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 (395) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,269 0 6
Proteins 5,068 0 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 process0.0039853.424e-12Least InformativeInherited
Biological Process (BP)regulation of cellular process0.0014110Least InformativeInherited
Biological Process (BP)regulation of signal transduction1.627e-090Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process1.178e-073.749e-11Moderately InformativeDirect
Biological Process (BP)regulation of catalytic activity0.00041790Moderately InformativeDirect
Biological Process (BP)positive regulation of molecular function0.023565.483e-11Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process10Moderately InformativeInherited
Biological Process (BP)regulation of nucleoside metabolic process00InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process1.874e-140InformativeDirect
Biological Process (BP)positive regulation of hydrolase activity5.084e-140InformativeDirect
Biological Process (BP)regulation of cellular catabolic process4.269e-130InformativeDirect
Biological Process (BP)positive regulation of Ras GTPase activity0.00018141.403e-06Highly InformativeDirect
Molecular Function (MF)enzyme regulator activity3.831e-110Moderately InformativeDirect
Molecular Function (MF)GTPase regulator activity00InformativeDirect
Molecular Function (MF)guanyl-nucleotide exchange factor activity00Highly InformativeDirect
Molecular Function (MF)small GTPase regulator activity0.0015130.007184Highly 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 cellular process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 3.424e-12 Least Informative Direct
Biological Process (BP) developmental process 4.321e-05 Least Informative Direct
Biological Process (BP) multicellular organismal process 1.605e-05 Least Informative Direct
Biological Process (BP) single-organism cellular process 6.916e-11 Least Informative Direct
Biological Process (BP) response to stimulus 3.432e-13 Least Informative Direct
Biological Process (BP) localization 0.6261 Least Informative Inherited
Biological Process (BP) regulation of signal transduction 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 3.749e-11 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 5.483e-11 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) signal transduction 3.86e-10 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0008013 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 0.3896 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.06412 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.02498 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.8831 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.03916 Moderately Informative Inherited
Biological Process (BP) organ development 0.5136 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.1556 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1364 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.9917 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.4999 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.869 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1364 Moderately Informative Inherited
Biological Process (BP) tissue development 0.7038 Moderately Informative Inherited
Biological Process (BP) immune system process 0.04138 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 nucleoside metabolic 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) intracellular signal transduction 6.33e-14 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 9.17e-08 Informative Direct
Biological Process (BP) positive regulation of protein modification process 1.963e-07 Informative Direct
Biological Process (BP) generation of neurons 4.016e-07 Informative Direct
Biological Process (BP) locomotion 1.781e-06 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 3.537e-06 Informative Direct
Biological Process (BP) regulation of cell development 5.676e-06 Informative Direct
Biological Process (BP) localization of cell 3.106e-05 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.0002246 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0003331 Informative Direct
Biological Process (BP) response to wounding 0.0004892 Informative Direct
Biological Process (BP) cellular component movement 0.0007765 Informative Direct
Biological Process (BP) regulation of nervous system development 0.006061 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.2201 Informative Inherited
Biological Process (BP) regulation of locomotion 0.3583 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.1835 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.4478 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 apoptotic process 0.06363 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.03947 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.6477 Informative Inherited
Biological Process (BP) reproductive system development 0.247 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.6819 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.0105 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.001054 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.002113 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.0223 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 1 Informative Inherited
Biological Process (BP) epithelium development 0.03517 Informative Inherited
Biological Process (BP) response to nutrient levels 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) regulation of system process 0.05583 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.02229 Informative Inherited
Biological Process (BP) microtubule-based process 0.4375 Informative Inherited
Biological Process (BP) organelle localization 0.01719 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) secretion by cell 0.005957 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.03855 Informative Inherited
Biological Process (BP) regulation of ion transport 0.07395 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1309 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) central nervous system development 0.2083 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.1675 Informative Inherited
