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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 (176) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 951 0 17
Proteins 951 0 17


Enzyme Commission (EC)

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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 face0.004416Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.004481Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.01313Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.0247Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.0581Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.08936Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1904Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.676Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the orbital region0.000006559Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the lower limb0.001316Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.002081Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.004337Moderately InformativeInherited
Phenotypic Abnormality (PA)Localized skin lesion0.00915Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.01027Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal heart morphology0.0173Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.04152Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.04321Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.04982Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.09199Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.2356Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4707Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.5115Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the oral cavity0.8317Moderately InformativeInherited
Phenotypic Abnormality (PA)Strabismus0.00003548InformativeDirect
Phenotypic Abnormality (PA)Abnormal cardiac septum morphology0.0000627InformativeDirect
Phenotypic Abnormality (PA)Lower extremity joint dislocation0.0001207InformativeDirect
Phenotypic Abnormality (PA)Microcephaly0.0009279InformativeDirect
Phenotypic Abnormality (PA)Abnormal cardiac ventricle morphology0.003257InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the radius0.004462InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.01259InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the scalp hair0.04498InformativeInherited
Phenotypic Abnormality (PA)Abnormality of upper limb joint0.04828InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.07098InformativeInherited
Phenotypic Abnormality (PA)Abnormality of facial skeleton0.2266InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.4046InformativeInherited
Phenotypic Abnormality (PA)Congenital abnormal hair pattern0.6291InformativeInherited
Phenotypic Abnormality (PA)Hypoplastic male external genitalia0.000008513Highly InformativeDirect
Phenotypic Abnormality (PA)Downturned corners of mouth0.00001478Highly InformativeDirect
Phenotypic Abnormality (PA)Ventricular septal defect0.00002393Highly InformativeDirect
Phenotypic Abnormality (PA)Atrial septal defect0.00002862Highly InformativeDirect
Phenotypic Abnormality (PA)Precocious puberty0.0001441Highly InformativeDirect
Phenotypic Abnormality (PA)Micrognathia0.0003668Highly InformativeDirect
Phenotypic Abnormality (PA)Talipes0.0005404Highly InformativeDirect
Phenotypic Abnormality (PA)Hypothyroidism0.0008469Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the ulna0.001703Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the sacrum0.002403Highly InformativeInherited
Phenotypic Abnormality (PA)Skin dimples0.0143Highly InformativeInherited
Phenotypic Abnormality (PA)Synostosis of joints0.04158Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.003189Least InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.3544Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.8037Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.241InformativeInherited
Mammalian Phenotype (MP)abnormal spermatogenesis0.4022InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.001778Highly InformativeInherited
Mammalian Phenotype (MP)abnormal spermiogenesis0.01329Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.002659Least InformativeInherited
Worm Phenotype (WP)cell development variant0.008552Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.275Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.001183Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2039Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.7481Moderately InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.0001737InformativeDirect
Worm Phenotype (WP)organism stress response variant0.002229InformativeInherited
Worm Phenotype (WP)vulva development variant0.00553InformativeInherited
Worm Phenotype (WP)multivulva0.0000004887Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00001992Highly InformativeDirect
Worm Phenotype (WP)organism UV response variant0.00002752Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.0006563Highly 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 variegation0.000000001152InformativeDirect

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)trunk0.005402Least InformativeInherited
Xenopus ANatomical entity (XAN)genital system0.007628Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.03408Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.00009449Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot apex0.006649Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue0.0987Least InformativeInherited
Plant ANatomical entity (PAN)shoot apical meristem0.000002644Highly InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.0009517Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferases0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.9698Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.000209Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.08339Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.0000001262InformativeDirect
Enzyme Commission (EC)DNA helicase0.000001961InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0001741InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0Highly InformativeDirect
Enzyme Commission (EC)With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors7.268e-16Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.0000002303Highly 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 cycle0.000004337Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processBiological rhythms0.0000000000227InformativeDirect
Biological processApoptosis0.000000001647InformativeDirect
Biological processGrowth regulation0.0000000000000151Highly InformativeDirect
Biological processMeiosis0.0000000003917Highly InformativeDirect
Biological processAutophagy0.000002037Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0.0000000000001875InformativeDirect
Coding sequence diversityAlternative splicing0.00000001686Least InformativeDirect
Coding sequence diversityChromosomal rearrangement0.00000004412InformativeDirect
DiseaseTumor suppressor0.000001177Moderately InformativeDirect
DiseaseMental retardation0.00009656InformativeDirect
DomainRepeat0.00000009168Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.000000000005968Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationTransferase0.02755Least InformativeInherited
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDNA-binding3.476e-16Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000001484Moderately InformativeDirect
Post-translational modificationOxidoreductase0.04052Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationMethyltransferase0.000004273InformativeDirect
Post-translational modificationAcyltransferase0.0001066InformativeDirect
Post-translational modificationHelicase0.0003145InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationCitrullination0.0000004655Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · 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) ]

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 · 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) · Internal database links ]