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) cellular macromolecule metabolic process 1.211e-08 Least Informative Direct
Biological Process (BP) protein metabolic process 4.414e-05 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.0009606 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.1264 Least Informative Inherited
Biological Process (BP) localization 0.9537 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.02188 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.763 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) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of cellular process 3.79e-05 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.07174 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.06396 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.4275 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.3443 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.0692 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.5462 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.07589 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.03073 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1974 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1448 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.4259 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.007156 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.002853 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.6075 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.04759 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 0.616 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) positive regulation of signal transduction 2.136e-09 Informative Direct
Biological Process (BP) regulation of intracellular transport 8.81e-05 Informative Direct
Biological Process (BP) protein localization to organelle 0.0002704 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0005311 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0008787 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0009649 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0009891 Informative Direct
Biological Process (BP) negative regulation of cell death 0.1801 Informative Inherited
Biological Process (BP) regulation of establishment of protein localization 0.006207 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.01414 Informative Inherited
Biological Process (BP) regulation of apoptotic process 1 Informative Inherited
Biological Process (BP) positive regulation of transport 0.6437 Informative Inherited
Biological Process (BP) protein catabolic process 0.004603 Informative Inherited
Biological Process (BP) proteolysis 0.2364 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.2721 Informative Inherited
Biological Process (BP) regulation of immune response 0.04864 Informative Inherited
Biological Process (BP) DNA metabolic process 1 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.02259 Informative Inherited
Biological Process (BP) RNA processing 0.002208 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.08325 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.02973 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3205 Informative Inherited
Biological Process (BP) RNA splicing 3.89e-07 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 4.596e-07 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 2.039e-05 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 5.875e-05 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0001225 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0001334 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.0001571 Highly Informative Direct
Biological Process (BP) immune response-regulating cell surface receptor signaling pathway 0.000431 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.0008339 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.0008427 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.3779 Highly Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 0.03188 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.002844 Highly Informative Inherited
Molecular Function (MF) binding 0.0009853 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.2189 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 6.31e-05 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.002762 Moderately Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 3.484e-05 Informative Direct
Molecular Function (MF) RNA binding 0.0003832 Informative Direct
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) peptidase activity 0.001279 Informative Inherited
Molecular Function (MF) thiolester hydrolase activity 5.78e-08 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 3.322e-06 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.0009502 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.008591 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.083 Least Informative Inherited
Cellular Component (CC) membrane 0.8521 Least Informative Inherited
Cellular Component (CC) protein complex 0.4053 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.002176 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.1017 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0001413 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 0.007723 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.011 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.7918 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 2.973e-07 Informative Direct
Cellular Component (CC) integral to membrane 0.3701 Informative Inherited
Cellular Component (CC) endosome 0.3082 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) nuclear envelope 0.147 Informative Inherited
Cellular Component (CC) pore complex 2.115e-06 Highly Informative Direct
Cellular Component (CC) nuclear body 0.000219 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0008412 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 disease0.1915Least InformativeInherited
Disease Ontology (DO)organ system cancer0.5867Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.05788Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.182Moderately InformativeInherited
Disease Ontology (DO)cell type cancer0.7581Moderately InformativeInherited
Disease Ontology (DO)retinal disease0.02953InformativeInherited
Disease Ontology (DO)retinal cancer0.0005515Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.02827Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.07929Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1147Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.3409Least InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.01223Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.01578Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.01613Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.3965Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal response to radiation0.0001368InformativeDirect
Mammalian Phenotype (MP)decreased leukocyte cell number0.00141InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.01796InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.03702InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.1335InformativeInherited
Mammalian Phenotype (MP)abnormal mature B cell morphology0.1401InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation2.863e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cell nucleus morphology1.363e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal B-1 B cell number0.001228Highly InformativeInherited
Mammalian Phenotype (MP)decreased mature B cell number0.4221Highly 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)Hydrolases5.406e-05Least InformativeDirect
Enzyme Commission (EC)Lyases0.02671Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)6.233e-12Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.002526Moderately InformativeInherited
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases6.492e-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

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 ]