SUPERFAMILY 1.75 HMM library and genome assignments server

Ran binding protein zinc finger-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Rubredoxin-like [ 57769] (17)
Superfamily:   Ran binding protein zinc finger-like [ 90209]
Families:   Ran binding protein zinc finger-like [ 90210] (6)


Superfamily statistics
Genomes (504) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,804 7,903 7
Proteins 5,661 5,298 7


Functional annotation
General category Regulation
Detailed category Other regulatory function

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) cellular macromolecule metabolic process 0.000000003882 Least Informative Direct
Biological Process (BP) protein metabolic process 0.00003026 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.01964 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.001448 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.284 Least Informative Inherited
Biological Process (BP) localization 0.9923 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.001336 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.0002888 Moderately Informative Direct
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3018 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.009019 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1254 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.3368 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1645 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.003171 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.1276 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1353 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.4424 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3326 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.3852 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.001136 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.09895 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.4712 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.01918 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.07799 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.00009654 Informative Direct
Biological Process (BP) protein localization to organelle 0.0002909 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0004005 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0004486 Informative Direct
Biological Process (BP) positive regulation of transport 0.6493 Informative Inherited
Biological Process (BP) negative regulation of cell death 0.2161 Informative Inherited
Biological Process (BP) regulation of protein localization 0.01839 Informative Inherited
Biological Process (BP) positive regulation of intracellular signal transduction 0.06386 Informative Inherited
Biological Process (BP) protein catabolic process 0.001973 Informative Inherited
Biological Process (BP) proteolysis 0.1574 Informative Inherited
Biological Process (BP) regulation of immune response 0.04699 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.2597 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.02198 Informative Inherited
Biological Process (BP) RNA processing 0.001522 Informative Inherited
Biological Process (BP) ribonucleoprotein complex biogenesis 0.001093 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.07283 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.002507 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3443 Informative Inherited
Biological Process (BP) regulation of mRNA processing 0.00000006331 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0000004041 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0.0000004187 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.000003576 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.00001344 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0001424 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0001679 Highly Informative Direct
Biological Process (BP) immune response-regulating cell surface receptor signaling pathway 0.0004365 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.3851 Highly Informative Inherited
Biological Process (BP) positive regulation of intracellular transport 0.001133 Highly Informative Inherited
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.0115 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-templated 0.001638 Highly Informative Inherited
Molecular Function (MF) binding 0.00113 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.2132 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000008454 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.00007834 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.004119 Informative Inherited
Molecular Function (MF) peptidase activity 0.001308 Informative Inherited
Molecular Function (MF) nuclease activity 0.03276 Informative Inherited
Molecular Function (MF) thiolester hydrolase activity 0.000001331 Highly Informative Direct
Molecular Function (MF) ubiquitin-protein transferase activity 0.000002944 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.006823 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0006187 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.08473 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.1375 Least Informative Inherited
Cellular Component (CC) membrane 0.8486 Least Informative Inherited
Cellular Component (CC) protein complex 0.2644 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00003221 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.00004422 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 1 Moderately Informative Inherited
Cellular Component (CC) plasma membrane part 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.00256 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.7877 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0.0000006086 Informative Direct
Cellular Component (CC) side of membrane 0.006608 Informative Inherited
Cellular Component (CC) endosome 0.2987 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) integral component of membrane 0.908 Informative Inherited
Cellular Component (CC) nuclear envelope 0.06462 Informative Inherited
Cellular Component (CC) pore complex 0.000002025 Highly Informative Direct
Cellular Component (CC) nuclear body 0.0002073 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0008131 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.00000000009655Least InformativeDirect
Enzyme Commission (EC)Omega peptidases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.5926Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.0613Moderately InformativeInherited
Disease Ontology (DO)cell type cancer0.7453Moderately InformativeInherited
Disease Ontology (DO)retinal cancer0.0005487Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.03028Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.08071Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1165Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.3439Least InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.01227Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.01589Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.5619Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal response to radiation0.00013InformativeDirect
Mammalian Phenotype (MP)decreased leukocyte cell number0.001429InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.01839InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.03735InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.136InformativeInherited
Mammalian Phenotype (MP)abnormal mature B cell morphology0.1374InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.000002858Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cell nucleus morphology0.00001433Highly InformativeDirect
Mammalian Phenotype (MP)abnormal B-1 B cell number0.001244Highly InformativeInherited
Mammalian Phenotype (MP)decreased mature B cell number0.4131Highly 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

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.00005385Least InformativeDirect
Enzyme Commission (EC)Lyases0.0266Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.000000000006148Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.002517Moderately InformativeInherited
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0.00000006456Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.6123Least InformativeInherited
Biological processApoptosis0.000000008091Moderately InformativeDirect
Biological processProtein transport0.000003904Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processmRNA splicing2.372e-16InformativeDirect
Biological processWnt signaling pathway0.0000000000001806InformativeDirect
Biological processmRNA transport0.000000000004368Highly InformativeDirect
Biological processTranslocation0.0006681Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0.0000000007391InformativeDirect
Coding sequence diversityAlternative splicing0.0004778Least InformativeDirect
DiseaseProto-oncogene0.0000009227Moderately InformativeDirect
DomainRepeat0.000002102Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainANK repeat0.00005761InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding0.0002263Moderately InformativeDirect
Post-translational modificationHydrolase0.2295Least InformativeInherited
Post-translational modificationProtease0.00000842Moderately InformativeDirect
Post-translational modificationLigase0.00004444Moderately InformativeDirect
Post-translational modificationThiol protease0.00000000000003862InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0001141Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein sumoylation0.0000002425Highly InformativeDirect
UniPathway (UP)protein degradation0.000003232Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 6 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 Ran binding protein zinc finger-like 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 6 hidden Markov models representing the Ran binding protein zinc finger-like 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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]