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 (444) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 14,795 11,616 7
Proteins 9,526 7,773 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 4.008e-15 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1.896e-14 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 7.681e-13 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.15e-10 Least Informative Direct
Biological Process (BP) regulation of metabolic process 3.225e-10 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 4.474e-07 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 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) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) gene expression 7.648e-09 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 3.138e-06 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 6.473e-06 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 5.59e-05 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.6078 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.758 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.9648 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.9926 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.9608 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.01657 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8696 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.06895 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.4121 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 9.554e-12 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 3.541e-07 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 1.49e-06 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 3.981e-06 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 9.695e-06 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 8.578e-05 Informative Direct
Biological Process (BP) nucleocytoplasmic transport 0.000149 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0003933 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.01015 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.04235 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.04436 Informative Inherited
Biological Process (BP) regulation of protein localization 0.005485 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.05813 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.001956 Informative Inherited
Biological Process (BP) regulation of cell development 0.1704 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.2353 Informative Inherited
Biological Process (BP) positive regulation of transport 0.1677 Informative Inherited
Biological Process (BP) negative regulation of cellular metabolic process 0.8621 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.006693 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.0982 Informative Inherited
Biological Process (BP) ribonucleoprotein complex subunit organization 1.2e-11 Highly Informative Direct
Biological Process (BP) negative regulation of phosphorylation 1.021e-05 Highly Informative Direct
Biological Process (BP) regulation of peptidyl-tyrosine phosphorylation 1.454e-05 Highly Informative Direct
Biological Process (BP) nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay 0.0001155 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0002679 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.0002925 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.000602 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.0007571 Highly Informative Direct
Biological Process (BP) negative regulation of signal transduction 0.03438 Highly Informative Inherited
Biological Process (BP) positive regulation of protein transport 0.001042 Highly Informative Inherited
Biological Process (BP) regulation of intracellular protein transport 0.04352 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.002013 Highly Informative Inherited
Biological Process (BP) regulation of lymphocyte activation 0.003324 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.9086 Highly Informative Inherited
Biological Process (BP) negative regulation of gene expression 1 Highly Informative Inherited
Biological Process (BP) RNA splicing, via transesterification reactions 0.002525 Highly Informative Inherited
Molecular Function (MF) binding 0.03175 Least Informative Inherited
Molecular Function (MF) heterocyclic compound binding 1.038e-14 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 2.182e-14 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.9763 Moderately Informative Inherited
Molecular Function (MF) RNA binding 7.217e-12 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0.0001248 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.0001061 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.3857 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 organelle part 0.6723 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 8.226e-12 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.2868 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.1936 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.1027 Informative Inherited
Cellular Component (CC) protein serine/threonine phosphatase complex 5.506e-07 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 9.307e-07 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)immune system phenotype0.1778Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.01271Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.02962Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.0001847InformativeDirect
Mammalian Phenotype (MP)abnormal thymus morphology0.0006023InformativeDirect
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.001014InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.004883InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.004904InformativeInherited
Mammalian Phenotype (MP)enlarged lymph nodes9.187e-06Highly InformativeDirect
Mammalian Phenotype (MP)T cell derived lymphoma3.968e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus development0.0001985Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen size0.001837Highly InformativeInherited

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 defective2.951e-10Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene1.035e-05Highly 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) 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
Zebrafish Anatomy (ZA)eye0Moderately InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)animal pole2.856e-08Highly InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0.004697Moderately InformativeInherited
Biological processUbl conjugation pathway0InformativeDirect
Biological processNeurogenesis0.0001572InformativeDirect
Biological processmRNA splicing0.05285InformativeInherited
Biological processSpliceosome0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentHost cytoplasm6.272e-06InformativeDirect
DomainRepeat0Least InformativeDirect
DomainCoiled coil1.675e-11Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionZinc-finger0Moderately InformativeDirect
Molecular functionRNA-binding4.583e-10Moderately InformativeDirect
Post-translational modificationDevelopmental protein1.801e-07Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least 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) · 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) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]