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 5.106e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.023e-08 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.1268 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.00101 Least Informative Inherited
Biological Process (BP) localization 0.9388 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.0189 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7744 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) regulation of programmed cell death 1.056e-06 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 3.419e-05 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.07258 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.06356 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.4163 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.338 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.0796 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.03137 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1964 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1412 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.4155 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.006931 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.003106 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.6032 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.008553 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.04474 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) organic cyclic compound catabolic process 0.6115 Moderately Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.0008302 Informative Direct
Biological Process (BP) positive regulation of signal transduction 2.426e-09 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0005559 Informative Direct
Biological Process (BP) regulation of intracellular transport 7.764e-05 Informative Direct
Biological Process (BP) protein localization to organelle 0.000268 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0009209 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0009492 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) negative regulation of cell death 0.1781 Informative Inherited
Biological Process (BP) regulation of establishment of protein localization 0.0059 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.0141 Informative Inherited
Biological Process (BP) positive regulation of transport 0.6484 Informative Inherited
Biological Process (BP) proteolysis 0.2312 Informative Inherited
Biological Process (BP) protein catabolic process 0.004339 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.2691 Informative Inherited
Biological Process (BP) regulation of immune response 0.04878 Informative Inherited
Biological Process (BP) DNA metabolic process 1 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.02238 Informative Inherited
Biological Process (BP) RNA processing 0.002231 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.08314 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3155 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.02879 Informative Inherited
Biological Process (BP) immune response-regulating cell surface receptor signaling pathway 0.0004374 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0001214 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0001358 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 1.89e-05 Highly Informative Direct
Biological Process (BP) RNA splicing 3.926e-07 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.00086 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.0008707 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 4.292e-07 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.000154 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 6.119e-05 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.3759 Highly Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 0.03313 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.002615 Highly Informative Inherited
Molecular Function (MF) binding 0.0007615 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.2087 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 5.515e-05 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.002356 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0003777 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 3.784e-05 Informative Direct
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) peptidase activity 0.001241 Informative Inherited
Molecular Function (MF) thiolester hydrolase activity 6.491e-08 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 4.082e-06 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.0009025 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.008189 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.06957 Least Informative Inherited
Cellular Component (CC) membrane 0.8486 Least Informative Inherited
Cellular Component (CC) protein complex 0.4069 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.002069 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.0785 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0001018 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 0.006082 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.01188 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.8048 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 2.957e-07 Informative Direct
Cellular Component (CC) nucleolus 3.012e-08 Informative Direct
Cellular Component (CC) integral to membrane 0.3808 Informative Inherited
Cellular Component (CC) endosome 0.3074 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) nuclear envelope 0.1575 Informative Inherited
Cellular Component (CC) nuclear body 0.0002174 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0009118 Highly Informative Direct
Cellular Component (CC) pore complex 2.17e-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 disease0.2565Least InformativeInherited
Disease Ontology (DO)organ system cancer0.6677Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.03409Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.08916Moderately InformativeInherited
Disease Ontology (DO)cell type cancer0.6385Moderately InformativeInherited
Disease Ontology (DO)retinal disease0.02255InformativeInherited
Disease Ontology (DO)retinal cancer0.0003636Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.02646Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.07886Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1142Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.3405Least InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.01212Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.01595Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.01602Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.3963Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal response to radiation0.00014InformativeDirect
Mammalian Phenotype (MP)decreased leukocyte cell number0.001427InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.01783InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.03704InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.132InformativeInherited
Mammalian Phenotype (MP)abnormal mature B cell morphology0.141InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation2.896e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cell nucleus morphology1.386e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal B-1 B cell number0.001241Highly InformativeInherited
Mammalian Phenotype (MP)decreased mature B cell number0.422Highly 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)Hydrolases5.214e-05Least InformativeDirect
Enzyme Commission (EC)Lyases0.02633Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)6.239e-12Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.002527Moderately InformativeInherited
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases6.509e-08Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.611Least InformativeInherited
Biological processApoptosis8.05e-09Moderately InformativeDirect
Biological processProtein transport3.901e-06Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processmRNA splicing2.37e-16InformativeDirect
Biological processWnt signaling pathway1.81e-13InformativeDirect
Biological processmRNA transport4.399e-12Highly InformativeDirect
Biological processTranslocation0.0006741Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome7.436e-10InformativeDirect
Coding sequence diversityAlternative splicing0.0002006Least InformativeDirect
DiseaseProto-oncogene9.268e-07Moderately InformativeDirect
DomainRepeat2.031e-06Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainANK repeat5.834e-05InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding0.0002306Moderately InformativeDirect
Post-translational modificationHydrolase0.2255Least InformativeInherited
Post-translational modificationProtease8.463e-06Moderately InformativeDirect
Post-translational modificationLigase4.453e-05Moderately InformativeDirect
Post-translational modificationRepressor0.0009801Moderately InformativeDirect
Post-translational modificationThiol protease3.856e-14InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0001135Least 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 sumoylation2.435e-07Highly InformativeDirect
UniPathway (UP)protein degradation3.245e-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 ]