0.01247 Highly Informative Inherited
Molecular Function (MF) binding 8.993e-08 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.0001459 Moderately Informative Direct
Molecular Function (MF) cytoskeletal protein binding 2.557e-10 Informative Direct
Molecular Function (MF) receptor binding 0.1761 Informative Inherited
Molecular Function (MF) protein complex binding 0.002359 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 8.155e-06 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.01513 Least Informative Inherited
Cellular Component (CC) cell projection 2.901e-12 Moderately Informative Direct
Cellular Component (CC) cell leading edge 0 Informative Direct
Cellular Component (CC) contractile fiber part 0 Informative Direct
Cellular Component (CC) neuron projection 1 Informative Inherited
Cellular Component (CC) cell-cell junction 1 Informative Inherited
Cellular Component (CC) adherens junction 0 Highly Informative Direct
Cellular Component (CC) cell-substrate junction 0.0004547 Highly Informative Direct
Cellular Component (CC) cell-cell contact zone 1.413e-10 Highly Informative Direct

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)cardiovascular system phenotype0.03933Least InformativeInherited
Mammalian Phenotype (MP)muscle phenotype0.0005164Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.009113Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.03364Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle fiber morphology6.051e-05Highly InformativeDirect
Mammalian Phenotype (MP)dilated heart0.0003835Highly InformativeDirect
Mammalian Phenotype (MP)cardiomyopathy0.0005814Highly InformativeDirect

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
Fly Anatomy (FA)acellular anatomical structure0Moderately InformativeDirect
Fly Anatomy (FA)prepupa0InformativeDirect

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)genital 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)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately 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 processDifferentiation3.277e-10Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Cellular componentMembrane9.875e-13Least InformativeDirect
Cellular componentCytoplasm1.416e-09Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentCell junction0Moderately InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentCell projection2.52e-15Moderately InformativeDirect
Molecular functionActin-binding0InformativeDirect
Post-translational modificationDevelopmental protein1.321e-09Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least 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 ]