SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Ras GEF superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Ras GEF [ 48365]
Superfamily:   Ras GEF [ 48366]
Families:   Ras GEF [ 48367]


Superfamily statistics
Genomes (408) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 5,754 13,926 6
Proteins 5,544 13,544 6


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Molecular Function (MF)molecular function regulator0.000000011490Moderately InformativeDirect
Molecular Function (MF)guanyl-nucleotide exchange factor activity00Highly InformativeDirect

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) multicellular organismal process 0.0003609 Least Informative Direct
Biological Process (BP) biological regulation 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.000000000137 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.457 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.4545 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single organism signaling 0 Moderately Informative Direct
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.00000000000004085 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.0000000001822 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.0000000002878 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00000005073 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.7031 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1903 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.8025 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.3394 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.01565 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.4626 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.5922 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.5882 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1198 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.9254 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.6164 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.1577 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1315 Moderately Informative Inherited
Biological Process (BP) tissue development 0.7104 Moderately Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.000000000000007296 Informative Direct
Biological Process (BP) regulation of protein modification process 0.000000000001279 Informative Direct
Biological Process (BP) intracellular signal transduction 0.000000000007771 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 0.0000002737 Informative Direct
Biological Process (BP) generation of neurons 0.0000009998 Informative Direct
Biological Process (BP) locomotion 0.00001449 Informative Direct
Biological Process (BP) localization of cell 0.00001574 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.00002348 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0.00003887 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.00005932 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0003014 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.000968 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.219 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.02917 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.2339 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.008038 Informative Inherited
Biological Process (BP) regulation of transferase activity 1 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.2191 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.2104 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.454 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.6869 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.04812 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.01148 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.03837 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.01623 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.5375 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.4096 Informative Inherited
Biological Process (BP) post-embryonic development 0.8846 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.1599 Informative Inherited
Biological Process (BP) regulation of locomotion 0.1693 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.7703 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.92 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) phosphorylation 0.001631 Informative Inherited
Biological Process (BP) central nervous system development 0.02726 Informative Inherited
Biological Process (BP) cell development 0.289 Informative Inherited
Biological Process (BP) epithelium development 0.09372 Informative Inherited
Biological Process (BP) circulatory system development 0.002332 Informative Inherited
Biological Process (BP) regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0 Highly Informative Direct
Biological Process (BP) response to organophosphorus 0.000000003512 Highly Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.00000008344 Highly Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.000000122 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.000001454 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.000001731 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.000001989 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.0000307 Highly Informative Direct
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.00003918 Highly Informative Direct
Biological Process (BP) response to growth factor 0.00006013 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0001948 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.05622 Highly Informative Inherited
Biological Process (BP) positive regulation of cell development 0.1184 Highly Informative Inherited
Biological Process (BP) positive regulation of apoptotic process 0.003841 Highly Informative Inherited
Biological Process (BP) positive regulation of protein serine/threonine kinase activity 0.00226 Highly Informative Inherited
Biological Process (BP) negative regulation of nervous system development 0.1039 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.3582 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.7771 Highly Informative Inherited
Biological Process (BP) second-messenger-mediated signaling 0.3589 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 1 Highly Informative Inherited
Biological Process (BP) negative regulation of cell development 0.1875 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.1467 Highly Informative Inherited
Biological Process (BP) appendage development 0.1642 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.003372 Highly Informative Inherited
Biological Process (BP) regulation of binding 0.3807 Highly Informative Inherited
Biological Process (BP) neuron development 0.2343 Highly Informative Inherited
Biological Process (BP) forebrain development 0.05351 Highly Informative Inherited
Biological Process (BP) biological adhesion 0.00328 Highly Informative Inherited
Biological Process (BP) epithelial cell differentiation 0.003219 Highly Informative Inherited
Molecular Function (MF) binding 0.0735 Least Informative Inherited
Molecular Function (MF) molecular function regulator 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.005495 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.0448 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.006441 Moderately Informative Inherited
Molecular Function (MF) enzyme binding 0.00000005683 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.00001612 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.0000204 Informative Direct
Molecular Function (MF) receptor binding 0.2769 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0 Highly Informative Direct
Molecular Function (MF) small GTPase binding 0 Highly Informative Direct
Molecular Function (MF) GTPase regulator activity 0.00000004057 Highly Informative Direct
Molecular Function (MF) G-protein coupled receptor binding 0.0003923 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0.003439 Highly Informative Inherited
Cellular Component (CC) membrane 0.0005546 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.1266 Least Informative Inherited
Cellular Component (CC) protein complex 0.2247 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.0000005449 Moderately Informative Direct
Cellular Component (CC) vesicle 0.2501 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.9094 Moderately Informative Inherited
Cellular Component (CC) plasma membrane region 0.03297 Informative Inherited
Cellular Component (CC) endosome 0.02214 Informative Inherited
Cellular Component (CC) perinuclear region of cytoplasm 0.000003168 Highly Informative Direct
Cellular Component (CC) neuronal cell body 0.00002794 Highly Informative Direct
Cellular Component (CC) late endosome 0.0006796 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0.00000000000004467Moderately InformativeDirect
Biological processCell cycle0.00001006Moderately InformativeDirect
Biological processNeurogenesis0.00000002164InformativeDirect
Cellular componentMembrane0.00000002427Least InformativeDirect
Cellular componentCell junction0.0000000003393Moderately InformativeDirect
Cellular componentEndosome0.0000000005408Moderately InformativeDirect
Cellular componentGolgi apparatus0.000009807Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.00005489Moderately InformativeDirect
Cellular componentCell projection0.00008758Moderately InformativeDirect
Cellular componentCell membrane0.0003084Moderately InformativeDirect
Cellular componentSynapse0.6369InformativeInherited
Cellular componentSynaptosome0.00000000001577Highly InformativeDirect
Coding sequence diversityAlternative splicing0.00007758Least InformativeDirect
DomainRepeat0.000182Least InformativeDirect
DomainCoiled coil0.000000003342Moderately InformativeDirect
DomainZinc-finger0.0003868Moderately InformativeDirect
DomainSH2 domain0.00000000004521InformativeDirect
DomainSH3 domain0.00000003736InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionCalcium0Moderately InformativeDirect
Molecular functioncAMP-binding0.00000000004518Highly InformativeDirect
Molecular functioncAMP0.000000001875Highly InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation0.000000000004159InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.000668Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008937 SSF48366 Protein matches
Abstract

Small GTPases of the Ras family alternate between 2 conformations induced by the binding of either GTP or GDP. Guanine nucleotide exchange factors (GEFs) induce the dissociation of GDP to allow association of the more abundant GTP. The Ras-like family of small GTPases includes, among others, Ras, Rap1, R-ras, and Ral. The family is characterised by similarities in the effector domain. The Ras GTPase Rap1 is activated rapidly in response to activation of a variety of receptors. Rap1 activation is mediated by several second messengers, including calcium, diacylglycerol, and cAMP. GEFs have been identified that mediate these effects. One such GEF is Epac, an exchange protein directly activated by cAMP, which represents a novel cAMP-induced, protein kinase A-independent pathway [PubMed10579920].


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) · 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 1 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 Ras GEF 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 1 hidden Markov models representing the Ras GEF 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) · UniProtKB KeyWords (KW) · Internal database links ]