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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 (172) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 941 1,543 17
Proteins 941 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 Least Informative Direct
Biological Process (BP) biological regulation 0.000000000241 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9205 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.7325 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.7838 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.000000000002267 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.0000000006294 Moderately Informative Direct
Biological Process (BP) negative regulation of biological process 0.0000007117 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule metabolic process 0.0000008289 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) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.01075 Moderately Informative Inherited
Biological Process (BP) positive regulation of biological process 0.1324 Moderately Informative Inherited
Biological Process (BP) system development 0.01442 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.8746 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.1109 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of primary metabolic process 0.005626 Moderately Informative Inherited
Biological Process (BP) nucleic acid metabolic process 0.1011 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.02632 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.04907 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.4663 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) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) methylation 0 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.000000000005202 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.000000016 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.00000008149 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 0.00001758 Informative Direct
Biological Process (BP) animal organ development 0.000123 Informative Direct
Biological Process (BP) single organism reproductive process 0.0007482 Informative Direct
Biological Process (BP) regulation of protein modification process 0.000829 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.002577 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.4232 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.9381 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.4112 Informative Inherited
Biological Process (BP) positive regulation of cellular metabolic process 0.0436 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.04241 Informative Inherited
Biological Process (BP) negative regulation of macromolecule metabolic process 0.004242 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) regulation of multicellular organismal development 1 Informative Inherited
Biological Process (BP) tissue development 0.8399 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.3695 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 1 Informative Inherited
Biological Process (BP) positive regulation of biosynthetic process 0.08231 Informative Inherited
Biological Process (BP) positive regulation of macromolecule metabolic process 0.7209 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) nervous system development 0.7477 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.6604 Informative Inherited
Biological Process (BP) post-embryonic development 0.3121 Informative Inherited
Biological Process (BP) DNA metabolic process 0.002088 Informative Inherited
Biological Process (BP) reproductive system development 0.09675 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.03519 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) protein alkylation 0.00000000000004122 Highly Informative Direct
Biological Process (BP) gene silencing 0.00000000002231 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0.000000001119 Highly Informative Direct
Biological Process (BP) chromosome organization 0.0000000254 Highly Informative Direct
Biological Process (BP) homeostasis of number of cells 0.000001405 Highly Informative Direct
Biological Process (BP) negative regulation of nucleobase-containing compound metabolic process 0.0004715 Highly Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.000672 Highly Informative Direct
Biological Process (BP) leukocyte cell-cell adhesion 0.0006778 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.05872 Highly Informative Inherited
Biological Process (BP) negative regulation of organelle organization 0.4589 Highly Informative Inherited
Biological Process (BP) regulation of autophagy 0.1424 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.01943 Highly Informative Inherited
Biological Process (BP) positive regulation of nucleic acid-templated transcription 0.5859 Highly Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.2185 Highly Informative Inherited
Biological Process (BP) neuron differentiation 0.6065 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.008087 Highly Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Highly Informative Inherited
Biological Process (BP) embryonic morphogenesis 1 Highly Informative Inherited
Biological Process (BP) cell morphogenesis 0.0432 Highly Informative Inherited
Biological Process (BP) hemopoiesis 0.1459 Highly Informative Inherited
Biological Process (BP) lymphocyte activation 0.4319 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.02875 Highly Informative Inherited
Biological Process (BP) head development 0.1532 Highly Informative Inherited
Biological Process (BP) central nervous system development 0.7607 Highly Informative Inherited
Biological Process (BP) cell projection organization 0.5229 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000000009493 Least Informative Direct
Molecular Function (MF) transferase activity 0.0000000002871 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) protein binding 0.000000001509 Moderately Informative Direct
Molecular Function (MF) cation binding 0.00000000321 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 0.1214 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.07936 Moderately Informative Inherited
Molecular Function (MF) methyltransferase activity 0.00000000000001949 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0000000000002598 Informative Direct
Molecular Function (MF) nucleic acid binding 0.000000000008052 Informative Direct
Molecular Function (MF) zinc ion binding 0.0000000006889 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.1914 Informative Inherited
Molecular Function (MF) lipid binding 0.4151 Informative Inherited
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.00000004278 Highly Informative Direct
Molecular Function (MF) N-methyltransferase activity 0.0000002414 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000001831 Highly Informative Direct
Molecular Function (MF) ubiquitin-like protein transferase activity 0.000002222 Highly Informative Direct
Molecular Function (MF) phospholipid binding 0.002729 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 0.0001282 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 0.000000000003015 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) chromatin 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome 0.0000000000009896 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 integument0.0822Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.08897Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.1238Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.001059Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the orbital region0.002916Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa0.00519Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.1709Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of upper lip0.0001704InformativeDirect
Phenotypic Abnormality (PA)Leukemia0.01475InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the forehead0.05522InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the scalp hair0.151InformativeInherited
Phenotypic Abnormality (PA)Congenital abnormal hair pattern0.6301InformativeInherited
Phenotypic Abnormality (PA)Acute myeloid leukemia0.0002091Highly InformativeDirect
Phenotypic Abnormality (PA)High anterior hairline0.00046Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.002464Least InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.8418Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.2342InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.3817InformativeInherited
Mammalian Phenotype (MP)abnormal spermatogenesis0.4002InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.001752Highly InformativeInherited
Mammalian Phenotype (MP)abnormal spermiogenesis0.01322Highly 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 variant0.007987Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.2191Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.001125Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.774Moderately InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.0001602InformativeDirect
Worm Phenotype (WP)organism stress response variant0.002293InformativeInherited
Worm Phenotype (WP)vulva development variant0.005436InformativeInherited
Worm Phenotype (WP)multivulva0.0000005192Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00001147Highly InformativeDirect
Worm Phenotype (WP)organism UV response variant0.00005398Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.0006045Highly 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 variegation0.00000001801InformativeDirect
Fly Phenotype (FP)homeotic0.0009659InformativeDirect

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 organism0.00000443Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0.00002164Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0.00007475Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.0005428Least InformativeDirect
Xenopus ANatomical entity (XAN)egg0.0001338Moderately 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)Transferases0.000000000002275Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.6537Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.00000000155Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.000001076Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.01648Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.000000005879InformativeDirect
Enzyme Commission (EC)Acting on ATP; involved in cellular and subcellular movement0.00001186InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.08851InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.4102InformativeInherited
Enzyme Commission (EC)With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0Highly InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0Highly InformativeDirect
Enzyme Commission (EC)HECT-type E3 ubiquitin transferase0.00000000172Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.00000005509Highly 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 cycle0.000002482Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processBiological rhythms0.00000000002132InformativeDirect
Biological processApoptosis0.00000000153InformativeDirect
Biological processGrowth regulation0.000000000000007168Highly InformativeDirect
Biological processMeiosis0.0000000002785Highly InformativeDirect
Biological processAutophagy0.000001772Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0.000000000005759InformativeDirect
Coding sequence diversityAlternative splicing0.00000003682Least InformativeDirect
Coding sequence diversityChromosomal rearrangement0.00000005293InformativeDirect
DiseaseTumor suppressor0.0000003053Moderately InformativeDirect
DomainRepeat0.0000001122Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.000000000003415Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0.00000006798Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0004571InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000001083Moderately InformativeDirect
Post-translational modificationOxidoreductase0.03594Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationMethyltransferase0.00000005086InformativeDirect
Post-translational modificationAcyltransferase0.00001627InformativeDirect
Post-translational modificationHelicase0.0003184InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationCitrullination0.0000003445Highly 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 sumoylation0.000004048Highly 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 ]