SUPERFAMILY 1.75 HMM library and genome assignments server

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PH domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   PH domain-like barrel [ 50728] (2)
Superfamily:   PH domain-like [ 50729] (13)
Families:   Pleckstrin-homology domain (PH domain) [ 50730] (47)
  Phosphotyrosine-binding domain (PTB) [ 50755] (12)
  Ran-binding domain [ 50764] (4)
  Enabled/VASP homology 1 domain (EVH1 domain) [ 50767] (6)
  Dcp1 [ 101836]
  Third domain of FERM [ 50776] (8)
  PreBEACH PH-like domain [ 82146] (2)
  GRAM domain [ 101839]
  TFIIH domain [ 110272] (2)
  SSRP1-like [ 141436]
  Necap1 N-terminal domain-like [ 141439]
  VPS36 N-terminal domain-like [ 141442]
  BPHL domain [ 159216] (2)


Superfamily statistics
Genomes (922) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 75,120 226,141 146
Proteins 66,982 203,244 145


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides1Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.05493Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep1Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases0.02837Moderately InformativeInherited
Enzyme Commission (EC)Phosphoinositide phospholipase C0InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.00000004532InformativeDirect
Enzyme Commission (EC)Diacylglycerol kinase0Highly InformativeDirect
Enzyme Commission (EC)Acting on GTP; involved in cellular and subcellula0.00000000000001873Highly InformativeDirect
Enzyme Commission (EC)Protein kinase C0.000003652Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)muscle tissue disease0.8903InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Gonosomal inheritance0.0119InformativeInherited
Mode of Inheritance (MI)X-linked recessive inheritance0.0003499Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.2839Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.9466Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal peripheral myelination0.0006175Highly 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 phenotype0.1604Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.2751Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.4544Least InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.6194Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood coagulation0.1355InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology1InformativeInherited
Mammalian Phenotype (MP)abnormal brain pia mater morphology0.00001034Highly InformativeDirect
Mammalian Phenotype (MP)abnormal bone marrow cell morphology/development0.4782Highly InformativeInherited
Mammalian Phenotype (MP)abnormal respiratory epithelium morphology0.9275Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.00000000006017Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0000000005989Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.000000001474Least InformativeDirect
Worm Phenotype (WP)cell development variant0.00002085Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00002258Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.00004221Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.002487Least InformativeInherited
Worm Phenotype (WP)apoptosis variant0.0000001743Moderately InformativeDirect
Worm Phenotype (WP)protein expression variant0.00000624Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.000007599Moderately InformativeDirect
Worm Phenotype (WP)metabolic pathway variant0.001055Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.08015Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.08535Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.2911Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.321Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.5055Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.6416Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.8977Moderately InformativeInherited
Worm Phenotype (WP)muscle cell physiology variant0.00000000009768InformativeDirect
Worm Phenotype (WP)mitochondria morphology variant0.000001756InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.00004596InformativeDirect
Worm Phenotype (WP)organism pathogen response variant0.0003059InformativeDirect
Worm Phenotype (WP)level of protein expression variant0.0004642InformativeDirect
Worm Phenotype (WP)pharyngeal pumping variant0.0004836InformativeDirect
Worm Phenotype (WP)locomotor coordination variant0.004999InformativeInherited
Worm Phenotype (WP)tail morphology variant0.006147InformativeInherited
Worm Phenotype (WP)defecation variant0.03471InformativeInherited
Worm Phenotype (WP)neuronal outgrowth variant0.03491InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.21InformativeInherited
Worm Phenotype (WP)cell stress response variant0.313InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.3236InformativeInherited
Worm Phenotype (WP)cell number increased0.5593InformativeInherited
Worm Phenotype (WP)protein modification variant0.6835InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.762InformativeInherited
Worm Phenotype (WP)chemotaxis variant0.8537InformativeInherited
Worm Phenotype (WP)endocytic transport defect1InformativeInherited
Worm Phenotype (WP)gonad sheath contractions variant0.000000007113Highly InformativeDirect
Worm Phenotype (WP)bacterially unswollen0.0000008238Highly InformativeDirect
Worm Phenotype (WP)growth rate variant0.000002343Highly InformativeDirect
Worm Phenotype (WP)osmotic stress response variant0.000002476Highly InformativeDirect
Worm Phenotype (WP)ovulation variant0.00001244Highly InformativeDirect
Worm Phenotype (WP)response to injury variant0.00003383Highly InformativeDirect
Worm Phenotype (WP)extra excretory cells0.00009335Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes0.00009757Highly InformativeDirect
Worm Phenotype (WP)coelomocyte uptake defective0.0001432Highly InformativeDirect
Worm Phenotype (WP)defecation contraction variant0.0002209Highly InformativeDirect
Worm Phenotype (WP)axon morphology variant0.0003785Highly InformativeDirect
Worm Phenotype (WP)protein phosphorylation variant0.0003957Highly InformativeDirect
Worm Phenotype (WP)axon development variant0.0004473Highly InformativeDirect
Worm Phenotype (WP)forward locomotion decreased0.0005949Highly InformativeDirect
Worm Phenotype (WP)drug induced gene expression variant0.0007632Highly InformativeDirect
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.06616Highly InformativeInherited
Worm Phenotype (WP)post hermaphrodite contact variant0.1185Highly InformativeInherited
Worm Phenotype (WP)odorant positive chemotaxis variant0.1261Highly InformativeInherited
Worm Phenotype (WP)male mating defective0.1624Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.02775Moderately InformativeInherited
Yeast Phenotype (YP)subcellular morphology0.3799InformativeInherited

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)anatomical group0.01157Least InformativeInherited
Fly Anatomy (FA)embryo0.07612Least InformativeInherited
Fly Anatomy (FA)acellular anatomical structure0.005409Moderately InformativeInherited
Fly Anatomy (FA)developing embryonic structure0.01185Moderately InformativeInherited
Fly Anatomy (FA)endocuticle0.0006506InformativeDirect
Fly Anatomy (FA)presumptive embryonic/larval digestive system0.2754InformativeInherited
Fly Anatomy (FA)embryonic foregut0.0004886Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0.7864Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.9063Least InformativeInherited
Zebrafish Anatomy (ZA)cardiovascular system0.2363Moderately InformativeInherited
Zebrafish Anatomy (ZA)post-vent region0.2472InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)nervous system0.09153Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.2828Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.4587Least InformativeInherited
Xenopus ANatomical entity (XAN)brain0.00005274Moderately 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)sporangium0.0003822Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0.03623Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll0.6563Least InformativeInherited
Plant ANatomical entity (PAN)pollen tube cell0.00001534InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.00004503Moderately InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.00000000001118Least InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.0004297Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.02951Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor1Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides1Moderately InformativeInherited
Enzyme Commission (EC)Protein-tyrosine kinases0InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0.00000000000009397InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.00001059InformativeDirect
Enzyme Commission (EC)Diacylglycerol kinase (ATP)0Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0Highly InformativeDirect

Document: EC 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 Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 94 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 PH domain-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 94 hidden Markov models representing the PH domain-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 Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]