SUPERFAMILY 1.75 HMM library and genome assignments server


Rap/Ran-GAP superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Rap/Ran-GAP [ 111346]
Superfamily:   Rap/Ran-GAP [ 111347]
Families:   Rap/Ran-GAP [ 111348]


Superfamily statistics
Genomes (350) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,969 2,280 1
Proteins 1,877 2,213 1


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)single-organism cellular process06.462e-05Least InformativeDirect
Biological Process (BP)response to stimulus05.135e-08Least InformativeDirect
Biological Process (BP)response to endogenous stimulus00.03462Moderately InformativeInherited
Biological Process (BP)response to organic substance00.8039Moderately InformativeInherited
Biological Process (BP)response to organonitrogen compound01.037e-08InformativeDirect
Biological Process (BP)locomotion00.0002615InformativeDirect
Biological Process (BP)chemotaxis00.0001613Highly 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) regulation of metabolic process 0.0002075 Least Informative Direct
Biological Process (BP) single-organism cellular process 6.462e-05 Least Informative Direct
Biological Process (BP) response to stimulus 5.135e-08 Least Informative Direct
Biological Process (BP) localization 0.05279 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3984 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.007244 Least Informative Inherited
Biological Process (BP) developmental process 0.04467 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.07292 Least Informative Inherited
Biological Process (BP) tissue development 0.0008239 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 3.657e-06 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of localization 3.328e-05 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0008038 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0003698 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.01255 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.03832 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2867 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.0399 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.9928 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.7717 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.03462 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.008849 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.8039 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.02919 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.0132 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.3419 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.8643 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.9179 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.001169 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.003226 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.0236 Moderately Informative Inherited
Biological Process (BP) organ development 0.648 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 2.958e-11 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 3.295e-10 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0004509 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 3.898e-06 Informative Direct
Biological Process (BP) response to organonitrogen compound 1.037e-08 Informative Direct
Biological Process (BP) cytoplasmic transport 4.533e-07 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0 Informative Direct
Biological Process (BP) tube development 1.136e-05 Informative Direct
Biological Process (BP) intracellular signal transduction 5.512e-05 Informative Direct
Biological Process (BP) locomotion 0.0002615 Informative Direct
Biological Process (BP) embryonic morphogenesis 3.369e-05 Informative Direct
Biological Process (BP) tissue morphogenesis 2.788e-05 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 5.728e-06 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0 Informative Direct
Biological Process (BP) regulation of nervous system development 1.077e-05 Informative Direct
Biological Process (BP) regulation of cell development 3.34e-05 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 1.75e-06 Informative Direct
Biological Process (BP) cardiovascular system development 0.0001769 Informative Direct
Biological Process (BP) regulation of anatomical structure size 4.3e-05 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.004585 Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0.001189 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.00298 Informative Inherited
Biological Process (BP) regulation of protein localization 0.02369 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.003186 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.001219 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 1 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.7696 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.04372 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.08451 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.04848 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.1207 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 1 Informative Inherited
Biological Process (BP) protein localization to organelle 0.001714 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.06078 Informative Inherited
Biological Process (BP) regulation of growth 0.314 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.005698 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.004495 Informative Inherited
Biological Process (BP) protein transport 0.001656 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.407 Informative Inherited
Biological Process (BP) epithelium development 0.1043 Informative Inherited
Biological Process (BP) response to hypoxia 9.477e-12 Highly Informative Direct
Biological Process (BP) chemotaxis 0.0001613 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 2.029e-12 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 8.255e-11 Highly Informative Direct
Biological Process (BP) carbohydrate transport 4.319e-10 Highly Informative Direct
Biological Process (BP) morphogenesis of embryonic epithelium 1.92e-11 Highly Informative Direct
Biological Process (BP) protein import 5.8e-10 Highly Informative Direct
Biological Process (BP) neural tube development 3.742e-11 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 1.017e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cell growth 4.89e-05 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0001783 Highly Informative Direct
Biological Process (BP) regulation of Ras GTPase activity 2.261e-09 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 3.043e-12 Highly Informative Direct
Biological Process (BP) negative regulation of phosphorylation 8.871e-05 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 2.014e-10 Highly Informative Direct
Biological Process (BP) positive regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 3.197e-13 Highly Informative Direct
Biological Process (BP) nuclear import 3.501e-11 Highly Informative Direct
Biological Process (BP) multi-organism behavior 1.813e-06 Highly Informative Direct
Biological Process (BP) regulation of protein kinase B signaling cascade 2.148e-08 Highly Informative Direct
Biological Process (BP) epithelial tube formation 4.286e-14 Highly Informative Direct
Biological Process (BP) regulation of cellular response to insulin stimulus 0 Highly Informative Direct
Biological Process (BP) cellular response to peptide 5.691e-06 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.006384 Highly Informative Inherited
Biological Process (BP) regulation of cell size 0.0498 Highly Informative Inherited
Biological Process (BP) small GTPase mediated signal transduction 0.003845 Highly Informative Inherited
Molecular Function (MF) binding 0.01986 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) enzyme activator activity 0 Informative Direct
Molecular Function (MF) enzyme binding 0.0004539 Informative Direct
Molecular Function (MF) GTPase regulator activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0002507 Informative Direct
Molecular Function (MF) GTPase activator activity 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0009521 Highly Informative Direct
Molecular Function (MF) small GTPase regulator activity 0.003485 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.1267 Least Informative Inherited
Cellular Component (CC) cytosol 0.001769 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)tumorigenesis0.002514Moderately InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
DomainCoiled coil1.543e-13Moderately InformativeDirect
Post-translational modificationGTPase activation0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · 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 Rap/Ran-GAP 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 Rap/Ran-GAP 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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]