Biological Process (BP) regulation of body fluid levels 0.06014 Informative Inherited
Biological Process (BP) defense response 0.3437 Informative Inherited
Biological Process (BP) leukocyte activation 0.2125 Informative Inherited
Biological Process (BP) immune effector process 0.1355 Informative Inherited
Biological Process (BP) immune response 0.7917 Informative Inherited
Biological Process (BP) cardiovascular system development 0.01861 Informative Inherited
Biological Process (BP) positive regulation of Ras GTPase activity 1.403e-06 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 2.303e-10 Highly Informative Direct
Biological Process (BP) exocytosis 6.076e-07 Highly Informative Direct
Biological Process (BP) regulation of synaptic transmission 2.37e-06 Highly Informative Direct
Biological Process (BP) MAPK cascade 4.905e-06 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 5.101e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 5.796e-06 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 9.217e-06 Highly Informative Direct
Biological Process (BP) fruiting body development 1.534e-05 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 1.561e-05 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 1.683e-05 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 2.316e-05 Highly Informative Direct
Biological Process (BP) regulation of ERK1 and ERK2 cascade 0.0001266 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0001948 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0001989 Highly Informative Direct
Biological Process (BP) hemostasis 0.0003482 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.0004149 Highly Informative Direct
Biological Process (BP) regulation of protein kinase B signaling cascade 0.0006306 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 0.8007 Highly Informative Inherited
Biological Process (BP) positive regulation of protein kinase activity 0.05487 Highly Informative Inherited
Biological Process (BP) microtubule-based movement 0.03384 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.06332 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.001128 Highly Informative Inherited
Biological Process (BP) regulation of Rho GTPase activity 1 Highly Informative Inherited
Biological Process (BP) regulation of transmembrane transport 0.004365 Highly Informative Inherited
Biological Process (BP) regulation of binding 1 Highly Informative Inherited
Biological Process (BP) regulation of transporter activity 0.132 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.2783 Highly Informative Inherited
Biological Process (BP) coagulation 0.007345 Highly Informative Inherited
Biological Process (BP) wound healing 0.4663 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.1597 Highly Informative Inherited
Biological Process (BP) inflammatory response 0.002246 Highly Informative Inherited
Molecular Function (MF) binding 0.001985 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.08611 Moderately Informative Inherited
Molecular Function (MF) GTPase regulator activity 0 Informative Direct
Molecular Function (MF) enzyme binding 2.04e-07 Informative Direct
Molecular Function (MF) nucleotide binding 0.0004437 Informative Direct
Molecular Function (MF) receptor binding 0.2271 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 0.005806 Highly Informative Inherited
Molecular Function (MF) small GTPase regulator activity 0.007184 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1253 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.8127 Least Informative Inherited
Cellular Component (CC) membrane 0.005199 Least Informative Inherited
Cellular Component (CC) cytosol 1.091e-06 Moderately Informative Direct
Cellular Component (CC) plasma membrane 7.568e-05 Moderately Informative Direct
Cellular Component (CC) cell projection 0.0009139 Moderately Informative Direct
Cellular Component (CC) lytic vacuole 0.0103 Informative Inherited
Cellular Component (CC) endosome 0.01404 Informative Inherited
Cellular Component (CC) cell body 2.278e-06 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0001622 Highly Informative Direct
Cellular Component (CC) late endosome 0.0009364 Highly Informative Direct
Cellular Component (CC) lysosome 0.004684 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 phenotype0.4081Least InformativeInherited
Mammalian Phenotype (MP)abnormal cell adhesion0.0006247Highly 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

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)Hydrolases0.01191Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases1.198e-09InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C2.117e-13Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation1.136e-14Moderately InformativeDirect
Biological processCell cycle9.487e-06Moderately InformativeDirect
Biological processNeurogenesis9.459e-09InformativeDirect
Biological processMitosis0.0006982InformativeDirect
Cellular componentMembrane4.977e-08Least InformativeDirect
Cellular componentCell junction6.435e-11Moderately InformativeDirect
Cellular componentEndosome9.246e-11Moderately InformativeDirect
Cellular componentGolgi apparatus6.07e-06Moderately InformativeDirect
Cellular componentEndoplasmic reticulum2.413e-05Moderately InformativeDirect
Cellular componentCell membrane0.000378Moderately InformativeDirect
Cellular componentSynapse0.6756InformativeInherited
Cellular componentSynaptosome4.834e-12Highly InformativeDirect
DomainRepeat0.0002556Least InformativeDirect
DomainCoiled coil1.787e-09Moderately InformativeDirect
DomainZinc-finger0.0004026Moderately InformativeDirect
DomainSH2 domain4.286e-11InformativeDirect
DomainSH3 domain3.532e-08InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionCalcium4.35e-14Moderately InformativeDirect
Molecular functioncAMP-binding2.003e-11Highly InformativeDirect
Molecular functioncAMP1.027e-09Highly InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation3.648e-12InformativeDirect
Post-translational modificationPhosphoprotein2.541e-14Least InformativeDirect
Post-translational modificationUbl conjugation7.084e-06Moderately 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 ]