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)response to stimulus00.00000005108Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis00.005387Least InformativeInherited
Biological Process (BP)response to external stimulus00.01918Moderately InformativeInherited
Biological Process (BP)response to endogenous stimulus00.0351Moderately InformativeInherited
Biological Process (BP)response to organic substance00.8131Moderately InformativeInherited
Biological Process (BP)response to organonitrogen compound00.00000001038InformativeDirect
Biological Process (BP)locomotion00.0002606InformativeDirect
Biological Process (BP)chemotaxis00.0001599Highly 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) response to stimulus 0.00000005108 Least Informative Direct
Biological Process (BP) positive regulation of biological process 0.000005382 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.0004361 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.04923 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.01021 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.005387 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.002201 Least Informative Inherited
Biological Process (BP) localization 0.06213 Least Informative Inherited
Biological Process (BP) developmental process 0.04446 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 catalytic activity 0 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.00000000000008678 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000005473 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0000009637 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.00004242 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0005811 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0006523 Moderately Informative Direct
Biological Process (BP) tissue development 0.0008308 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.009294 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.03618 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.8131 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.0351 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.09083 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.01918 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.03822 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.6859 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.0032 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.0292 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.01531 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.9606 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.00134 Moderately Informative Inherited
Biological Process (BP) organ development 0.6197 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.01989 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.5386 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.0128 Moderately Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.00000001038 Informative Direct
Biological Process (BP) locomotion 0.0002606 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of catabolic process 0 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.00000000003367 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.0000000003248 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.00000006063 Informative Direct
Biological Process (BP) intracellular signal transduction 0.00000008549 Informative Direct
Biological Process (BP) cytoplasmic transport 0.000000705 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.000002129 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.000003949 Informative Direct
Biological Process (BP) tube development 0.00000861 Informative Direct
Biological Process (BP) regulation of nervous system development 0.00001105 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.0000132 Informative Direct
Biological Process (BP) single-organism membrane organization 0.00001832 Informative Direct
Biological Process (BP) regulation of anatomical structure size 0.0000463 Informative Direct
Biological Process (BP) tissue morphogenesis 0.00007285 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.00007383 Informative Direct
Biological Process (BP) single-organism cellular localization 0.00008225 Informative Direct
Biological Process (BP) cardiovascular system development 0.0001845 Informative Direct
Biological Process (BP) protein transport 0.000929 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.002112 Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0.00118 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.004669 Informative Inherited
Biological Process (BP) regulation of protein localization 0.0247 Informative Inherited
Biological Process (BP) regulation of transferase activity 1 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.04498 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.07514 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.09047 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of RNA metabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.07309 Informative Inherited
Biological Process (BP) protein localization to organelle 0.001657 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.04507 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.004789 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.00913 Informative Inherited
Biological Process (BP) regulation of growth 0.2957 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.001849 Informative Inherited
Biological Process (BP) epithelium development 0.1986 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.004363 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.003073 Informative Inherited
Biological Process (BP) chemotaxis 0.0001599 Highly Informative Direct
Biological Process (BP) positive regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) regulation of cellular response to insulin stimulus 0 Highly Informative Direct
Biological Process (BP) epithelial tube formation 0.0000000000000406 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0.0000000000002493 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.0000000000003172 Highly Informative Direct
Biological Process (BP) single-organism nuclear import 0.0000000000003231 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.000000000001964 Highly Informative Direct
Biological Process (BP) plasma membrane organization 0.00000000001509 Highly Informative Direct
Biological Process (BP) response to hypoxia 0.00000000001582 Highly Informative Direct
Biological Process (BP) morphogenesis of embryonic epithelium 0.00000000001871 Highly Informative Direct
Biological Process (BP) neural tube development 0.0000000000234 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.00000000005649 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.0000000002009 Highly Informative Direct
Biological Process (BP) carbohydrate transport 0.0000000003326 Highly Informative Direct
Biological Process (BP) protein import 0.0000000004064 Highly Informative Direct
Biological Process (BP) regulation of Ras GTPase activity 0.000000002297 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 0.0000007114 Highly Informative Direct
Biological Process (BP) cellular response to peptide 0.000005546 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.00002462 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0.00003767 Highly Informative Direct
Biological Process (BP) negative regulation of cell growth 0.00004124 Highly Informative Direct
Biological Process (BP) negative regulation of protein phosphorylation 0.00005088 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-templated 0.008421 Highly Informative Inherited
Biological Process (BP) regulation of cell size 0.05002 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.08925 Highly Informative Inherited
Biological Process (BP) small GTPase mediated signal transduction 0.01186 Highly Informative Inherited
Molecular Function (MF) binding 0.02157 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) protein dimerization activity 0.000252 Informative Direct
Molecular Function (MF) enzyme binding 0.0004736 Informative Direct
Molecular Function (MF) GTPase activator activity 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.000975 Highly Informative Direct
Molecular Function (MF) small GTPase regulator activity 0.003417 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.1223 Least Informative Inherited
Cellular Component (CC) cytosol 0.001837 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 coil0.0000000000001543Moderately 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 ]