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.


HD-domain/PDEase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   HD-domain/PDEase-like [ 109603]
Superfamily:   HD-domain/PDEase-like [ 109604] (5)
Families:   HD domain [ 101340] (13)
  PDEase [ 48548] (6)
  modified HD domain [ 116973]
  MioX-like [ 140769]
  Ppx associated domain [ 140773]


Superfamily statistics
Genomes (3,167) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 34,365 255,448 45
Proteins 33,692 250,821 45


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.7809Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)In phosphorous-containing anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Diphosphotransferases0InformativeDirect
Enzyme Commission (EC)Acting on single donors with incorporation of mole0.0000002853InformativeDirect
Enzyme Commission (EC)[Protein-PII] uridylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)GTP diphosphokinase0Highly InformativeDirect
Enzyme Commission (EC)3',5'-cyclic-nucleotide phosphodiesterase0Highly InformativeDirect
Enzyme Commission (EC)Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.689Least InformativeInherited
Disease Ontology (DO)hematologic cancer0.1187Moderately InformativeInherited
Disease Ontology (DO)lymphoblastic leukemia0.001203InformativeInherited
Disease Ontology (DO)chronic lymphocytic leukemia0.00002434Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.1879Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1975Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.01599Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.02777InformativeInherited
Phenotypic Abnormality (PA)Glucose intolerance0.00002987Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.5439Least InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.2836Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.3199Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.3945Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.03181InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.08261InformativeInherited
Mammalian Phenotype (MP)abnormal neuron number0.09739InformativeInherited
Mammalian Phenotype (MP)abnormal retinal photoreceptor morphology0.005476Highly InformativeInherited
Mammalian Phenotype (MP)decreased sensory neuron number0.007126Highly InformativeInherited
Mammalian Phenotype (MP)neuron degeneration0.03976Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism behavior variant0.0688Least InformativeInherited
Worm Phenotype (WP)movement variant0.03824Moderately InformativeInherited
Worm Phenotype (WP)locomotion variant0.2994Moderately InformativeInherited
Worm Phenotype (WP)thermotaxis variant0.00000001995Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.1436Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.2722Least InformativeInherited
Plant ANatomical entity (PAN)root system0.4044Least InformativeInherited
Plant ANatomical entity (PAN)portion of ground tissue0.00002324InformativeDirect
Plant ANatomical entity (PAN)fruit0.0004237InformativeDirect
Plant ANatomical entity (PAN)root stele0.000002639Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases2.561e-16Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups0.000000009827Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.2053Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0InformativeDirect
Enzyme Commission (EC)In phosphorus-containing anhydrides0InformativeDirect
Enzyme Commission (EC)Forming carbon-oxygen bonds0InformativeDirect
Enzyme Commission (EC)Acting on single donors with incorporation of molecular oxygen (oxygenases). The oxygen incorporated0.0000001075InformativeDirect
Enzyme Commission (EC)Diphosphotransferases0Highly InformativeDirect
Enzyme Commission (EC)Diphosphoric monoester hydrolases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationHydrolase0Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · 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

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.


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.


Browse and view proteins in genomes which have different domain combinations including a HD-domain/PDEase-like domain.


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.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 41 hidden Markov models representing the HD-domain/PDEase-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · 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 ]