SUPERFAMILY 1.75 HMM library and genome assignments server


ENTH/VHS domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   alpha-alpha superhelix [ 48370] (24)
Superfamily:   ENTH/VHS domain [ 48464] (4)
Families:   ENTH domain [ 48465]
  VHS domain [ 48468] (5)
  Phosphoinositide-binding clathrin adaptor, N-terminal domain [ 100911] (2)
  RPR domain (SMART 00582 ) [ 109975]


Superfamily statistics
Genomes (497) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,688 9,644 14
Proteins 9,655 9,623 14


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)developmental process0.00073221Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0015460.976Least InformativeInherited
Biological Process (BP)single-organism cellular process0.014360.008983Least InformativeInherited
Biological Process (BP)response to stimulus0.055151Least InformativeInherited
Biological Process (BP)regulation of cellular process0.67040.8592Least InformativeInherited
Biological Process (BP)single-organism developmental process0.010541Moderately InformativeInherited
Biological Process (BP)organ development0.14091Moderately InformativeInherited
Biological Process (BP)signal transduction0.00074430.2377Moderately InformativeInherited
Biological Process (BP)embryonic organ development1.01e-070.0004575InformativeDirect
Biological Process (BP)embryo development ending in birth or egg hatching9.115e-070.01816InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) localization 3.752e-15 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.8592 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.008983 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.5321 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.976 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) system process 0.0004647 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.3845 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.5034 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.001792 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.01853 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.3668 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.2098 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2845 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.5857 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.4375 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.09551 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.9158 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.8807 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1158 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.4958 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.06801 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.2377 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1632 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2831 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1626 Moderately Informative Inherited
Biological Process (BP) embryonic organ development 0.0004575 Informative Direct
Biological Process (BP) secretion by cell 6.205e-13 Informative Direct
Biological Process (BP) vesicle-mediated transport 4.135e-12 Informative Direct
Biological Process (BP) synaptic transmission 2.158e-11 Informative Direct
Biological Process (BP) protein transport 6.456e-09 Informative Direct
Biological Process (BP) cellular membrane organization 0.0001591 Informative Direct
Biological Process (BP) RNA processing 0.0005255 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0007909 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.000829 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.009273 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.1862 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.1912 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.2504 Informative Inherited
Biological Process (BP) protein localization to organelle 0.9738 Informative Inherited
Biological Process (BP) dephosphorylation 0.06784 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) organelle localization 0.003881 Informative Inherited
Biological Process (BP) transmembrane transport 0.002923 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.003004 Informative Inherited
Biological Process (BP) protein complex assembly 0.7613 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.1522 Informative Inherited
Biological Process (BP) protein catabolic process 0.1733 Informative Inherited
Biological Process (BP) proteolysis 0.3182 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.4288 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.9248 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.06564 Informative Inherited
Biological Process (BP) cytoplasmic transport 1 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.001935 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.01816 Informative Inherited
Biological Process (BP) actin filament-based process 0.01588 Informative Inherited
Biological Process (BP) establishment of synaptic vesicle localization 0 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 0 Highly Informative Direct
Biological Process (BP) vesicle organization 9.888e-14 Highly Informative Direct
Biological Process (BP) neurotransmitter transport 6.292e-13 Highly Informative Direct
Biological Process (BP) autophagy 8.506e-09 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 2.648e-05 Highly Informative Direct
Biological Process (BP) signal release 3.296e-05 Highly Informative Direct
Biological Process (BP) mRNA processing 6.132e-05 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 7.184e-05 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.0001146 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.0002055 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.001116 Highly Informative Inherited
Biological Process (BP) establishment of protein localization to organelle 0.07448 Highly Informative Inherited
Biological Process (BP) protein dephosphorylation 0.003281 Highly Informative Inherited
Biological Process (BP) protein import 0.00117 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.0623 Highly Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.0754 Highly Informative Inherited
Molecular Function (MF) binding 0.0002478 Least Informative Direct
Molecular Function (MF) anion binding 5.594e-06 Moderately Informative Direct
Molecular Function (MF) lipid binding 1.456e-11 Informative Direct
Molecular Function (MF) enzyme binding 0.005735 Informative Inherited
Molecular Function (MF) protein complex binding 0.03055 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.001812 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.07118 Least Informative Inherited
Cellular Component (CC) protein complex 0.06454 Least Informative Inherited
Cellular Component (CC) membrane 0.07406 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1322 Least Informative Inherited
Cellular Component (CC) endomembrane system 1.164e-05 Moderately Informative Direct
Cellular Component (CC) vesicle 1.771e-05 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.01502 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.7441 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.1414 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.4115 Moderately Informative Inherited
Cellular Component (CC) cell cortex 8.584e-08 Informative Direct
Cellular Component (CC) endosome 9.063e-08 Informative Direct
Cellular Component (CC) coated vesicle 3.481e-07 Informative Direct
Cellular Component (CC) Golgi apparatus 1.973e-05 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 7.832e-05 Informative Direct
Cellular Component (CC) actin cytoskeleton 0.001932 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.04249 Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 0 Highly Informative Direct
Cellular Component (CC) cortical cytoskeleton 1.684e-09 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 1.77e-07 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0001687 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.5523 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)growth/size/body phenotype0.01414Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.959Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.3777Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal circulating glucose level0.05441InformativeInherited
Mammalian Phenotype (MP)decreased body size0.07407InformativeInherited
Mammalian Phenotype (MP)abnormal total tissue mass0.7216InformativeInherited
Mammalian Phenotype (MP)postnatal growth retardation1.403e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased birth weight0.0007288Highly InformativeDirect
Mammalian Phenotype (MP)hypoglycemia0.0008656Highly InformativeDirect
Mammalian Phenotype (MP)decreased body weight0.02401Highly InformativeInherited

