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 (503) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,722 7,903 7
Proteins 5,613 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) protein metabolic process 2.806e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 4.559e-09 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.0008198 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.2012 Least Informative Inherited
Biological Process (BP) localization 0.9613 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01424 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6692 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) positive regulation of cellular process 4.938e-05 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.1296 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.0821 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.4278 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.3252 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.06449 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.532 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.07803 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.02892 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1362 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1453 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.4308 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.009146 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.002681 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.5093 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.06122 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.1026 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) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.0008318 Informative Direct
Biological Process (BP) positive regulation of signal transduction 2.079e-09 Informative Direct
Biological Process (BP) regulation of intracellular transport 8.94e-05 Informative Direct
Biological Process (BP) protein localization to organelle 0.0002794 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0003622 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) negative regulation of cell death 0.1039 Informative Inherited
Biological Process (BP) regulation of protein localization 0.01702 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.001178 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.01504 Informative Inherited
Biological Process (BP) positive regulation of transport 0.6676 Informative Inherited
Biological Process (BP) proteolysis 0.1599 Informative Inherited
Biological Process (BP) protein catabolic process 0.001921 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.2721 Informative Inherited
Biological Process (BP) regulation of immune response 0.0476 Informative Inherited
Biological Process (BP) DNA metabolic process 1 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.02209 Informative Inherited
Biological Process (BP) RNA processing 0.00224 Informative Inherited
Biological Process (BP) ribonucleoprotein complex biogenesis 0.001136 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.08133 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.335 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.0286 Informative Inherited
Biological Process (BP) immune response-regulating cell surface receptor signaling pathway 0.000441 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0001721 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0001412 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 3.147e-06 Highly Informative Direct
Biological Process (BP) RNA splicing 4.225e-07 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.0007927 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 4.409e-07 Highly Informative Direct
Biological Process (BP) regulation of mRNA processing 8.533e-08 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.0001586 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 6.883e-05 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.3813 Highly Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 0.03178 Highly Informative Inherited
Biological Process (BP) positive regulation of programmed cell death 0.001637 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.002749 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.2184 Least Informative Inherited
Molecular Function (MF) binding 0.001085 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 6.479e-05 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.00266 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0003512 Informative Direct
Molecular Function (MF) ligase activity 0.0006546 Informative Direct
Molecular Function (MF) peptidase activity 0.00132 Informative Inherited
Molecular Function (MF) thiolester hydrolase activity 5.942e-08 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 3.297e-06 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.007014 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.08257 Least Informative Inherited
Cellular Component (CC) membrane 0.8609 Least Informative Inherited
Cellular Component (CC) protein complex 0.4098 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.002238 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.09956 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0001361 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 1 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.007413 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.01676 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.7903 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 2.965e-07 Informative Direct
Cellular Component (CC) integral to membrane 0.3694 Informative Inherited
Cellular Component (CC) endosome 0.3086 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) nuclear envelope 0.1421 Informative Inherited
Cellular Component (CC) nuclear body 0.0002136 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0008215 Highly Informative Direct
Cellular Component (CC) pore complex 2.112e-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)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 radiation2.858e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cell nucleus morphology1.433e-05Highly 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)Hydrolases5.385e-05Least InformativeDirect
Enzyme Commission (EC)Lyases0.0266Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)6.148e-12Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.002517Moderately InformativeInherited
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases6.456e-08Highly 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 processApoptosis8.091e-09Moderately InformativeDirect
Biological processProtein transport3.904e-06Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processmRNA splicing2.372e-16InformativeDirect
Biological processWnt signaling pathway1.806e-13InformativeDirect
Biological processmRNA transport4.368e-12Highly InformativeDirect
Biological processTranslocation0.0006681Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome7.391e-10InformativeDirect
Coding sequence diversityAlternative splicing0.0004778Least InformativeDirect
DiseaseProto-oncogene9.227e-07Moderately InformativeDirect
DomainRepeat2.102e-06Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainANK repeat5.761e-05InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding0.0002263Moderately InformativeDirect
Post-translational modificationHydrolase0.2295Least InformativeInherited
Post-translational modificationProtease8.42e-06Moderately InformativeDirect
Post-translational modificationLigase4.444e-05Moderately InformativeDirect
Post-translational modificationThiol protease3.862e-14InformativeDirect
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 sumoylation2.425e-07Highly InformativeDirect
UniPathway (UP)protein degradation3.232e-06Highly 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 ]