SUPERFAMILY 1.75 HMM library and genome assignments server

CCCH zinc finger superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   CCCH zinc finger [ 90228]
Superfamily:   CCCH zinc finger [ 90229]
Families:   CCCH zinc finger [ 90230] (4)


Superfamily statistics
Genomes (498) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 17,740 16,537 7
Proteins 11,175 11,033 4


Functional annotation
General category Regulation
Detailed category DNA-binding

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) heterocycle metabolic process 0.0000000000005896 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000000000001405 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.000000000005297 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000000000486 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000004802 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000001138 Least Informative Direct
Biological Process (BP) positive regulation of biological process 0.4066 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3809 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000001309 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000147 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0002123 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.09569 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.17 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1276 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.7178 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.873 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.3272 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.002603 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.8684 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3843 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.9716 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8641 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.2923 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.5752 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.0000000009942 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0000003135 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.00001117 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.00001148 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.00002755 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.00003798 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.00004669 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0002307 Informative Direct
Biological Process (BP) positive regulation of RNA metabolic process 0.006583 Informative Inherited
Biological Process (BP) negative regulation of immune system process 0.001227 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.0147 Informative Inherited
Biological Process (BP) positive regulation of intracellular signal transduction 0.1243 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.441 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.001872 Informative Inherited
Biological Process (BP) regulation of protein localization 0.01673 Informative Inherited
Biological Process (BP) positive regulation of transport 0.4681 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.001458 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.08242 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.1019 Informative Inherited
Biological Process (BP) positive regulation of catabolic process 0.06429 Informative Inherited
Biological Process (BP) regulation of cell activation 0.04832 Informative Inherited
Biological Process (BP) leukocyte activation 0.005381 Informative Inherited
Biological Process (BP) growth 0.1714 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.9818 Informative Inherited
Biological Process (BP) cell proliferation 0.003594 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.2667 Informative Inherited
Biological Process (BP) cell division 0.4646 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.01733 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3189 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.3391 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.02496 Informative Inherited
Biological Process (BP) immune response 0.2858 Informative Inherited
Biological Process (BP) immune effector process 0.03232 Informative Inherited
Biological Process (BP) RNA processing 0.003053 Informative Inherited
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0000000000254 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 0.0000000001968 Highly Informative Direct
Biological Process (BP) T cell differentiation 0.000003133 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.000006981 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 0.00001677 Highly Informative Direct
Biological Process (BP) negative regulation of protein phosphorylation 0.00002673 Highly Informative Direct
Biological Process (BP) regulation of peptidyl-tyrosine phosphorylation 0.00003186 Highly Informative Direct
Biological Process (BP) RNA splicing 0.00004396 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.00006078 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 0.00007361 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0.00009966 Highly Informative Direct
Biological Process (BP) negative regulation of leukocyte activation 0.0001812 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0001847 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.0004353 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.001133 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 0.001221 Highly Informative Inherited
Biological Process (BP) gene silencing 0.01277 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.9012 Highly Informative Inherited
Biological Process (BP) stem cell development 0.01607 Highly Informative Inherited
Biological Process (BP) regulation of mRNA processing 0.007758 Highly Informative Inherited
Biological Process (BP) regulation of translation 0.04175 Highly Informative Inherited
Biological Process (BP) mRNA catabolic process 0.005353 Highly Informative Inherited
Molecular Function (MF) binding 0.0000004548 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 1 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0.0005029 Informative Direct
Molecular Function (MF) mRNA binding 0.07236 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.2597 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.776 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.7409 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.000000000002761 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.01358 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.01249 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.002679 Informative Inherited
Cellular Component (CC) cytoplasmic ribonucleoprotein granule 0.00000000000004089 Highly Informative Direct
Cellular Component (CC) protein serine/threonine phosphatase complex 0.0000004157 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.00002099 Highly Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.1459Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1852Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.6864Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.006992Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal protein level0.05945Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.06168Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.1004Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.1056Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.00003776InformativeDirect
Mammalian Phenotype (MP)abnormal thymus morphology0.002056InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.002177InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.002273InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.002627InformativeInherited
Mammalian Phenotype (MP)abnormal circulating cytokine level0.003936InformativeInherited
Mammalian Phenotype (MP)enlarged lymph nodes0.000001001Highly InformativeDirect
Mammalian Phenotype (MP)increased T cell derived lymphoma incidence0.00009502Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.0001157Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus development0.0002886Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.02055Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.0002533Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.01352Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.4851Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.8275Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.01127InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.01322InformativeInherited
Worm Phenotype (WP)P granule defective0.0000000002951Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00001035Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.001341Highly InformativeInherited
Worm Phenotype (WP)pharyngeal development variant0.01199Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)head0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect

Document: ZA 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)animal pole0.0000003417Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0.005664Moderately InformativeInherited
Biological processUbl conjugation pathway0.0000000000001535InformativeDirect
Biological processNeurogenesis0.0002147InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Cellular componentHost cytoplasm0.000008017InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.0000007247Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding0.00000000000154Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000000238Moderately InformativeDirect
Post-translational modificationRepressor0.00001141Moderately InformativeDirect
Post-translational modificationPhosphoprotein9.055e-16Least 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 ubiquitination0Moderately InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 CCCH zinc finger 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 CCCH zinc finger 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]