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)cell physiology variant0.0006634Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.1134Least InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.005458Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.005993Moderately InformativeInherited
Worm Phenotype (WP)drug resistant0.1295InformativeInherited
Worm Phenotype (WP)coelomocyte uptake defective4.753e-06Highly InformativeDirect
Worm Phenotype (WP)aldicarb resistant0.0002594Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.0009348InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)multi-tissue structure0.435Least InformativeInherited
Fly Anatomy (FA)larva0.5413Least InformativeInherited
Fly Anatomy (FA)cell0.7464Least InformativeInherited
Fly Anatomy (FA)epithelium0.1853Moderately InformativeInherited
Fly Anatomy (FA)developing material anatomical entity0.3457Moderately InformativeInherited
Fly Anatomy (FA)epithelial cell0.002844InformativeInherited
Fly Anatomy (FA)imaginal precursor0.02012InformativeInherited
Fly Anatomy (FA)prepupa0.02386InformativeInherited
Fly Anatomy (FA)pupa0.02722InformativeInherited
Fly Anatomy (FA)cuboidal/columnar epithelium0.1008InformativeInherited

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) 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
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
DomainZinc-finger2.457e-06Moderately InformativeDirect
DomainCoiled coil6.695e-05Moderately InformativeDirect
DomainSH3 domain0InformativeDirect
Molecular functionZinc0.0006704Least InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Molecular functionActin-binding1.119e-06InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0005132Least InformativeDirect
Post-translational modificationUbl conjugation5.83e-08Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008942 SSF48464 Protein matches
Abstract

This entry represents domains with a multi-helical, alpha-alpha 2-layered structural fold as found in: the ENTH domain of Epsin; the VHS domain of Hrs, Tom1, and ADP-ribosylation factors; the RPR domain of PCF11 protein; and the N-terminal domain of phosphoinositide-binding clathrin adaptor.

The epsin NH2-terminal homology (ENTH) domain is a membrane interacting module composed of a superhelix of alpha-helices. It is present at the NH2-terminus of proteins that often contain consensus sequences for binding to clathrin coat components and their accessory factors, and therefore function as endocytic adaptors. ENTH domain containing proteins have additional roles in signalling and actin regulation and may have yet other actions in the nucleus. The ENTH domain is structurally similar to the VHS domain.

The ENTH domain is approximately 150 amino acids long. The ENTH domain forms a compact globular structure, composed of eight alpha-helices connected by loops of varying length. Three helical hairpins that are stacked consecutively with a right-handed twist determine the general topology of the domain. This stacking gives the ENTH domain a rectangular appearance when viewed face on. The most highly conserved amino acids fall roughly into two classes: internal residues that are involved in packing and therefore are necessary for structural integrity, and solvent accessible residues that may be involved in protein-protein interactions [PubMed11911874].

VHS domains are found at the N-termini of select proteins involved in intracellular membrane trafficking. The domain consists of eight helices arranged in a superhelix. The surface of the domain has two main features: a basic patch on one side due to several conserved positively charged residues on helix 3 and a negatively charged ridge on the opposite side, formed by residues on helix 2. Comparison of the two VHS domains and the ENTH domain reveals a conserved surface, composed of helices 2 and 4, that is utilised for protein-protein interactions. In addition, VHS domain-containing proteins are also often localized to membranes. It has therefore been suggested that the conserved positively charged surface of helix 3 in VHS and ENTH domains plays a role in membrane binding [PubMed10985773].


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-quality) · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · 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 10 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 ENTH/VHS 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 10 hidden Markov models representing the ENTH/VHS 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-quality) · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]