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 (156) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,392 4,547 19
Proteins 1,256 1,371 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) multicellular organismal process 0.00009192 Least Informative Direct
Biological Process (BP) developmental process 0.000002858 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0002027 Least Informative Direct
Biological Process (BP) localization 0.00004681 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000000000001752 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.8845 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.00004285 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.00000001568 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.000002118 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.00004514 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0002187 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.00008225 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0.0000007039 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.003348 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.02565 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2845 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.01778 Moderately Informative Inherited
Biological Process (BP) organ development 0.8897 Moderately Informative Inherited
Biological Process (BP) tissue development 0.4718 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.004508 Moderately Informative Inherited
Biological Process (BP) cellular component movement 0.0000396 Informative Direct
Biological Process (BP) cytoskeleton organization 0.00000000000001752 Informative Direct
Biological Process (BP) synaptic transmission 0.00002933 Informative Direct
Biological Process (BP) organ morphogenesis 0.0006374 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0001233 Informative Direct
Biological Process (BP) biological adhesion 0 Informative Direct
Biological Process (BP) actin filament-based process 0.000837 Informative Direct
Biological Process (BP) cell projection organization 0.000000008794 Informative Direct
Biological Process (BP) locomotion 0.000001858 Informative Direct
Biological Process (BP) regulation of locomotion 0.000000001191 Informative Direct
Biological Process (BP) generation of neurons 0.00000006153 Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.00006413 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.000002663 Informative Direct
Biological Process (BP) localization of cell 0.00001314 Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.00004035 Informative Direct
Biological Process (BP) epithelium development 0.00003626 Informative Direct
Biological Process (BP) muscle structure development 0.0006382 Informative Direct
Biological Process (BP) tissue morphogenesis 0.01854 Informative Inherited
Biological Process (BP) central nervous system development 0.04652 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.008351 Informative Inherited
Biological Process (BP) tube development 0.1289 Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.00191 Informative Inherited
Biological Process (BP) sexual reproduction 0.3906 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.03284 Informative Inherited
Biological Process (BP) single organism reproductive process 0.0271 Informative Inherited
Biological Process (BP) phagocytosis 0.00001222 Highly Informative Direct
Biological Process (BP) cell adhesion 0 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.0003899 Highly Informative Direct
Biological Process (BP) female gamete generation 0.00001289 Highly Informative Direct
Biological Process (BP) cell junction organization 0 Highly Informative Direct
Biological Process (BP) branching morphogenesis of an epithelial tube 0.000005184 Highly Informative Direct
Biological Process (BP) maintenance of location 0.000000000000197 Highly Informative Direct
Biological Process (BP) neuron projection development 0.1945 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.05114 Highly Informative Inherited
Biological Process (BP) cell projection morphogenesis 0.2603 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.002759 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.1953 Highly Informative Inherited
Biological Process (BP) epithelial cell development 0.01668 Highly Informative Inherited
Biological Process (BP) cell projection assembly 0.01332 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.002735 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.01809 Highly Informative Inherited
Biological Process (BP) germ cell development 0.03929 Highly Informative Inherited
Biological Process (BP) columnar/cuboidal epithelial cell differentiation 0.01562 Highly Informative Inherited
Molecular Function (MF) binding 0.00000001542 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.000214 Moderately Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.000000000001401 Informative Direct
Molecular Function (MF) protein complex binding 0.00000003991 Informative Direct
Molecular Function (MF) receptor binding 0.01558 Informative Inherited
Molecular Function (MF) cell adhesion molecule binding 0.000000000000001593 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0000009408 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.04185 Least Informative Inherited
Cellular Component (CC) cell projection 0.00000000000443 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 0.00000001089 Informative Direct
Cellular Component (CC) neuron projection 1 Informative Inherited
Cellular Component (CC) adherens junction 0 Highly Informative Direct
Cellular Component (CC) cell-cell contact zone 0.0000000002396 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 phenotype0.0415Least InformativeInherited
Mammalian Phenotype (MP)muscle phenotype0.0005391Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.01088Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.03481Moderately 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
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 processDifferentiation0.0000000003652Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Cellular componentMembrane0.0000000000009268Least InformativeDirect
Cellular componentCytoplasm0.000000001486Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentCell junction0Moderately InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentCell projection0.0000000000000035Moderately InformativeDirect
Molecular functionActin-binding0InformativeDirect
Post-translational modificationDevelopmental protein0.000000001285Moderately 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 ]