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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 (401) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,605 6,034 6
Proteins 5,397 5,895 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 regulator0.000000002810Moderately 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) biological regulation 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000000000002474 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00000000002567 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.366 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) signaling 0 Moderately Informative Direct
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.00000000000005013 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.000000000002749 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.0000000003009 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.00000001272 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00000002371 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.8017 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2374 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.2128 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.07988 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.3438 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.04087 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.9304 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.5636 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.1751 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.3605 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to stress 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.06545 Moderately Informative Inherited
Biological Process (BP) system development 0.7549 Moderately Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.0000000000002191 Informative Direct
Biological Process (BP) regulation of protein modification process 0.000000000001988 Informative Direct
Biological Process (BP) intracellular signal transduction 0.000000000006884 Informative Direct
Biological Process (BP) generation of neurons 0.0000001675 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 0.0000004376 Informative Direct
Biological Process (BP) locomotion 0.00000476 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0.00007174 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.0002747 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.0006723 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0009023 Informative Direct
Biological Process (BP) regulation of locomotion 0.1501 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.3703 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.0403 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.1524 Informative Inherited
Biological Process (BP) positive regulation of cell death 0.1018 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.003113 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.3005 Informative Inherited
Biological Process (BP) regulation of transferase activity 1 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.4016 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.1573 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.03027 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) circulatory system development 0.001234 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.002194 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.001909 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.2636 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.7316 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.8577 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.03138 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.6423 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0145 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.2933 Informative Inherited
Biological Process (BP) epithelium development 0.09813 Informative Inherited
Biological Process (BP) post-embryonic development 0.9047 Informative Inherited
Biological Process (BP) regulation of organelle organization 1 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.132 Informative Inherited
Biological Process (BP) phosphorylation 0.001863 Informative Inherited
Biological Process (BP) central nervous system development 0.04513 Informative Inherited
Biological Process (BP) cell adhesion 0.002017 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) cell development 0.09403 Informative Inherited
Biological Process (BP) small GTPase mediated signal transduction 0 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0 Highly Informative Direct
Biological Process (BP) positive regulation of GTPase activity 0.000000000003346 Highly Informative Direct
Biological Process (BP) response to organophosphorus 0.000000001149 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.0000002274 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.000009012 Highly Informative Direct
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.00001391 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.00003478 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.00007593 Highly Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.00008703 Highly Informative Direct
Biological Process (BP) regulation of cell shape 0.0001832 Highly Informative Direct
Biological Process (BP) cell projection organization 0.0003662 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.0006915 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.04143 Highly Informative Inherited
Biological Process (BP) positive regulation of cell development 0.06976 Highly Informative Inherited
Biological Process (BP) regulation of protein serine/threonine kinase activity 0.007169 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.4117 Highly Informative Inherited
Biological Process (BP) positive regulation of apoptotic process 0.003766 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.6279 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.9878 Highly Informative Inherited
Biological Process (BP) negative regulation of cell development 0.1358 Highly Informative Inherited
Biological Process (BP) appendage development 0.1816 Highly Informative Inherited
Biological Process (BP) regulation of binding 0.2916 Highly Informative Inherited
Biological Process (BP) neuron development 0.1667 Highly Informative Inherited
Biological Process (BP) brain development 0.005599 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.2989 Highly Informative Inherited
Biological Process (BP) cellular response to external stimulus 0.0309 Highly Informative Inherited
Biological Process (BP) response to nutrient levels 1 Highly Informative Inherited
Biological Process (BP) epithelial cell differentiation 0.001522 Highly Informative Inherited
Molecular Function (MF) binding 0.0136 Least Informative Inherited
Molecular Function (MF) molecular function regulator 0 Moderately Informative Direct
Molecular Function (MF) protein binding 0.00000009115 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.008548 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.006767 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.0316 Moderately Informative Inherited
Molecular Function (MF) enzyme binding 0.00000004242 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.000004661 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.000005875 Informative Direct
Molecular Function (MF) receptor binding 0.2793 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 0.00000001365 Highly Informative Direct
Molecular Function (MF) G-protein coupled receptor binding 0.0004051 Highly Informative Direct
Cellular Component (CC) membrane 0.0005546 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.04326 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.000001184 Moderately Informative Direct
Cellular Component (CC) vesicle 0.1301 Moderately Informative Inherited
Cellular Component (CC) site of polarized growth 0.000002293 Informative Direct
Cellular Component (CC) synapse 0.0003816 Informative Direct
Cellular Component (CC) plasma membrane region 0.01649 Informative Inherited
Cellular Component (CC) endosome 0.01156 Informative Inherited
Cellular Component (CC) perinuclear region of cytoplasm 0.000001579 Highly Informative Direct
Cellular Component (CC) neuronal cell body 0.00005331 Highly Informative Direct
Cellular Component (CC) late endosome 0.0006713 Highly Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.0342Moderately InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.5737Least InformativeInherited
Mammalian Phenotype (MP)abnormal cell adhesion0.0006243Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect
Zebrafish Anatomy (ZA)trunk0Moderately InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.003367Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.000000000005514InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0.00000000000003159Moderately InformativeDirect
Biological processCell cycle0.00001004Moderately InformativeDirect
Biological processNeurogenesis0.00000001937InformativeDirect
Biological processMitosis0.0008359InformativeDirect
Cellular componentMembrane0.0000001569Least InformativeDirect
Cellular componentCell junction0.0000000002867Moderately InformativeDirect
Cellular componentEndosome0.0000000004101Moderately InformativeDirect
Cellular componentGolgi apparatus0.000009906Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.00004708Moderately InformativeDirect
Cellular componentCell membrane0.0005815Moderately InformativeDirect
Cellular componentSynapse0.6324InformativeInherited
Cellular componentSynaptosome0.00000000001318Highly InformativeDirect
Coding sequence diversityAlternative splicing0.0000873Least InformativeDirect
DomainRepeat0.0001767Least InformativeDirect
DomainCoiled coil0.000000003285Moderately InformativeDirect
DomainZinc-finger0.0003905Moderately InformativeDirect
DomainSH2 domain0.00000000004547InformativeDirect
DomainSH3 domain0.00000003654InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionCalcium0Moderately InformativeDirect
Molecular functioncAMP-binding0.00000000004447Highly InformativeDirect
Molecular functioncAMP0.000000001757Highly InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation0.000000000007008InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.00008275Moderately 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]