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PYP-like sensor domain (PAS domain) 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:   PYP-like sensor domain (PAS domain) [ 55785] (7)
Families:   PYP-like [ 55786] (2)
  Heme-binding PAS domain [ 55789] (2)
  Flavin-binding PAS domain [ 88853] (3)
  N-terminal PAS domain of Pas kinase [ 82764]
  Hypoxia-inducible factor Hif2a, C-terminal domain [ 103184]
  PAS domain of steroid receptor coactivator 1A, NCo-A1 [ 103187]
  BphP N-terminal domain-like [ 160669] (3)


Superfamily statistics
Genomes (2,787) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 71,046 436,778 30
Proteins 45,859 288,328 30


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) biological regulation 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01743 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) reproduction 0.00007501 Moderately Informative Direct
Biological Process (BP) ion transport 0.0002748 Moderately Informative Direct
Biological Process (BP) cell communication 0.00000005333 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) single organism signaling 0.000000006698 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0003817 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.2036 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.001682 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.234 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.9553 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.04053 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.8059 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.01608 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.2788 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.6581 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.7276 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.8918 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.009519 Moderately Informative Inherited
Biological Process (BP) gene expression 0.6257 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.06221 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.8728 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0.00000004145 Informative Direct
Biological Process (BP) response to oxidative stress 0.0001269 Informative Direct
Biological Process (BP) behavior 0.000002187 Informative Direct
Biological Process (BP) response to radiation 0.00001983 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0 Informative Direct
Biological Process (BP) positive regulation of gene expression 0 Informative Direct
Biological Process (BP) regulation of hormone levels 0.00000004061 Informative Direct
Biological Process (BP) response to organic cyclic compound 0 Informative Direct
Biological Process (BP) metal ion transport 0.0001019 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.0005667 Informative Direct
Biological Process (BP) intracellular signal transduction 0.00005977 Informative Direct
Biological Process (BP) single organism reproductive process 0.000009442 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.8418 Informative Inherited
Biological Process (BP) positive regulation of developmental process 1 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.6003 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.04923 Informative Inherited
Biological Process (BP) microtubule-based process 0.6671 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.9076 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 1 Informative Inherited
Biological Process (BP) regulation of cellular amide metabolic process 1 Informative Inherited
Biological Process (BP) transmembrane transport 0.09677 Informative Inherited
Biological Process (BP) generation of neurons 0.4676 Informative Inherited
Biological Process (BP) regulation of ion transport 0.004268 Informative Inherited
Biological Process (BP) regulation of transmembrane transport 0.005685 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) cell death 0.06596 Informative Inherited
Biological Process (BP) system process 0.05606 Informative Inherited
Biological Process (BP) regulation of protein localization 0.01723 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) intracellular transport 1 Informative Inherited
Biological Process (BP) regulation of secretion 0.007223 Informative Inherited
Biological Process (BP) phosphorylation 0.2515 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 1 Informative Inherited
Biological Process (BP) regulation of cell differentiation 1 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.2498 Informative Inherited
Biological Process (BP) epithelium development 0.02559 Informative Inherited
Biological Process (BP) organelle localization 0.09367 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.7637 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.8953 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.6072 Informative Inherited
Biological Process (BP) central nervous system development 0.1053 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.03956 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.129 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.5356 Informative Inherited
Biological Process (BP) chromosome organization 0.8795 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.6723 Informative Inherited
Biological Process (BP) proteolysis 0.1285 Informative Inherited
Biological Process (BP) post-embryonic development 0.855 Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Informative Inherited
Biological Process (BP) localization of cell 0.07393 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.002604 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.016 Informative Inherited
Biological Process (BP) regulation of peptide transport 0.007945 Informative Inherited
Biological Process (BP) regulation of system process 0.03382 Informative Inherited
Biological Process (BP) reproductive system development 0.008402 Informative Inherited
Biological Process (BP) embryo development 0.8381 Informative Inherited
Biological Process (BP) locomotion 0.01327 Informative Inherited
Biological Process (BP) response to hypoxia 0 Highly Informative Direct
Biological Process (BP) lactate metabolic process 0.0000007124 Highly Informative Direct
Biological Process (BP) xenobiotic metabolic process 0.000000003189 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.0002364 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.000000001669 Highly Informative Direct
Biological Process (BP) photoperiodism 0 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.0002465 Highly Informative Direct
Biological Process (BP) response to hydrogen peroxide 0.0000002762 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) modification-dependent macromolecule catabolic process 0.0001289 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.0005147 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.0007072 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 0.00000000000001254 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.00009478 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.3009 Highly Informative Inherited
Biological Process (BP) regulation of binding 0.06898 Highly Informative Inherited
Biological Process (BP) microtubule-based movement 0.04935 Highly Informative Inherited
Biological Process (BP) inorganic cation transmembrane transport 0.02719 Highly Informative Inherited
Biological Process (BP) response to red or far red light 0.1042 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.7271 Highly Informative Inherited
Biological Process (BP) histone modification 0.02346 Highly Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter in response to stress 0.008054 Highly Informative Inherited
Biological Process (BP) cellular response to decreased oxygen levels 0.9222 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription from RNA polymerase II promoter 1 Highly Informative Inherited
Biological Process (BP) positive regulation of cellular component biogenesis 1 Highly Informative Inherited
Biological Process (BP) anatomical structure homeostasis 0.05118 Highly Informative Inherited
Biological Process (BP) cell-cell signaling 0.9239 Highly Informative Inherited
Biological Process (BP) apoptotic process 0.004933 Highly Informative Inherited
Biological Process (BP) nervous system process 0.6452 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.06652 Highly Informative Inherited
Biological Process (BP) appendage development 0.0561 Highly Informative Inherited
Biological Process (BP) establishment of organelle localization 0.02747 Highly Informative Inherited
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0.1628 Highly Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.1461 Highly Informative Inherited
Biological Process (BP) response to carbohydrate 0.5045 Highly Informative Inherited
Biological Process (BP) aging 0.1205 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.9162 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.02197 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.2159 Highly Informative Inherited
Biological Process (BP) germ cell development 0.8786 Highly Informative Inherited
Biological Process (BP) female gamete generation 1 Highly Informative Inherited
Biological Process (BP) epithelial cell differentiation 0.8759 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.3812 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) transferase activity 0.003148 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.00000000000001973 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.0000000000393 Moderately Informative Direct
Molecular Function (MF) small molecule binding 1 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.2589 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.4917 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0 Informative Direct
Molecular Function (MF) signal transducer activity 0 Informative Direct
Molecular Function (MF) receptor binding 0.0000000000002843 Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0.0000000000000531 Informative Direct
Molecular Function (MF) kinase activity 0.000251 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.00004332 Informative Direct
Molecular Function (MF) passive transmembrane transporter activity 0.000000000009987 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 0.0000000000006051 Informative Direct
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) enzyme binding 0.1767 Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.3522 Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.000001872 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.00001161 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.000000003015 Highly Informative Direct
Molecular Function (MF) ion channel activity 0.0000000000005049 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.0008554 Highly Informative Direct
Molecular Function (MF) gated channel activity 0.000221 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.0000000004007 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.001304 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000001443 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.3837 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.03078 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2299 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.000001402 Informative Direct
Cellular Component (CC) transporter complex 0.2825 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.1502 Informative Inherited
Cellular Component (CC) nuclear body 0.000000000436 Highly Informative Direct
Cellular Component (CC) receptor complex 0 Highly Informative Direct
Cellular Component (CC) RNA polymerase II transcription factor complex 0.000000000007068 Highly Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.4176 Highly Informative Inherited

