SUPERFAMILY 1.75 HMM library and genome assignments server

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 (400) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,586 6,034 6
Proteins 5,378 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)
Biological Process (BP)regulation of metabolic process0.022980.00000000004685Least InformativeInherited
Biological Process (BP)regulation of cellular process0.039910Least InformativeInherited
Biological Process (BP)regulation of signal transduction0.000003840Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.000093110.00000000008733Moderately InformativeDirect
Biological Process (BP)positive regulation of molecular function0.078840.0000000001768Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity0.0040250Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process10Moderately InformativeInherited
Biological Process (BP)regulation of nucleoside metabolic process0.00000000013430InformativeDirect
Biological Process (BP)regulation of cellular catabolic process0.000000012540InformativeDirect
Biological Process (BP)positive regulation of hydrolase activity0.0000000020480InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process0.0000000010750InformativeDirect
Biological Process (BP)positive regulation of GTPase activity0.0000000000075450Highly InformativeDirect
Molecular Function (MF)enzyme regulator activity0.000000000053280Moderately InformativeDirect
Molecular Function (MF)GTPase regulator activity00InformativeDirect
Molecular Function (MF)guanyl-nucleotide exchange factor activity00Highly InformativeDirect
Molecular Function (MF)small GTPase regulator activity0.0016470.009833Highly InformativeInherited

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) regulation of metabolic process 0.00000000004685 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00002262 Least Informative Direct
Biological Process (BP) developmental process 0.00005909 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00000000006675 Least Informative Direct
Biological Process (BP) regulation of cellular process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000000000009977 Least Informative Direct
Biological Process (BP) localization 0.6625 Least Informative Inherited
Biological Process (BP) signal transduction 0.00000000006076 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000000008733 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0008573 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.0000000001768 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.4118 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.09358 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.05948 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.9203 Moderately Informative Inherited
Biological Process (BP) organ development 0.5157 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.131 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.117 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.9615 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.4685 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.8301 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1402 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.713 Moderately Informative Inherited
Biological Process (BP) immune system process 0.04543 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.000004432 Informative Direct
Biological Process (BP) cellular component movement 0.0007033 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.0000001273 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) response to wounding 0.0005169 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0002913 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0 Informative Direct
Biological Process (BP) intracellular signal transduction 0.00000000000002458 Informative Direct
Biological Process (BP) locomotion 0.000002066 Informative Direct
Biological Process (BP) generation of neurons 0.0000004121 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0.000007042 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0 Informative Direct
Biological Process (BP) localization of cell 0.00003207 Informative Direct
Biological Process (BP) regulation of cell development 0.000007325 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.0003997 Informative Direct
Biological Process (BP) regulation of nervous system development 0.005996 Informative Inherited
Biological Process (BP) regulation of locomotion 0.3295 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.1964 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.1669 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.407 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 1 Informative Inherited
Biological Process (BP) regulation of cell proliferation 1 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.03915 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.6595 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.6963 Informative Inherited
Biological Process (BP) reproductive system development 0.2599 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.009088 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.002139 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.001859 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.02077 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 1 Informative Inherited
Biological Process (BP) epithelium development 0.03359 Informative Inherited
Biological Process (BP) response to nutrient levels 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) regulation of system process 0.06022 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.02257 Informative Inherited
Biological Process (BP) microtubule-based process 0.4389 Informative Inherited
Biological Process (BP) organelle localization 0.01764 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.9882 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.04019 Informative Inherited
Biological Process (BP) secretion by cell 0.006201 Informative Inherited
Biological Process (BP) regulation of ion transport 0.07572 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1293 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) central nervous system development 0.2203 Informative Inherited
Biological Process (BP) regulation of body fluid levels 0.05945 Informative Inherited
Biological Process (BP) defense response 0.3394 Informative Inherited
Biological Process (BP) leukocyte activation 0.2134 Informative Inherited
Biological Process (BP) immune effector process 0.1329 Informative Inherited
Biological Process (BP) immune response 0.7829 Informative Inherited
Biological Process (BP) cardiovascular system development 0.01793 Informative Inherited
Biological Process (BP) MAPK cascade 0.000004732 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.0004198 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 0.000005258 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.00001796 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.000195 Highly Informative Direct
Biological Process (BP) exocytosis 0.0000006639 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0 Highly Informative Direct
Biological Process (BP) hemostasis 0.0003675 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.000005873 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.0000000002869 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0002098 Highly Informative Direct
Biological Process (BP) cytoskeleton-dependent intracellular transport 0.00003009 Highly Informative Direct
Biological Process (BP) regulation of Ras GTPase activity 0.000006016 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.00002674 Highly Informative Direct
Biological Process (BP) positive regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) regulation of synaptic transmission 0.000003384 Highly Informative Direct
Biological Process (BP) regulation of protein kinase B signaling cascade 0.0005637 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.00002035 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 0.0000106 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.04599 Highly Informative Inherited
Biological Process (BP) microtubule-based movement 0.03246 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.2653 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.06067 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.001114 Highly Informative Inherited
Biological Process (BP) regulation of Rho protein signal transduction 1 Highly Informative Inherited
Biological Process (BP) regulation of transmembrane transport 0.004066 Highly Informative Inherited
Biological Process (BP) regulation of binding 1 Highly Informative Inherited
Biological Process (BP) regulation of transporter activity 0.1171 Highly Informative Inherited
Biological Process (BP) wound healing 0.4822 Highly Informative Inherited
Biological Process (BP) coagulation 0.00762 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.1582 Highly Informative Inherited
Biological Process (BP) inflammatory response 0.002213 Highly Informative Inherited
Molecular Function (MF) binding 0.003479 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.08158 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0004636 Informative Direct
Molecular Function (MF) enzyme binding 0.0000003498 Informative Direct
Molecular Function (MF) GTPase regulator activity 0 Informative Direct
Molecular Function (MF) receptor binding 0.2242 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0 Highly Informative Direct
Molecular Function (MF) Ras GTPase binding 0 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0.005791 Highly Informative Inherited
Molecular Function (MF) small GTPase regulator activity 0.009833 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.137 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.8139 Least Informative Inherited
Cellular Component (CC) membrane 0.009189 Least Informative Inherited
Cellular Component (CC) cytosol 0.000001863 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.0001876 Moderately Informative Direct
Cellular Component (CC) lytic vacuole 0.01033 Informative Inherited
Cellular Component (CC) endosome 0.0148 Informative Inherited
Cellular Component (CC) late endosome 0.0009798 Highly Informative Direct
Cellular Component (CC) cell body 0.000002396 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0001819 Highly Informative Direct
Cellular Component (CC) lysosome 0.004757 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)cellular phenotype0.4321Least InformativeInherited
Mammalian Phenotype (MP)abnormal cell adhesion0.0006011Highly 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

