SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (497) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 17,528 16,537 7
Proteins 11,031 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 0.0000000000001099 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000000000002674 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.000000000007278 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000001062 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000001133 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000000421 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3044 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) single-organism cellular 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 0.000000001647 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000004931 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00024 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.204 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.5033 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1288 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1301 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.8728 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.2096 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.9734 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.7072 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8113 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.2335 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.3561 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.08859 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.527 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.002792 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.0000000008144 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0000002455 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.000009321 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.00001329 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.00001606 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.00002181 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.00002188 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000298 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.2798 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.2027 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.2363 Informative Inherited
Biological Process (BP) regulation of protein localization 0.0132 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.5167 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.001176 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.08818 Informative Inherited
Biological Process (BP) negative regulation of immune system process 0.002681 Informative Inherited
Biological Process (BP) regulation of cell activation 0.04894 Informative Inherited
Biological Process (BP) growth 0.1743 Informative Inherited
Biological Process (BP) negative regulation of gene expression 1 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.01145 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.001484 Informative Inherited
Biological Process (BP) positive regulation of transport 0.4617 Informative Inherited
Biological Process (BP) leukocyte activation 0.005467 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.03287 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.07671 Informative Inherited
Biological Process (BP) immune effector process 0.0319 Informative Inherited
Biological Process (BP) immune response 0.2665 Informative Inherited
Biological Process (BP) RNA processing 0.006972 Informative Inherited
Biological Process (BP) ribonucleoprotein complex subunit organization 0.00000000001662 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 0.0000000001594 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.000001748 Highly Informative Direct
Biological Process (BP) T cell differentiation 0.000002806 Highly Informative Direct
Biological Process (BP) negative regulation of leukocyte activation 0.00001059 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 0.00001708 Highly Informative Direct
Biological Process (BP) regulation of peptidyl-tyrosine phosphorylation 0.00001798 Highly Informative Direct
Biological Process (BP) negative regulation of phosphorylation 0.00002657 Highly Informative Direct
Biological Process (BP) RNA splicing 0.00004273 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.00004459 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.00006071 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 0.0000803 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0001813 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.0003684 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.0007927 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.03178 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.003185 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 0.001048 Highly Informative Inherited
Biological Process (BP) gene silencing 0.01111 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.9286 Highly Informative Inherited
Biological Process (BP) stem cell development 0.01516 Highly Informative Inherited
Biological Process (BP) regulation of mRNA processing 0.02396 Highly Informative Inherited
Biological Process (BP) cell division 0.04403 Highly Informative Inherited
Biological Process (BP) mRNA catabolic process 0.005556 Highly Informative Inherited
Molecular Function (MF) binding 0.00003287 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.9934 Moderately Informative Inherited
Molecular Function (MF) RNA binding 8.006e-16 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0.0003639 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.0003485 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.2461 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9789 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.7857 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.000000000002588 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.03733 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.04359 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.05446 Informative Inherited
Cellular Component (CC) chromosome 0.2382 Informative Inherited
Cellular Component (CC) protein serine/threonine phosphatase complex 0.0000006505 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.00001226 Highly Informative Direct
Cellular Component (CC) chromatin 0.0003865 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 ]