SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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)

(
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 system0.001586Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.001849Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.02025Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.0406Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.09826Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.1152Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.1276Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.2052Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.2071Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.3489Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.5939Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal ocular adnexa morphology0.00000003219Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal muscle tone0.003377Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.008044Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.01709Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ear0.02186Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skull size0.03005Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.04908Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.0592Moderately InformativeInherited
Phenotypic Abnormality (PA)Localized skin lesion0.07008Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal inflammatory response0.08188Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.09274Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.1242Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental delay0.1243Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal heart morphology0.1572Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.1637Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.2644Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.4382Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal physiology0.5759Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.7261Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal conjugate eye movement0.00001244InformativeDirect
Phenotypic Abnormality (PA)Abnormality of male external genitalia0.00007077InformativeDirect
Phenotypic Abnormality (PA)Abnormal cardiac septum morphology0.0001298InformativeDirect
Phenotypic Abnormality (PA)Microcephaly0.0003366InformativeDirect
Phenotypic Abnormality (PA)Abnormality of calvarial morphology0.0004436InformativeDirect
Phenotypic Abnormality (PA)Abnormal lip morphology0.0007875InformativeDirect
Phenotypic Abnormality (PA)Regional abnormality of skin0.007809InformativeInherited
Phenotypic Abnormality (PA)Abnormal cardiac ventricle morphology0.01078InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.1862InformativeInherited
Phenotypic Abnormality (PA)Neoplasm by histology0.3406InformativeInherited
Phenotypic Abnormality (PA)Cryptorchidism0.000003209Highly InformativeDirect
Phenotypic Abnormality (PA)Atrial septal defect0.00001423Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal ureter physiology0.0001383Highly InformativeDirect
Phenotypic Abnormality (PA)Ventricular septal defect0.0001586Highly InformativeDirect
Phenotypic Abnormality (PA)Downturned corners of mouth0.000166Highly InformativeDirect
Phenotypic Abnormality (PA)Otitis media0.0003163Highly InformativeDirect
Phenotypic Abnormality (PA)Delayed speech and language development0.0004014Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal dermatoglyphics0.0006174Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the diaphragm0.0007113Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the ulna0.005431Highly InformativeInherited
Phenotypic Abnormality (PA)Skin pit0.01188Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the radius0.01497Highly InformativeInherited
Phenotypic Abnormality (PA)Urinary tract neoplasm0.02724Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of periauricular region0.1135Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.003239Least InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.3529Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.8007Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.2406InformativeInherited
Mammalian Phenotype (MP)abnormal spermatogenesis0.4009InformativeInherited
Mammalian Phenotype (MP)increased mortality induced by ionizing radiation0.001771Highly InformativeInherited
Mammalian Phenotype (MP)abnormal spermiogenesis0.01341Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.0113Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.1089Least InformativeInherited
Worm Phenotype (WP)blast cell physiology variant0.1089Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1557Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.00116Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.01327Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.1058Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.6881Moderately InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.0001433InformativeDirect
Worm Phenotype (WP)vulva development variant0.005028InformativeInherited
Worm Phenotype (WP)organism stress response variant0.007168InformativeInherited
Worm Phenotype (WP)protein metabolism variant0.1989InformativeInherited
Worm Phenotype (WP)multivulva0.0000004734Highly InformativeDirect
Worm Phenotype (WP)organism UV response variant0.00001488Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00002173Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.0007126Highly 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 variegation0.0000000006983InformativeDirect
Fly Phenotype (FP)homeotic0.0009275Highly 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)embryo0.001688Least InformativeInherited
Xenopus ANatomical entity (XAN)urogenital system0.002116Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.006619Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.03623Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.06325Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.00009343Moderately 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)Transferases0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.9312Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0005162Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.008618Moderately InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0.0000000001715InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.0000001762InformativeDirect
Enzyme Commission (EC)Acting on ATP; involved in cellular and subcellular movement0.0001136InformativeDirect
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 donors9.184e-16Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.0000002117Highly 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 ]