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.01208Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.000000001199InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0.0000000000002092Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0.00000000000001226Moderately InformativeDirect
Biological processCell cycle0.000008275Moderately InformativeDirect
Biological processNeurogenesis0.000000009577InformativeDirect
Biological processMitosis0.0006411InformativeDirect
Cellular componentMembrane0.00000005312Least InformativeDirect
Cellular componentCell junction0.00000000006365Moderately InformativeDirect
Cellular componentEndosome0.00000000009828Moderately InformativeDirect
Cellular componentGolgi apparatus0.000006185Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.00002537Moderately InformativeDirect
Cellular componentCell membrane0.0004213Moderately InformativeDirect
Cellular componentSynapse0.678InformativeInherited
Cellular componentSynaptosome0.000000000004768Highly InformativeDirect
Coding sequence diversityAlternative splicing0.00007456Least InformativeDirect
DomainRepeat0.0002589Least InformativeDirect
DomainCoiled coil0.000000001824Moderately InformativeDirect
DomainZinc-finger0.0003891Moderately InformativeDirect
DomainSH2 domain0.00000000004159InformativeDirect
DomainSH3 domain0.0000000343InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionCalcium0.00000000000005329Moderately InformativeDirect
Molecular functioncAMP-binding0.00000000002071Highly InformativeDirect
Molecular functioncAMP0.000000001061Highly InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation0.000000000003182InformativeDirect
Post-translational modificationPhosphoprotein0.00000000000002723Least InformativeDirect
Post-translational modificationUbl conjugation0.000008127Moderately 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]