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 (453) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 7,462 5,730 7
Proteins 4,786 3,769 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) protein metabolic process 7.617e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.086e-09 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.1408 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.001044 Least Informative Inherited
Biological Process (BP) localization 0.942 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01718 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7482 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule catabolic process 0.0001305 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 5.937e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 2.467e-05 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.08707 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.06411 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.404 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.1917 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.07669 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.5854 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.07864 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.03243 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1383 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1182 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.3644 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.006988 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.002888 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.6108 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.04001 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.9846 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.448 Moderately Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.000688 Informative Direct
Biological Process (BP) positive regulation of signal transduction 2.138e-09 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0006124 Informative Direct
Biological Process (BP) regulation of intracellular transport 7.329e-05 Informative Direct
Biological Process (BP) protein localization to organelle 0.000223 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0004038 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0007911 Informative Direct
Biological Process (BP) negative regulation of cell death 0.1727 Informative Inherited
Biological Process (BP) regulation of establishment of protein localization 0.004262 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.01384 Informative Inherited
Biological Process (BP) positive regulation of transport 0.6169 Informative Inherited
Biological Process (BP) proteolysis 0.23 Informative Inherited
Biological Process (BP) protein catabolic process 0.005359 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.1627 Informative Inherited
Biological Process (BP) regulation of immune response 0.05487 Informative Inherited
Biological Process (BP) DNA metabolic process 1 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.008348 Informative Inherited
Biological Process (BP) RNA processing 0.001127 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.0919 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.2887 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.02469 Informative Inherited
Biological Process (BP) immune response-regulating signaling pathway 0.0002798 Highly Informative Direct
Biological Process (BP) DNA catabolic process 1.373e-05 Highly Informative Direct
Biological Process (BP) mRNA processing 5.746e-05 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 1.459e-05 Highly Informative Direct
Biological Process (BP) RNA splicing 3.087e-08 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.0009079 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.0007239 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 3.66e-07 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.000182 Highly Informative Direct
Biological Process (BP) positive regulation of protein transport 0.0001874 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 6.51e-05 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.3739 Highly Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 0.03697 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.002129 Highly Informative Inherited
Molecular Function (MF) binding 0.0001275 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.1751 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 8.723e-06 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.001896 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0002218 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 3.142e-05 Informative Direct
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) peptidase activity 0.001061 Informative Inherited
Molecular Function (MF) thiolester hydrolase activity 6.172e-08 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 3.391e-06 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.0007083 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.005925 Highly Informative Inherited
Cellular Component (CC) membrane 0.5989 Least Informative Inherited
Cellular Component (CC) protein complex 0.3852 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.005092 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.3024 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.5315 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 1 Moderately Informative Inherited
Cellular Component (CC) plasma membrane part 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.05424 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.001414 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.008272 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.7652 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 2.882e-07 Informative Direct
Cellular Component (CC) nucleolus 6.669e-07 Informative Direct
Cellular Component (CC) integral to membrane 0.3302 Informative Inherited
Cellular Component (CC) endosome 0.2907 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) nuclear envelope 0.06836 Informative Inherited
Cellular Component (CC) internal side of plasma membrane 7.239e-06 Highly Informative Direct
Cellular Component (CC) nuclear body 0.0001845 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0005039 Highly Informative Direct
Cellular Component (CC) pore complex 2.054e-06 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)9.655e-11Least 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)nervous system disease0.2048Least InformativeInherited
Disease Ontology (DO)organ system cancer0.5847Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.05714Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.1666Moderately InformativeInherited
Disease Ontology (DO)cell type cancer0.7599Moderately InformativeInherited
Disease Ontology (DO)retinal disease0.02836InformativeInherited
Disease Ontology (DO)ocular cancer1InformativeInherited

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.03364Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.05166Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.07802Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.2444Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.009773Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.1209Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.3896Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.5772Moderately InformativeInherited
Mammalian Phenotype (MP)increased apoptosis0.0005877InformativeDirect
Mammalian Phenotype (MP)decreased hematopoietic cell number0.00207InformativeInherited
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.008258InformativeInherited
Mammalian Phenotype (MP)abnormal mature B cell morphology0.1397InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.1492InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation2.192e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cell nucleus morphology8.581e-06Highly InformativeDirect
Mammalian Phenotype (MP)decreased B cell number2.597e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal B-1 B cell number0.00104Highly 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)Hydrolases5.579e-05Least InformativeDirect
Enzyme Commission (EC)Lyases0.02658Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)6.928e-12Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.002552Moderately InformativeInherited
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases6.369e-08Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.6119Least InformativeInherited
Biological processApoptosis8.017e-09Moderately InformativeDirect
Biological processProtein transport3.92e-06Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processmRNA splicing2.365e-16InformativeDirect
Biological processWnt signaling pathway1.902e-13InformativeDirect
Biological processmRNA transport4.418e-12Highly InformativeDirect
Biological processTranslocation0.0006851Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome5.457e-10InformativeDirect
Coding sequence diversityAlternative splicing0.0009796Least InformativeDirect
DiseaseProto-oncogene1.009e-06Moderately InformativeDirect
DomainRepeat2.145e-06Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainANK repeat6.056e-05InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding0.000251Moderately InformativeDirect
Post-translational modificationHydrolase0.2249Least InformativeInherited
Post-translational modificationProtease8.268e-06Moderately InformativeDirect
Post-translational modificationLigase4.653e-05Moderately InformativeDirect
Post-translational modificationRepressor0.0009354Moderately InformativeDirect
Post-translational modificationThiol protease4.028e-14InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0001113Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect

Document: KW 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) ]

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) · Internal database links ]