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.


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 2017_06 genome PDB chains (SCOP 1.75)
Domains 36,933 243,202 19
Proteins 31,601 210,910 15


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 0.000000005834 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00000004168 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000001113 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0000004404 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000005345 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00001752 Least Informative Direct
Biological Process (BP) biological regulation 0.003302 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9464 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5628 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.04921 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1651 Least Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000000000000001925 Moderately Informative Direct
Biological Process (BP) single organism signaling 0.00000001605 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00000003275 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0000001253 Moderately Informative Direct
Biological Process (BP) cell communication 0.0000002174 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000001025 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.000006085 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00000858 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000008806 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00001863 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00006221 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.0001011 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0001439 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.000827 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.03825 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.144 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.05591 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.07954 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.07812 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.05981 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.005717 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1483 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.003767 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.02009 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.2744 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.763 Moderately Informative Inherited
Biological Process (BP) tissue development 0.702 Moderately Informative Inherited
Biological Process (BP) organophosphate catabolic process 0 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0000000000001341 Informative Direct
Biological Process (BP) negative regulation of transport 0.0000000000001434 Informative Direct
Biological Process (BP) system process 0.00000002037 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.0000005752 Informative Direct
Biological Process (BP) mitochondrion organization 0.0000006552 Informative Direct
Biological Process (BP) regulation of cellular localization 0.0000008446 Informative Direct
Biological Process (BP) response to nitrogen compound 0.0000009426 Informative Direct
Biological Process (BP) regulation of protein localization 0.000005867 Informative Direct
Biological Process (BP) regulation of defense response 0.000009803 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0000112 Informative Direct
Biological Process (BP) protein localization to organelle 0.0000136 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.00003886 Informative Direct
Biological Process (BP) regulation of peptide transport 0.00007709 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.0001894 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0003039 Informative Direct
Biological Process (BP) protein transport 0.0008801 Informative Direct
Biological Process (BP) negative regulation of signaling 0.6482 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.7497 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.8758 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.002823 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.002604 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.08667 Informative Inherited
Biological Process (BP) response to radiation 0.05861 Informative Inherited
Biological Process (BP) intracellular transport 0.01812 Informative Inherited
Biological Process (BP) cell development 0.4523 Informative Inherited
Biological Process (BP) epithelium development 0.1258 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) purine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0 Highly Informative Direct
Biological Process (BP) response to organophosphorus 0 Highly Informative Direct
Biological Process (BP) regulation of protein import 0 Highly Informative Direct
Biological Process (BP) regulation of protein localization to nucleus 0 Highly Informative Direct
Biological Process (BP) nucleotide catabolic process 0.000000000000001925 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.000000000000003734 Highly Informative Direct
Biological Process (BP) negative regulation of establishment of protein localization 0.000000000000007296 Highly Informative Direct
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.000000000000007296 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.00000000000001079 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.00000000000001079 Highly Informative Direct
Biological Process (BP) establishment of protein localization to mitochondrion 0.00000000000003429 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.00000000003522 Highly Informative Direct
Biological Process (BP) mitochondrial transport 0.0000000001979 Highly Informative Direct
Biological Process (BP) protein targeting 0.000000001605 Highly Informative Direct
Biological Process (BP) response to drug 0.000000006193 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.000000006573 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0.000000007417 Highly Informative Direct
Biological Process (BP) second-messenger-mediated signaling 0.00000004804 Highly Informative Direct
Biological Process (BP) response to mechanical stimulus 0.0000003099 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0.0000007532 Highly Informative Direct
Biological Process (BP) response to red or far red light 0.0000484 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.0001383 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.0001494 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.002304 Highly Informative Inherited
Biological Process (BP) camera-type eye development 0.001889 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.000000000003929 Least Informative Direct
Molecular Function (MF) binding 0.5738 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000000001015 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.0000003373 Moderately Informative Direct
Molecular Function (MF) ribonucleotide binding 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0 Informative Direct
Molecular Function (MF) signal transducer activity 0.07435 Informative Inherited
Molecular Function (MF) kinase activity 1 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.002257 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.09371 Informative Inherited
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.05042 Highly Informative Inherited
Cellular Component (CC) membrane 0.0373 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.02285 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.5337 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.254 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.8592 Moderately Informative Inherited
Cellular Component (CC) plasma membrane region 0.000001509 Informative Direct
Cellular Component (CC) neuron projection 1 Informative Inherited
Cellular Component (CC) cilium 0.01856 Informative Inherited
Cellular Component (CC) perinuclear region of cytoplasm 0.0000000000949 Highly Informative Direct
Cellular Component (CC) photoreceptor cell cilium 0.00003137 Highly Informative Direct
Cellular Component (CC) presynapse 0.0007572 Highly Informative Direct

Document: GO annotation of SCOP domains

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processStress response0InformativeDirect
Biological processSensory transduction0InformativeDirect
Biological processNitrogen fixation9.645e-16InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Biological processEthylene signaling pathway0Highly InformativeDirect
Cellular componentEndoplasmic reticulum0.0000006898Moderately InformativeDirect
DomainRepeat0.0000003302Least InformativeDirect
Molecular functionNucleotide-binding0.07208Least InformativeInherited
Molecular functionCopper0InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functioncGMP0Highly InformativeDirect
Molecular functioncGMP-binding0Highly InformativeDirect
Molecular functioncAMP7.437e-16Highly InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDNA-binding2.221e-16Moderately InformativeDirect
Post-translational modificationActivator0.000000004583Moderately InformativeDirect
Post-translational modificationKinase0.00000001158Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.0000000000005746Least InformativeDirect
Post-translational modificationPrenylation0InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · 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 15 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 15 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]