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 bonds0.4681Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.0000000376Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.000007319Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.7839Moderately InformativeInherited
Enzyme Commission (EC)Protein-histidine kinases0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)3',5'-cyclic-nucleotide phosphodiesterase0.0001609Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDifferentiation0.0000000003124Moderately InformativeDirect
Biological processVirulence0.0000006992Moderately InformativeDirect
Biological processIon transport0.000001568Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processNitrogen fixation0InformativeDirect
Biological processSensory transduction0InformativeDirect
Biological processNeurogenesis0.000000000006078InformativeDirect
Biological processAngiogenesis0.00001163InformativeDirect
Biological processSporulation0.0004272InformativeDirect
Biological processPotassium transport0Highly InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Biological processGluconeogenesis0.000000001354Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane0.009838Least InformativeInherited
Cellular componentCell membrane0.000002672Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionNucleotide-binding0.02268Least InformativeInherited
Molecular functionFlavoprotein0.00000004669Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionPotassium0InformativeDirect
Molecular functionFMN0.000000004619InformativeDirect
Molecular functioncAMP0.000002316Highly InformativeDirect
Post-translational modificationTransferase0.00000003667Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000000003437Moderately InformativeDirect
Post-translational modificationRepressor0.0000006464Moderately InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationCalmodulin-binding0.000008566InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationVoltage-gated channel0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.0000000000718Moderately InformativeDirect
Post-translational modificationHydroxylation0.000000000002217InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · 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 16 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 PYP-like sensor domain (PAS domain) 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 16 hidden Markov models representing the PYP-like sensor domain (PAS domain) 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]