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PHD domain family

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   FYVE/PHD zinc finger [ 57902]
Superfamily:   FYVE/PHD zinc finger [ 57903] (3)
Family:   PHD domain [ 57911] (13)


Family statistics
Genomes (176) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 951 2,535 17
Proteins 951 2,535 17


Gene Ontology (high-quality)

(
show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000000002259 Least Informative Direct
Biological Process (BP) biological regulation 0.00000004948 Least Informative Direct
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.987 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 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) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule modification 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular protein metabolic process 0.00000000000001449 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.0000000001269 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule metabolic process 0.00000002118 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.000003686 Moderately Informative Direct
Biological Process (BP) reproduction 0.00004823 Moderately Informative Direct
Biological Process (BP) negative regulation of biological process 0.0001175 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.2127 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.5878 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of primary metabolic process 0.001123 Moderately Informative Inherited
Biological Process (BP) system development 0.0188 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.5587 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.02443 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.02229 Moderately Informative Inherited
Biological Process (BP) nucleic acid metabolic process 0.299 Moderately Informative Inherited
Biological Process (BP) response to chemical 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.0545 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.08169 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) methylation 0 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) regulation of organelle organization 0 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.000000000001153 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0000001199 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.0000003205 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 0.000004188 Informative Direct
Biological Process (BP) single organism reproductive process 0.00002816 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 1 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.7322 Informative Inherited
Biological Process (BP) regulation of catabolic process 1 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.4265 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.007905 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.01208 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.3558 Informative Inherited
Biological Process (BP) negative regulation of macromolecule metabolic process 0.05012 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) cellular component morphogenesis 1 Informative Inherited
Biological Process (BP) nervous system development 0.9087 Informative Inherited
Biological Process (BP) regulation of multicellular organismal development 1 Informative Inherited
Biological Process (BP) tissue development 0.9899 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.5369 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 1 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.1049 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.1396 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.995 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.002198 Informative Inherited
Biological Process (BP) cell activation 0.122 Informative Inherited
Biological Process (BP) reproductive system development 0.02656 Informative Inherited
Biological Process (BP) post-embryonic development 0.2001 Informative Inherited
Biological Process (BP) DNA metabolic process 0.006488 Informative Inherited
Biological Process (BP) embryo development 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.006251 Informative Inherited
Biological Process (BP) macromolecule methylation 0 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.00000000000001727 Highly Informative Direct
Biological Process (BP) protein alkylation 0.0000000000000627 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0.00000000007268 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0.0000000001562 Highly Informative Direct
Biological Process (BP) negative regulation of organelle organization 0.000005174 Highly Informative Direct
Biological Process (BP) myeloid cell homeostasis 0.0003859 Highly Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0007967 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.07009 Highly Informative Inherited
Biological Process (BP) negative regulation of catabolic process 0.1723 Highly Informative Inherited
Biological Process (BP) regulation of protein complex disassembly 0.02498 Highly Informative Inherited
Biological Process (BP) cell morphogenesis 0.01618 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.08588 Highly Informative Inherited
Biological Process (BP) myeloid cell differentiation 0.002199 Highly Informative Inherited
Biological Process (BP) negative regulation of nucleobase-containing compound metabolic process 0.006015 Highly Informative Inherited
Biological Process (BP) neuron differentiation 0.5472 Highly Informative Inherited
Biological Process (BP) sex differentiation 0.8859 Highly Informative Inherited
Biological Process (BP) leukocyte differentiation 0.08994 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-templated 0.1659 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.4318 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.03199 Highly Informative Inherited
Biological Process (BP) brain development 0.4403 Highly Informative Inherited
Biological Process (BP) lymphocyte activation 0.06677 Highly Informative Inherited
Biological Process (BP) cell projection organization 0.5965 Highly Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 1 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.8758 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.04855 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000003426 Least Informative Direct
Molecular Function (MF) binding 0.000000002026 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) metal ion binding 0.00000000007535 Moderately Informative Direct
Molecular Function (MF) protein binding 0.000000005813 Moderately Informative Direct
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.2944 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.3789 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) methyltransferase activity 0.0000000000002432 Informative Direct
Molecular Function (MF) zinc ion binding 0.00000000004839 Informative Direct
Molecular Function (MF) DNA binding 0.0000000005672 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.3597 Informative Inherited
Molecular Function (MF) lipid binding 0.5008 Informative Inherited
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.00000003089 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.0000009759 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.5841 Highly Informative Inherited
Molecular Function (MF) phospholipid binding 0.007719 Highly Informative Inherited
Cellular Component (CC) macromolecular complex 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0001259 Least Informative Direct
Cellular Component (CC) catalytic complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) neuron part 1 Informative Inherited
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 1 Informative Inherited
Cellular Component (CC) ATPase complex 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.00000001591 Highly Informative Direct
Cellular Component (CC) chromatin 0.00005941 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)Transferring one-carbon groups0.0000000003076Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.07112Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases0.4996Least InformativeInherited
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.00000000007186Moderately InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0.0000000007451Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.0002735Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)With 2-oxoglutarate as one donor, and incorporatio0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processCell cycle0.000002653Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processBiological rhythms0.00000000002321InformativeDirect
Biological processApoptosis0.000000001676InformativeDirect
Biological processGrowth regulation0.00000000000001102Highly InformativeDirect
Biological processMeiosis0.0000000003645Highly InformativeDirect
Biological processAutophagy0.000002041Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0.000000000009007InformativeDirect
Coding sequence diversityAlternative splicing0.00000002695Least InformativeDirect
Coding sequence diversityChromosomal rearrangement0.00000004576InformativeDirect
DiseaseTumor suppressor0.0000007127Moderately InformativeDirect
DiseaseMental retardation0.0003349InformativeDirect
DomainRepeat0.00000008722Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.000000000004262Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationTransferase0.03603Least InformativeInherited
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDNA-binding3.42e-16Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000001316Moderately InformativeDirect
Post-translational modificationOxidoreductase0.0382Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationMethyltransferase0.0000002542InformativeDirect
Post-translational modificationAcyltransferase0.00009255InformativeDirect
Post-translational modificationHelicase0.0003134InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationCitrullination0.0000003968Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

   
Superfamily level     Family level

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.


   
Superfamily level     Family level

Alignments of sequences to 22 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.


Superfamily level

Browse and view proteins in genomes which have different domain combinations including a FYVE/PHD zinc finger domain.


   
Superfamily level     Family level

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.


Jump to [ Top of page · SCOP classification · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]