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 5,590 6,034 6
Proteins 5,383 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 cellular process0.045430Least InformativeInherited
Biological Process (BP)positive regulation of biological process0.017790Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.028820.000000000082Least InformativeInherited
Biological Process (BP)regulation of signal transduction0.0000044210Moderately InformativeDirect
Biological Process (BP)regulation of phosphorus metabolic process0.0000063040Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00010290.00000000001332Moderately InformativeDirect
Biological Process (BP)positive regulation of metabolic process0.00014590Moderately InformativeDirect
Biological Process (BP)positive regulation of molecular function0.080270.0000000003045Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity0.0031610Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.0073370Moderately InformativeInherited
Biological Process (BP)regulation of nucleoside metabolic process0.00000000019880InformativeDirect
Biological Process (BP)positive regulation of catabolic process0.00000000037870InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process0.0000000014450InformativeDirect
Biological Process (BP)positive regulation of hydrolase activity0.0000000023110InformativeDirect
Biological Process (BP)regulation of cellular catabolic process0.000000029390InformativeDirect
Biological Process (BP)positive regulation of phosphate metabolic process0.00000040570.0000000000001924InformativeDirect
Biological Process (BP)positive regulation of GTPase activity0.0000000000074610Highly 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) positive regulation of biological process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.000000000082 Least Informative Direct
Biological Process (BP) regulation of cellular process 0 Least Informative Direct
Biological Process (BP) developmental process 0.0000582 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00001265 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000000000009774 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000569 Least Informative Direct
Biological Process (BP) localization 0.7152 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of signal transduction 0 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000000001332 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.0000000003045 Moderately Informative Direct
Biological Process (BP) signal transduction 0.00000000005809 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.001014 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.4277 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.06215 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.0971 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.715 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.9236 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.9411 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.9275 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.317 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.5036 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8623 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.3454 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.9954 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1578 Moderately Informative Inherited
Biological Process (BP) organ development 0.4707 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.1865 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) defense response 0.2967 Moderately Informative Inherited
Biological Process (BP) immune system process 0.002269 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of catabolic process 0 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.0000000000001924 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0000000000003672 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.000000124 Informative Direct
Biological Process (BP) generation of neurons 0.0000004395 Informative Direct
Biological Process (BP) locomotion 0.000002044 Informative Direct
Biological Process (BP) epithelium development 0.0000288 Informative Direct
Biological Process (BP) localization of cell 0.00003372 Informative Direct
Biological Process (BP) cellular component movement 0.0001478 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.0003957 Informative Direct
Biological Process (BP) cell projection organization 0.0004033 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.1945 Informative Inherited
Biological Process (BP) regulation of locomotion 0.3318 Informative Inherited
Biological Process (BP) positive regulation of developmental process 1 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) regulation of transferase activity 1 Informative Inherited
Biological Process (BP) regulation of ion transport 0.08072 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.6145 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.6348 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.06057 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.04731 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.001827 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.002182 Informative Inherited
Biological Process (BP) regulation of MAPK cascade 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) response to nutrient levels 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) organelle localization 0.01979 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.02104 Informative Inherited
Biological Process (BP) regulation of cell development 0.01956 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.06369 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.6811 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.1403 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.3941 Informative Inherited
Biological Process (BP) microtubule-based process 0.3366 Informative Inherited
Biological Process (BP) leukocyte activation 0.4063 Informative Inherited
Biological Process (BP) positive regulation of intracellular signal transduction 1 Informative Inherited
Biological Process (BP) secretion by cell 0.002574 Informative Inherited
Biological Process (BP) positive regulation of cell death 0.9467 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.06895 Informative Inherited
Biological Process (BP) reproductive structure development 0.2481 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) phosphorylation 0.1586 Informative Inherited
Biological Process (BP) central nervous system development 0.2357 Informative Inherited
Biological Process (BP) biological adhesion 0.005885 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.06561 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.005955 Informative Inherited
Biological Process (BP) regulation of body fluid levels 0.07381 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.04115 Informative Inherited
Biological Process (BP) immune effector process 0.3261 Informative Inherited
Biological Process (BP) immune response 0.7812 Informative Inherited
Biological Process (BP) cardiovascular system development 0.0187 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.2341 Informative Inherited
Biological Process (BP) positive regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) regulation of Ras GTPase activity 0.000006207 Highly Informative Direct
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) response to purine-containing compound 0.0000000002742 Highly Informative Direct
Biological Process (BP) response to nerve growth factor 0.0000000009405 Highly Informative Direct
Biological Process (BP) exocytosis 0.0000006739 Highly Informative Direct
Biological Process (BP) regulation of transmembrane transporter activity 0.000001025 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 0.000005318 Highly Informative Direct
Biological Process (BP) regulation of ion transmembrane transport 0.000007711 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.00001786 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.00001831 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.00002232 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 0.0001266 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0002045 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0002109 Highly Informative Direct
Biological Process (BP) hemostasis 0.000362 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.0005868 Highly Informative Direct
Biological Process (BP) positive regulation of neurogenesis 0.4025 Highly Informative Inherited
Biological Process (BP) regulation of protein serine/threonine kinase activity 0.07151 Highly Informative Inherited
Biological Process (BP) positive regulation of protein kinase activity 0.04733 Highly Informative Inherited
Biological Process (BP) negative regulation of nervous system development 0.03951 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.1604 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 1 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.006603 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.2696 Highly Informative Inherited
Biological Process (BP) regulation of synaptic transmission 0.002491 Highly Informative Inherited
Biological Process (BP) regulation of binding 1 Highly Informative Inherited
Biological Process (BP) regulation of Rho protein signal transduction 1 Highly Informative Inherited
Biological Process (BP) cell adhesion 0.002153 Highly Informative Inherited
Biological Process (BP) microtubule-based movement 0.03238 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.08193 Highly Informative Inherited
Biological Process (BP) wound healing 0.006644 Highly Informative Inherited
Biological Process (BP) coagulation 0.008426 Highly Informative Inherited
Biological Process (BP) inflammatory response 0.001237 Highly Informative Inherited
Molecular Function (MF) binding 0.004061 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.0001647 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.02393 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.05337 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.08156 Moderately Informative Inherited
Molecular Function (MF) enzyme binding 0.0000003796 Informative Direct
Molecular Function (MF) nucleotide binding 0.0004628 Informative Direct
Molecular Function (MF) receptor binding 0.2227 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 0.005922 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.8006 Least Informative Inherited
Cellular Component (CC) membrane 0.00925 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1401 Least Informative Inherited
Cellular Component (CC) cytosol 0.000002026 Moderately Informative Direct
Cellular Component (CC) lytic vacuole 0.01022 Informative Inherited
Cellular Component (CC) cell body 0.000002435 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0001836 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)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 ]