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ArfGap/RecO-like zinc finger superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   ArfGap/RecO-like zinc finger [ 57862]
Superfamily:   ArfGap/RecO-like zinc finger [ 57863] (2)
Families:   Pyk2-associated protein beta ARF-GAP domain [ 57864]
  RecO C-terminal domain-like [ 118303]


Superfamily statistics
Genomes (2,682) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,035 20,294 2
Proteins 8,022 20,278 2


Functional annotation
General category General
Detailed category Ion binding

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) localization 0.0001171 Least Informative Direct
Biological Process (BP) response to stimulus 0.2879 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.4423 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.002139 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.0173 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02231 Least Informative Inherited
Biological Process (BP) developmental process 0.1032 Least Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.00000000000002284 Moderately Informative Direct
Biological Process (BP) cellular localization 0.000009023 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.0009731 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.238 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7628 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.03134 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.7441 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.7842 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.007664 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.01749 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2159 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.6209 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.006116 Moderately Informative Inherited
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 purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.00000000115 Informative Direct
Biological Process (BP) protein transport 0.0002165 Informative Direct
Biological Process (BP) single-organism behavior 0.0005991 Informative Direct
Biological Process (BP) cellular response to endogenous stimulus 0.1822 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.2346 Informative Inherited
Biological Process (BP) sensory organ development 0.2874 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.00765 Informative Inherited
Biological Process (BP) protein localization to organelle 0.04847 Informative Inherited
Biological Process (BP) response to oxidative stress 0.0585 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.435 Informative Inherited
Biological Process (BP) organ morphogenesis 0.3065 Informative Inherited
Biological Process (BP) cellular response to reactive oxygen species 0.00006259 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0001576 Highly Informative Direct
Biological Process (BP) nuclear import 0.0001918 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.001148 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.002089 Highly Informative Inherited
Biological Process (BP) positive regulation of Ras GTPase activity 1 Highly Informative Inherited
Biological Process (BP) eye morphogenesis 0.002492 Highly Informative Inherited
Molecular Function (MF) binding 0.08772 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000002118 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.2922 Moderately Informative Inherited
Molecular Function (MF) enzyme activator activity 0 Informative Direct
Molecular Function (MF) GTPase regulator activity 0 Informative Direct
Molecular Function (MF) lipid binding 0.000000002025 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.2368 Informative Inherited
Molecular Function (MF) GTPase activator activity 0.000000000000007513 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 0.2305 Highly Informative Inherited
Molecular Function (MF) small GTPase regulator activity 0.01941 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9824 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1739 Least Informative Inherited
Cellular Component (CC) membrane 0.5818 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.05152 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.1961 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.4262 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.000000002502 Informative Direct
Cellular Component (CC) cell junction 0.000001035 Informative Direct
Cellular Component (CC) cell leading edge 0.0004411 Informative Direct
Cellular Component (CC) endosome 0.001389 Informative Inherited
Cellular Component (CC) adherens junction 0.000000000008222 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0.0002253 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0003515 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)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA 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

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)pollen development stage0.0003282Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)L mature pollen stage0.00003075InformativeDirect
Plant structure DEvelopment stage (PDE)M germinated pollen stage0.000179InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processDNA damage0Moderately InformativeDirect
Biological processProtein transport0.0000006845Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentGolgi apparatus0.000000000000001278Moderately InformativeDirect
Cellular componentEndosome0.0001249Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.0000712Moderately InformativeDirect
DomainANK repeat0InformativeDirect
DomainSH3 domain0.000514InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationGTPase activation0InformativeDirect
Post-translational modificationPhosphoprotein0.000003487Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001164 SSF57863 Protein matches
Abstract

This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins [PubMed9446556]. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins.

The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved [PubMed10601011]. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis [PubMed10102276].

The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs [PubMed7637788]. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.


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) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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 ArfGap/RecO-like zinc finger 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 ArfGap/RecO-like zinc finger 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) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]