SUPERFAMILY 1.75 HMM library and genome assignments server

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GAF domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Profilin-like [ 55769] (10)
Superfamily:   GAF domain-like [ 55781] (4)
Families:   GAF domain [ 55782] (7)
  IclR ligand-binding domain-like [ 75513] (2)
  HrcA C-terminal domain-like [ 111115]
  Phytochrome-specific domain [ 160664] (2)

Superfamily statistics
Genomes (2,896) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 36,933 318,516 19
Proteins 31,601 276,982 15

Functional annotation
General category Regulation
Detailed category Signal transduction

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)Phosphoric diester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-histidine kinases0InformativeDirect

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 cardiovascular system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.1572Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1634Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.253Least InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the vasculature0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal posterior eye segment morphology0.02389Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.03233Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.1469Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature of the eye0.003081InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.003127InformativeInherited
Phenotypic Abnormality (PA)Abnormal retinal morphology0.009306InformativeInherited
Phenotypic Abnormality (PA)Abnormal electroretinogram0.00007766Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal retinal vascular morphology0.00009511Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of retinal pigmentation0.0003708Highly InformativeDirect
Phenotypic Abnormality (PA)Diabetes mellitus0.0009566Highly 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 phenotype0.01752Least InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.03906Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.07138Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.2609Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.0006406InformativeDirect
Mammalian Phenotype (MP)abnormal eye physiology0.001953InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.00222InformativeInherited
Mammalian Phenotype (MP)abnormal neuron number0.002783InformativeInherited
Mammalian Phenotype (MP)abnormal retinal photoreceptor morphology0.00007376Highly InformativeDirect
Mammalian Phenotype (MP)decreased sensory neuron number0.0001018Highly InformativeDirect
Mammalian Phenotype (MP)abnormal eye electrophysiology0.0001211Highly InformativeDirect
Mammalian Phenotype (MP)neuron degeneration0.0008495Highly InformativeDirect

Document: MP 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)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)fruit0.00001876InformativeDirect
Plant structure DEvelopment stage (PDE)seedling development stage0.0000001125InformativeDirect

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)Hydrolases0.00000003639Least InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0InformativeDirect
Enzyme Commission (EC)Protein-histidine kinases0Highly InformativeDirect

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · 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 26 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 GAF 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 26 hidden Markov models representing the GAF 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]