SUPERFAMILY 1.75 HMM library and genome assignments server


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 5.997e-15 Least Informative Direct
Biological Process (BP) biological regulation 4.353e-12 Least Informative Direct
Biological Process (BP) single-organism cellular process 1.301e-09 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 0.07827 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2034 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2147 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.05101 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 macromolecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 4.647e-08 Moderately Informative Direct
Biological Process (BP) regulation of primary metabolic process 8.877e-07 Moderately Informative Direct
Biological Process (BP) nucleic acid metabolic process 0.0003889 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 0.8182 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.2458 Moderately Informative Inherited
Biological Process (BP) organ development 0.002049 Moderately Informative Inherited
Biological Process (BP) immune system process 0.0908 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 0.4635 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.4892 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.5255 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.7523 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.04125 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.931 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 2.454e-09 Informative Direct
Biological Process (BP) regulation of transcription, DNA-dependent 6.024e-08 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 2.548e-07 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0001308 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0002017 Informative Direct
Biological Process (BP) negative regulation of macromolecule metabolic process 0.004474 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.2099 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 1 Informative Inherited
Biological Process (BP) cell development 0.8632 Informative Inherited
Biological Process (BP) neurogenesis 1 Informative Inherited
Biological Process (BP) cellular component morphogenesis 1 Informative Inherited
Biological Process (BP) embryo development 0.2182 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.5994 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.7014 Informative Inherited
Biological Process (BP) regulation of catabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.2786 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 0.479 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.1031 Informative Inherited
Biological Process (BP) positive regulation of biosynthetic process 0.3961 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 1 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.1346 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) cell activation 0.2143 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.001852 Informative Inherited
Biological Process (BP) cell projection organization 0.751 Informative Inherited
Biological Process (BP) behavior 0.09676 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) protein alkylation 7.896e-12 Highly Informative Direct
Biological Process (BP) transcription, DNA-dependent 3.851e-06 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 3.269e-05 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 6.515e-05 Highly Informative Direct
Biological Process (BP) lymphocyte differentiation 0.0006827 Highly Informative Direct
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.002109 Highly Informative Inherited
Biological Process (BP) protein ubiquitination 0.333 Highly Informative Inherited
Biological Process (BP) neuron projection development 0.01352 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.005447 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.1108 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.6172 Highly Informative Inherited
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 0.9992 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.029 Highly Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 0.06026 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.3985 Highly Informative Inherited
Biological Process (BP) T cell activation 0.001748 Highly Informative Inherited
Biological Process (BP) in utero embryonic development 0.005665 Highly Informative Inherited
Molecular Function (MF) binding 2.788e-11 Least Informative Direct
Molecular Function (MF) transferase activity 1.742e-06 Least Informative Direct
Molecular Function (MF) cation binding 1.983e-09 Moderately Informative Direct
Molecular Function (MF) protein binding 1.457e-05 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 0.04089 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.06186 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) methyltransferase activity 6.895e-14 Informative Direct
Molecular Function (MF) zinc ion binding 6.446e-10 Informative Direct
Molecular Function (MF) DNA binding 3.606e-08 Informative Direct
Molecular Function (MF) ligase activity 0.0003191 Informative Direct
Molecular Function (MF) lipid binding 0.4285 Informative Inherited
Molecular Function (MF) receptor binding 0.9979 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 9.26e-13 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 1.292e-10 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 1.764e-09 Highly Informative Direct
Molecular Function (MF) dioxygenase activity 1.357e-05 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.21 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.001541 Highly Informative Inherited
Molecular Function (MF) phospholipid binding 0.004979 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 5.221e-14 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 2.894e-06 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 4.595e-08 Informative Direct
Cellular Component (CC) neuron part 1 Informative Inherited
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0.7898 Informative Inherited
Cellular Component (CC) chromatin 3.99e-05 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 groups3.076e-10Least 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 groups7.186e-11Moderately InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red7.451e-10Moderately 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 integument0.04816Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.8302Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.0006371Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.007601Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa0.0096Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.02947Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.03682Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of leukocytes0.2718InformativeInherited
Phenotypic Abnormality (PA)Large hands2.699e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Acute myeloid leukemia0.0001302Highly InformativeDirect
Phenotypic Abnormality (PA)Hypothyroidism0.0004649Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.03745Least InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.2332Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal developmental patterning0.02089InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.2079InformativeInherited
Mammalian Phenotype (MP)abnormal mesoderm development0.0002462Highly InformativeDirect
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.001749Highly 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 hypersensitive9.22e-10Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene4.93e-06Highly InformativeDirect
Worm Phenotype (WP)multivulva6.125e-06Highly 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 variegation2.993e-08InformativeDirect
Fly Phenotype (FP)homeotic0.0008889Highly 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)cell0.0003707Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0.0005618Least 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 meristem2.636e-06Highly 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)Transferases5.677e-11Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.5704Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1.365e-10Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases2.376e-05Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.01148Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1.5e-10InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen2.45e-09InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases2.71e-06InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular and subcellular movement6.66e-06InformativeDirect
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 kinase3.698e-08Highly 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 cycle6.088e-07Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processApoptosis2.021e-07InformativeDirect
Biological processGrowth regulation1.101e-15Highly InformativeDirect
Biological processMeiosis5.469e-11Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome4.932e-09InformativeDirect
Coding sequence diversityAlternative splicing2.193e-08Least InformativeDirect
Coding sequence diversityChromosomal rearrangement4.194e-08InformativeDirect
DiseaseTumor suppressor4.673e-07Moderately InformativeDirect
DomainRepeat1.196e-06Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil1.651e-11Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding1.728e-06Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0002755InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein1.812e-07Moderately InformativeDirect
Post-translational modificationOxidoreductase0.0182Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationMethyltransferase2.578e-08InformativeDirect
Post-translational modificationAcyltransferase0.0003884InformativeDirect
Post-translational modificationHelicase0.000739InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond5.509e-06Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0005432Moderately InformativeDirect
Post-translational modificationCitrullination3.349e-07Highly 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) · 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) ]

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) · Internal database links ]