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 genitourinary system0.001068Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.001438Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.01428Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.03206Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.08044Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.09697Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1734Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.1868Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.2551Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.3342Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.5844Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal ocular adnexa morphology0.00000001226Moderately InformativeDirect
Phenotypic Abnormality (PA)Muscular hypotonia0.0002296Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.00468Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebrum0.006413Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.01741Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skull size0.02389Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ear0.03865Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.07368Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental delay0.1194Moderately InformativeInherited
Phenotypic Abnormality (PA)Localized skin lesion0.1271Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.1628Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal heart morphology0.1653Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.1672Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.1836Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.2635Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal physiology0.6525Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.8229Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of male external genitalia0.00002579InformativeDirect
Phenotypic Abnormality (PA)Abnormal conjugate eye movement0.00003011InformativeDirect
Phenotypic Abnormality (PA)Abnormality of calvarial morphology0.0001516InformativeDirect
Phenotypic Abnormality (PA)Abnormal cardiac septum morphology0.0002683InformativeDirect
Phenotypic Abnormality (PA)Microcephaly0.0007267InformativeDirect
Phenotypic Abnormality (PA)Abnormal lip morphology0.0008314InformativeDirect
Phenotypic Abnormality (PA)Abnormal cardiac ventricle morphology0.0116InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.01361InformativeInherited
Phenotypic Abnormality (PA)Cryptorchidism0.0000008527Highly InformativeDirect
Phenotypic Abnormality (PA)Atrial septal defect0.00002968Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal ureter physiology0.0001822Highly InformativeDirect
Phenotypic Abnormality (PA)Downturned corners of mouth0.00023Highly InformativeDirect
Phenotypic Abnormality (PA)Delayed speech and language development0.0002487Highly InformativeDirect
Phenotypic Abnormality (PA)Ventricular septal defect0.0002959Highly InformativeDirect
Phenotypic Abnormality (PA)Otitis media0.000358Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal dermatoglyphics0.0008139Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the diaphragm0.0009429Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the ulna0.006419Highly InformativeInherited
Phenotypic Abnormality (PA)Skin pit0.01116Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the radius0.01725Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of periauricular region0.2538Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.003232Least InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.353Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.8009Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.2406InformativeInherited
Mammalian Phenotype (MP)abnormal spermatogenesis0.4009InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.001773Highly InformativeInherited
Mammalian Phenotype (MP)abnormal spermiogenesis0.01342Highly 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 variant0.00001587Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.0001429Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.0004333Least InformativeDirect
Worm Phenotype (WP)cell development variant0.01083Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.04404Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.001346Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.03714Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.1711Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.1866Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.5065Moderately InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.0002031InformativeDirect
Worm Phenotype (WP)vulva development variant0.006497InformativeInherited
Worm Phenotype (WP)protein metabolism variant0.1116InformativeInherited
Worm Phenotype (WP)multivulva0.000000768Highly InformativeDirect
Worm Phenotype (WP)organism UV response variant0.000002913Highly InformativeDirect
Worm Phenotype (WP)RNAi resistant0.0006247Highly 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 variegation0.0000000006378InformativeDirect
Fly Phenotype (FP)homeotic0.00091Highly InformativeDirect

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)embryo0.001668Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.006412Least InformativeInherited
Xenopus ANatomical entity (XAN)urogenital system0.01541Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.03535Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.06342Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.00008728Moderately 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 apex0.006653Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue0.09854Least InformativeInherited
Plant ANatomical entity (PAN)shoot meristem0.0000021Highly InformativeDirect
Plant ANatomical entity (PAN)apical meristem0.00001839Highly InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.0009562Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferases0.0000000000004718Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.64Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.001544Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.9853Moderately InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0.0000000000987InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.00000001941InformativeDirect
Enzyme Commission (EC)Acting on ATP; involved in cellular and subcellular movement0.00001485InformativeDirect
Enzyme Commission (EC)Methyltransferases0.03322InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1InformativeInherited
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 acetyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.00000005879Highly 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 41 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 ]