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 (149) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 860 1,326 17
Proteins 860 1,326 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 3.046e-15 Least Informative Direct
Biological Process (BP) biological regulation 8.545e-10 Least Informative Direct
Biological Process (BP) single-organism cellular process 1.089e-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 0.1046 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2512 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2636 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.06877 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 4.57e-07 Moderately Informative Direct
Biological Process (BP) regulation of primary metabolic process 3.434e-06 Moderately Informative Direct
Biological Process (BP) nucleic acid metabolic process 0.0008679 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 0.8262 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.1881 Moderately Informative Inherited
Biological Process (BP) system development 0.04571 Moderately Informative Inherited
Biological Process (BP) immune system process 0.06574 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 0.3902 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.432 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.4606 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.6943 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.0158 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.7864 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.9773 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) methylation 0 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) DNA metabolic process 1.613e-08 Informative Direct
Biological Process (BP) regulation of transcription, DNA-dependent 5.8e-07 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 3.549e-06 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 4.127e-05 Informative Direct
Biological Process (BP) negative regulation of macromolecule metabolic process 0.01161 Informative Inherited
Biological Process (BP) macromolecular complex assembly 0.776 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 1 Informative Inherited
Biological Process (BP) cell development 0.7912 Informative Inherited
Biological Process (BP) neurogenesis 1 Informative Inherited
Biological Process (BP) cellular component morphogenesis 1 Informative Inherited
Biological Process (BP) embryo development 0.3637 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.5394 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.8969 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.5152 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 0.5898 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.07198 Informative Inherited
Biological Process (BP) positive regulation of biosynthetic process 0.2608 Informative Inherited
Biological Process (BP) positive regulation of macromolecule metabolic process 0.7432 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.9659 Informative Inherited
Biological Process (BP) positive regulation of cellular metabolic process 0.05632 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.1617 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.6057 Informative Inherited
Biological Process (BP) cell activation 0.1999 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.001148 Informative Inherited
Biological Process (BP) cell projection organization 0.6831 Informative Inherited
Biological Process (BP) behavior 0.05788 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) protein alkylation 4.059e-10 Highly Informative Direct
Biological Process (BP) transcription, DNA-dependent 6.046e-06 Highly Informative Direct
Biological Process (BP) negative regulation of nucleobase-containing compound metabolic process 3.13e-05 Highly Informative Direct
Biological Process (BP) embryonic organ development 0.0002322 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0002884 Highly Informative Direct
Biological Process (BP) lymphocyte differentiation 0.0005555 Highly Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.001322 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.001663 Highly Informative Inherited
Biological Process (BP) protein ubiquitination 0.3646 Highly Informative Inherited
Biological Process (BP) neuron projection development 0.007813 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.006437 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.1021 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.3214 Highly Informative Inherited
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 0.9697 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.02219 Highly Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 0.1211 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.3298 Highly Informative Inherited
Biological Process (BP) T cell activation 0.0013 Highly Informative Inherited
Biological Process (BP) in utero embryonic development 0.001663 Highly Informative Inherited
Molecular Function (MF) binding 2.3e-14 Least Informative Direct
Molecular Function (MF) cation binding 2.466e-10 Moderately Informative Direct
Molecular Function (MF) protein binding 4.371e-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 0.07305 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.1067 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) transition metal ion binding 0 Informative Direct
Molecular Function (MF) DNA binding 5.098e-08 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 1.353e-06 Informative Direct
Molecular Function (MF) ligase activity 0.0005336 Informative Direct
Molecular Function (MF) lipid binding 0.4546 Informative Inherited
Molecular Function (MF) receptor binding 0.9474 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 2.769e-13 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 2.068e-09 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 8.742e-09 Highly Informative Direct
Molecular Function (MF) dioxygenase activity 1.267e-05 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.1814 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.001097 Highly Informative Inherited
Molecular Function (MF) phospholipid binding 0.003872 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 3.489e-12 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 3.113e-05 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 3.332e-07 Informative Direct
Cellular Component (CC) neuron part 1 Informative Inherited
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0.8319 Informative Inherited
Cellular Component (CC) chromatin 9.473e-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 integument0.04978Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.8318Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.007355Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa0.01075Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.03112Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.03967Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm by anatomical site0.000353InformativeDirect
Phenotypic Abnormality (PA)Abnormality of leukocytes0.2747InformativeInherited
Phenotypic Abnormality (PA)Large hands4.57e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Acute myeloid leukemia0.0001309Highly InformativeDirect
Phenotypic Abnormality (PA)Hypothyroidism0.0004419Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.01039Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.06246Least InformativeInherited
Mammalian Phenotype (MP)abnormal cell proliferation0.1692Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal developmental patterning0.02154InformativeInherited
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.04584InformativeInherited
Mammalian Phenotype (MP)abnormal mesoderm development0.0008996Highly InformativeDirect
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.007871Highly 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 variegation1.136e-08InformativeDirect
Fly Phenotype (FP)homeotic0.0007087Highly 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)cell0.0003508Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0.0005336Least 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)Transferases1.354e-11Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.5141Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups3.708e-10Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases2.05e-05Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.06432Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups7.799e-11InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen1.571e-09InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases2.214e-06InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular and subcellular movement0.0002435InformativeDirect
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 kinase3.003e-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 cycle5.019e-07Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processApoptosis1.732e-07InformativeDirect
Biological processGrowth regulation3.702e-16Highly InformativeDirect
Biological processMeiosis3.306e-11Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome2.808e-08InformativeDirect
Coding sequence diversityAlternative splicing7.302e-09Least InformativeDirect
Coding sequence diversityChromosomal rearrangement3.916e-08InformativeDirect
DiseaseTumor suppressor6.523e-05Moderately InformativeDirect
DomainRepeat1.766e-06Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil7.817e-12Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding6.501e-06Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0003723InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein7.016e-07Moderately InformativeDirect
Post-translational modificationOxidoreductase0.01512Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationMethyltransferase5.083e-08InformativeDirect
Post-translational modificationAcyltransferase0.0003483InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond4.328e-06Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0004755Moderately InformativeDirect
Post-translational modificationCitrullination3.546e-07Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)protein modification0Moderately 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 ]