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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 (173) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 942 1,543 17
Proteins 942 1,543 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 0.000000000000003104 Least Informative Direct
Biological Process (BP) biological regulation 0.0000000002277 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000000008867 Least Informative Direct
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8038 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8546 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9977 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0 Moderately Informative Direct
Biological Process (BP) macromolecule modification 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) cellular protein metabolic process 0.0000000000004673 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.000000000009531 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule metabolic process 0.00000005061 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.0000007889 Moderately Informative Direct
Biological Process (BP) negative regulation of biological process 0.00002299 Moderately Informative Direct
Biological Process (BP) regulation of primary metabolic process 0.0003122 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 1 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) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of biological process 0.2183 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.03045 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.1367 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.05879 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.04747 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.4464 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) nucleic acid metabolic process 0.1458 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) system development 0.03317 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) regulation of organelle organization 0 Informative Direct
Biological Process (BP) methylation 0 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.00000000000004476 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 0.000000003286 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.00000001687 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.00009469 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0002379 Informative Direct
Biological Process (BP) single organism reproductive process 0.0003755 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.7799 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.4773 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.2644 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) embryo development 0.8538 Informative Inherited
Biological Process (BP) regulation of multicellular organismal development 1 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.435 Informative Inherited
Biological Process (BP) cell activation 0.07862 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 1 Informative Inherited
Biological Process (BP) positive regulation of biosynthetic process 0.1126 Informative Inherited
Biological Process (BP) positive regulation of cellular metabolic process 0.1152 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.001222 Informative Inherited
Biological Process (BP) nervous system development 0.9495 Informative Inherited
Biological Process (BP) negative regulation of macromolecule metabolic process 0.00102 Informative Inherited
Biological Process (BP) DNA metabolic process 0.003032 Informative Inherited
Biological Process (BP) post-embryonic development 0.2219 Informative Inherited
Biological Process (BP) tissue development 0.861 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.02638 Informative Inherited
Biological Process (BP) reproductive system development 0.08268 Informative Inherited
Biological Process (BP) peptidyl-lysine modification 0 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.00000000000001462 Highly Informative Direct
Biological Process (BP) protein alkylation 0.00000000000007924 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0.0000000000275 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0.00000001168 Highly Informative Direct
Biological Process (BP) transcription, DNA-templated 0.00000003839 Highly Informative Direct
Biological Process (BP) negative regulation of organelle organization 0.000003131 Highly Informative Direct
Biological Process (BP) negative regulation of nucleobase-containing compound metabolic process 0.00005827 Highly Informative Direct
Biological Process (BP) myeloid cell homeostasis 0.0002856 Highly Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0006902 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.06302 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.004115 Highly Informative Inherited
Biological Process (BP) positive regulation of nucleic acid-templated transcription 0.7232 Highly Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.226 Highly Informative Inherited
Biological Process (BP) neuron differentiation 0.6775 Highly Informative Inherited
Biological Process (BP) cell projection organization 0.8547 Highly Informative Inherited
Biological Process (BP) embryonic morphogenesis 1 Highly Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Highly Informative Inherited
Biological Process (BP) cell morphogenesis 0.06189 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.5251 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.02668 Highly Informative Inherited
Biological Process (BP) head development 0.1915 Highly Informative Inherited
Biological Process (BP) central nervous system development 0.818 Highly Informative Inherited
Biological Process (BP) hemopoiesis 0.1286 Highly Informative Inherited
Biological Process (BP) lymphocyte activation 0.06754 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.8866 Highly Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 1 Highly Informative Inherited
Biological Process (BP) negative regulation of catabolic process 0.3619 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.01228 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000001271 Least Informative Direct
Molecular Function (MF) binding 0.00000000005493 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) cation binding 0.00000000002946 Moderately Informative Direct
Molecular Function (MF) protein binding 0.0000000009441 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.1223 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.1745 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) methyltransferase activity 0.00000000000005498 Informative Direct
