SUPERFAMILY 1.75 HMM library and genome assignments server

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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 943 1,543 17
Proteins 943 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 0.00000000000001173 Least Informative Direct
Biological Process (BP) biological regulation 0.000000000005883 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000001163 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0001084 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.07976 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2063 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2187 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.05196 Least Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000000000001819 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00000005046 Moderately Informative Direct
Biological Process (BP) regulation of primary metabolic process 0.000000821 Moderately Informative Direct
Biological Process (BP) nucleic acid metabolic process 0.0003678 Moderately Informative Direct
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.8491 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.2592 Moderately Informative Inherited
Biological Process (BP) organ development 0.002037 Moderately Informative Inherited
Biological Process (BP) immune system process 0.09513 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.5257 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.5513 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.5886 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.8023 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.05573 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.944 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) DNA metabolic process 0.00000000233 Informative Direct
Biological Process (BP) regulation of transcription, DNA-dependent 0.00000002962 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 0.0000002228 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0001224 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0001322 Informative Direct
Biological Process (BP) negative regulation of macromolecule metabolic process 0.004114 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.2229 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 1 Informative Inherited
Biological Process (BP) cell development 0.8686 Informative Inherited
Biological Process (BP) neurogenesis 1 Informative Inherited
Biological Process (BP) cellular component morphogenesis 1 Informative Inherited
Biological Process (BP) embryo development 0.2135 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.696 Informative Inherited
Biological Process (BP) regulation of catabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.2865 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 1 Informative Inherited
Biological Process (BP) protein catabolic process 1 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.4882 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.124 Informative Inherited
Biological Process (BP) positive regulation of biosynthetic process 0.4555 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 1 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.1388 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) central nervous system development 0.9855 Informative Inherited
Biological Process (BP) cell activation 0.2161 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.001917 Informative Inherited
Biological Process (BP) cell projection organization 0.7598 Informative Inherited
Biological Process (BP) behavior 0.1058 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) protein alkylation 0.000000000008813 Highly Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.000003715 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.00003425 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00003776 Highly Informative Direct
Biological Process (BP) lymphocyte differentiation 0.0006948 Highly Informative Direct
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.001493 Highly Informative Inherited
Biological Process (BP) protein ubiquitination 0.3369 Highly Informative Inherited
Biological Process (BP) neuron projection development 0.01367 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.005003 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.1105 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.6397 Highly Informative Inherited
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 1 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.02969 Highly Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 0.05889 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.3907 Highly Informative Inherited
Biological Process (BP) T cell activation 0.001779 Highly Informative Inherited
Biological Process (BP) in utero embryonic development 0.005528 Highly Informative Inherited
Molecular Function (MF) binding 0.00000000001791 Least Informative Direct
Molecular Function (MF) transferase activity 0.000001002 Least Informative Direct
Molecular Function (MF) cation binding 0.000000002372 Moderately Informative Direct
Molecular Function (MF) protein binding 0.00002267 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 0.03502 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.05395 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) methyltransferase activity 0.00000000000001075 Informative Direct
Molecular Function (MF) zinc ion binding 0.0000000006019 Informative Direct
Molecular Function (MF) DNA binding 0.000000003126 Informative Direct
Molecular Function (MF) ligase activity 0.0003525 Informative Direct
Molecular Function (MF) lipid binding 0.4443 Informative Inherited
Molecular Function (MF) receptor binding 1 Informative Inherited
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.0000000000009014 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.0000000001702 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 0.000000001868 Highly Informative Direct
Molecular Function (MF) dioxygenase activity 0.00001381 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.09721 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.001596 Highly Informative Inherited
Molecular Function (MF) phospholipid binding 0.005528 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) macromolecular complex 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000000000005596 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.000001798 Least Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) membrane-enclosed lumen 0 Moderately Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00000004328 Informative Direct
Cellular Component (CC) neuron part 1 Informative Inherited
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0.788 Informative Inherited
Cellular Component (CC) chromatin 0.00001572 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 integument0.04806Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.8299Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.0006331Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.007439Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa0.009553Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.02937Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.03674Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of leukocytes0.2716InformativeInherited
Phenotypic Abnormality (PA)Large hands0.00002672Highly InformativeDirect
Phenotypic Abnormality (PA)Acute myeloid leukemia0.0001292Highly InformativeDirect
Phenotypic Abnormality (PA)Hypothyroidism0.0004615Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.01905Least InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.2571Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal developmental patterning0.0205InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.2146InformativeInherited
Mammalian Phenotype (MP)abnormal mesoderm development0.0002478Highly InformativeDirect
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.001772Highly 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 variant0.1363Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.0005302Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.6569Moderately InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.0001087InformativeDirect
Worm Phenotype (WP)organism stress response variant0.000292InformativeDirect
Worm Phenotype (WP)protein expression variant0.112InformativeInherited
Worm Phenotype (WP)organism UV hypersensitive0.000000000922Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00000493Highly InformativeDirect
Worm Phenotype (WP)multivulva0.000006125Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.0003501Highly InformativeDirect
Worm Phenotype (WP)protein modification variant0.002848Highly InformativeInherited

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 variegation0.00000002982InformativeDirect
Fly Phenotype (FP)homeotic0.0008875Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cell0.00038Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0.0005666Least 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 apex0.01337Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue0.1516Least InformativeInherited
Plant ANatomical entity (PAN)shoot apical meristem0.000002636Highly InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.0007726Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferases0.00000000005561Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.5763Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.0000000001335Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.00002359Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.01137Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.0000000001477InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen0.000000002371InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases0.000002691InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular and subcellular movement0.00000658InformativeDirect
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)Non-specific protein-tyrosine kinase0.00000003672Highly 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 cycle0.0000005396Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processApoptosis0.000000204InformativeDirect
Biological processGrowth regulation0.000000000000001102Highly InformativeDirect
Biological processMeiosis0.00000000005689Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0.00000000495InformativeDirect
Coding sequence diversityAlternative splicing0.00000003745Least InformativeDirect
Coding sequence diversityChromosomal rearrangement0.00000004484InformativeDirect
DiseaseTumor suppressor0.0000004566Moderately InformativeDirect
DomainRepeat0.000001291Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.00000000001827Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0.000001603Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0002646InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000001804Moderately InformativeDirect
Post-translational modificationOxidoreductase0.01822Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationMethyltransferase0.0000000256InformativeDirect
Post-translational modificationAcyltransferase0.0003954InformativeDirect
Post-translational modificationHelicase0.0007519InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond0.000006081Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0005874Moderately InformativeDirect
Post-translational modificationCitrullination0.0000003316Highly 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 sumoylation0.00000501Highly 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) · 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]