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 (176) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 951 3,034 17
Proteins 951 3,034 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 face0.004686Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.004718Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.01398Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.02536Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.06096Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.09303Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.6759Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the orbital region0.000007232Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the lower limb0.001482Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.002287Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.002683Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.004718Moderately InformativeInherited
Phenotypic Abnormality (PA)Localized skin lesion0.009193Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.01054Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal heart morphology0.01912Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.04281Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.04432Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.2291Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4681Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.5039Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal cardiac ventricle morphology0.00003917InformativeDirect
Phenotypic Abnormality (PA)Abnormal conjugate eye movement0.00005734InformativeDirect
Phenotypic Abnormality (PA)Abnormal cardiac septum morphology0.00009541InformativeDirect
Phenotypic Abnormality (PA)Lower extremity joint dislocation0.0001186InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the radius0.004575InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.01287InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the scalp hair0.04182InformativeInherited
Phenotypic Abnormality (PA)Abnormality of upper limb joint0.04589InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.07085InformativeInherited
Phenotypic Abnormality (PA)Abnormality of facial skeleton0.2248InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.4021InformativeInherited
Phenotypic Abnormality (PA)Congenital abnormal hair pattern0.6301InformativeInherited
Phenotypic Abnormality (PA)Atrial septal defect0.000002219Highly InformativeDirect
Phenotypic Abnormality (PA)Ventricular septal defect0.000003127Highly InformativeDirect
Phenotypic Abnormality (PA)Hypoplastic male external genitalia0.00000855Highly InformativeDirect
Phenotypic Abnormality (PA)Downturned corners of mouth0.00001457Highly InformativeDirect
Phenotypic Abnormality (PA)Precocious puberty0.000143Highly InformativeDirect
Phenotypic Abnormality (PA)Micrognathia0.0003842Highly InformativeDirect
Phenotypic Abnormality (PA)Talipes0.0005343Highly InformativeDirect
Phenotypic Abnormality (PA)Hypothyroidism0.0008423Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the ulna0.001701Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the sacrum0.002373Highly InformativeInherited
Phenotypic Abnormality (PA)Skin dimples0.01437Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.00318Least 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 radiation0.001777Highly 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 variant0.002701Least InformativeInherited
Worm Phenotype (WP)cell development variant0.009435Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.2779Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.001223Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2039Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.7491Moderately InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.00016InformativeDirect
Worm Phenotype (WP)organism stress response variant0.002206InformativeInherited
Worm Phenotype (WP)vulva development variant0.005624InformativeInherited
Worm Phenotype (WP)multivulva0.0000005057Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00001976Highly InformativeDirect
Worm Phenotype (WP)organism UV response variant0.00002709Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.0006739Highly 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 variegation0.0000000009408InformativeDirect

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)trunk0.00549Least InformativeInherited
Xenopus ANatomical entity (XAN)genital system0.007611Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.03433Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.00009483Moderately 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)Oxidoreductases0.9707Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0005245Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.0832Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.0000001392InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.00004023InformativeDirect
Enzyme Commission (EC)Acting on ATP; involved in cellular and subcellular movement0.0001288InformativeDirect
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 donors3.655e-16Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.0000002298Highly InformativeDirect

Document: EC 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) ]

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) · Internal database links ]