Molecular Function (MF) zinc ion binding 0.00000000003563 Informative Direct
Molecular Function (MF) DNA binding 0.000000000194 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.2559 Informative Inherited
Molecular Function (MF) lipid binding 0.4427 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 0.00000004309 Highly Informative Direct
Molecular Function (MF) N-methyltransferase activity 0.000000232 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000002694 Highly Informative Direct
Molecular Function (MF) ubiquitin-like protein transferase activity 0.00001091 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.4288 Highly Informative Inherited
Molecular Function (MF) macromolecular complex binding 0.6742 Highly Informative Inherited
Molecular Function (MF) phospholipid binding 0.003924 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) macromolecular complex 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0002913 Least Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) catalytic complex 0 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) chromosome 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) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.000001323 Highly Informative Direct
Cellular Component (CC) chromatin 0.0002553 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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the integument0.08187Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.0881Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.1235Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal morphology of the ocular adnexa0.0002481Moderately InformativeDirect
Phenotypic Abnormality (PA)Neoplasm0.001023Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.002489Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.17Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of upper lip0.0001573InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the forehead0.05387InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the scalp hair0.1498InformativeInherited
Phenotypic Abnormality (PA)Congenital abnormal hair pattern0.6312InformativeInherited
Phenotypic Abnormality (PA)Acute myeloid leukemia0.0002295Highly InformativeDirect
Phenotypic Abnormality (PA)High anterior hairline0.0004373Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.003234Least InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.3529Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.8034Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.2442InformativeInherited
Mammalian Phenotype (MP)abnormal spermatogenesis0.4023InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.001775Highly InformativeInherited
Mammalian Phenotype (MP)abnormal spermiogenesis0.01329Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.008268Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.2528Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.001154Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.1816Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.7474Moderately InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.0001768InformativeDirect
Worm Phenotype (WP)organism stress response variant0.003973InformativeInherited
Worm Phenotype (WP)vulva development variant0.005668InformativeInherited
Worm Phenotype (WP)multivulva0.0000005291Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00001301Highly InformativeDirect
Worm Phenotype (WP)organism UV response variant0.00003057Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.0006501Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)modifier of variegation0.00000000119InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male organism0.000004437Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0.00002144Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0.00007257Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.0005664Least InformativeDirect
Xenopus ANatomical entity (XAN)egg0.0001267Moderately 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)shoot apex0.006649Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue0.0987Least InformativeInherited
Plant ANatomical entity (PAN)shoot apical meristem0.000002644Highly InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.0009517Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferases0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.9803Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.00004864Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.09222Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.0000001184InformativeDirect
Enzyme Commission (EC)DNA helicase0.000002404InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.00006326InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0Highly InformativeDirect
Enzyme Commission (EC)With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors5.443e-16Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.0000002618Highly 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 cycle0.000002589Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processBiological rhythms0.00000000002325InformativeDirect
Biological processApoptosis0.000000001642InformativeDirect
Biological processGrowth regulation0.00000000000001045Highly InformativeDirect
Biological processMeiosis0.0000000003384Highly InformativeDirect
Biological processAutophagy0.000002073Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0.000000000009035InformativeDirect
Coding sequence diversityAlternative splicing0.00000003761Least InformativeDirect
Coding sequence diversityChromosomal rearrangement0.00000004928InformativeDirect
DiseaseTumor suppressor0.0000007636Moderately InformativeDirect
DiseaseMental retardation0.0003162InformativeDirect
DomainRepeat0.00000009997Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.000000000004831Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationTransferase0.03696Least InformativeInherited
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDNA-binding3.415e-16Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000000132Moderately InformativeDirect
Post-translational modificationOxidoreductase0.03748Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationMethyltransferase0.0000002457InformativeDirect
Post-translational modificationAcyltransferase0.00009172InformativeDirect
Post-translational modificationHelicase0.0003203InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationCitrullination0.0000003614Highly 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 modification0Moderately InformativeDirect
UniPathway (UP)protein sumoylation0.000003919Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]