SUPERFAMILY 1.75 HMM library and genome assignments server

  Home > SCOP hierarchy > Ypt/Rab-GAP domain of gyp1p superfamily


Ypt/Rab-GAP domain of gyp1p superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Left-handed superhelix [ 47916] (4)
Superfamily:   Ypt/Rab-GAP domain of gyp1p [ 47923]
Families:   Ypt/Rab-GAP domain of gyp1p [ 47924]

 Superfamily statistics
Genomes (444) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 18,362 16,110 4
Proteins 10,106 8,879 2

 Functional annotation
General category Regulation
Detailed category Signal transduction

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of metabolic process 0.01144 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3323 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) localization 0.04268 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of molecular function 1.019e-13 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 4.617e-10 Moderately Informative Direct
Biological Process (BP) regulation of signaling 1.542e-09 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 3.601e-08 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.002009 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.002348 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.7217 Moderately Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 1.443e-07 Informative Direct
Biological Process (BP) vesicle-mediated transport 1.542e-06 Informative Direct
Biological Process (BP) biological adhesion 0.06098 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.4016 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.4785 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.5175 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.01676 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.07259 Informative Inherited
Biological Process (BP) sexual reproduction 0.01374 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.04362 Informative Inherited
Biological Process (BP) single organism reproductive process 0.06152 Informative Inherited
Biological Process (BP) cellular component movement 0.02973 Informative Inherited
Biological Process (BP) localization of cell 0.05686 Informative Inherited
Biological Process (BP) locomotion 0.1876 Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of Ras protein signal transduction 0 Highly Informative Direct
Biological Process (BP) regulation of purine nucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) female gamete generation 4.358e-05 Highly Informative Direct
Biological Process (BP) cell adhesion 0.04783 Highly Informative Inherited
Biological Process (BP) negative regulation of signal transduction 1 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) protein binding 0.8341 Moderately Informative Inherited
Molecular Function (MF) GTPase regulator activity 0 Informative Direct
Molecular Function (MF) enzyme activator activity 1.325e-14 Informative Direct
Molecular Function (MF) enzyme binding 0.01299 Informative Inherited
Molecular Function (MF) receptor binding 0.1189 Informative Inherited
Molecular Function (MF) GTPase activator activity 0 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.0005924 Highly Informative Direct
Molecular Function (MF) small GTPase regulator activity 0.01513 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.01512 Least Informative Inherited
Cellular Component (CC) vesicle 3.924e-08 Moderately Informative Direct
Cellular Component (CC) cell projection 0.3536 Moderately Informative Inherited
Cellular Component (CC) cell projection part 0.05962 Informative Inherited
Cellular Component (CC) neuron part 0.2134 Informative Inherited
Cellular Component (CC) synapse 0.03532 Informative Inherited
Cellular Component (CC) neuromuscular junction 2.875e-06 Highly Informative Direct
Cellular Component (CC) axon part 6.526e-05 Highly Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organ system development variant0.3247Moderately InformativeInherited
Worm Phenotype (WP)nervous system development variant0.0005769Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.0003188Moderately InformativeDirect
Cellular componentCytoplasm0.1089Least InformativeInherited
Cellular componentCytoplasmic vesicle1.266e-14Moderately InformativeDirect
Cellular componentGolgi apparatus3.743e-07Moderately InformativeDirect
Cellular componentCell projection0.000146Moderately InformativeDirect
Cellular componentCell junction0.000469Moderately InformativeDirect
Cellular componentCytoskeleton0.0008719Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.0006016Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainSH3 domain4.785e-06InformativeDirect
Post-translational modificationGTPase activation0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000195 SSF47923 Protein matches
Abstract Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, imply that these domains are GTPase activator proteins of Rab-like small GTPases [PubMed11013213].

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-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 2 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 Ypt/Rab-GAP domain of gyp1p 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 2 hidden Markov models representing the Ypt/Rab-GAP domain of gyp1p 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-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.