SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,135) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 55,277 143,070 30
Proteins 35,964 97,530 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) regulation of metabolic process 2.079e-07 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0004231 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.9336 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.01245 Least Informative Inherited
Biological Process (BP) developmental process 0.03508 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01131 Least Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 4.008e-15 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 7.654e-12 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 1.416e-11 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 2.239e-11 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 1.28e-06 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0001247 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0001416 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0002512 Moderately Informative Direct
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.544 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.9811 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.7681 Moderately Informative Inherited
Biological Process (BP) organ development 0.5356 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.4186 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.07451 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.009219 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.00177 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.04617 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.2336 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.00435 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.008138 Moderately Informative Inherited
Biological Process (BP) gene expression 0.03262 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) response to light stimulus 0 Informative Direct
Biological Process (BP) transcription, DNA-dependent 1.763e-12 Informative Direct
Biological Process (BP) positive regulation of gene expression 1.008e-10 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1.522e-09 Informative Direct
Biological Process (BP) embryonic organ development 1.572e-09 Informative Direct
Biological Process (BP) gland development 2.482e-09 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 2.098e-08 Informative Direct
Biological Process (BP) chordate embryonic development 1.631e-07 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 8.732e-07 Informative Direct
Biological Process (BP) locomotion 4.313e-06 Informative Direct
Biological Process (BP) reproductive system development 1.01e-05 Informative Direct
Biological Process (BP) tube development 6.892e-05 Informative Direct
Biological Process (BP) regulation of ion transport 0.0001164 Informative Direct
Biological Process (BP) metal ion transport 0.0001939 Informative Direct
Biological Process (BP) regulation of secretion 0.9909 Informative Inherited
Biological Process (BP) transmembrane transport 0.2396 Informative Inherited
Biological Process (BP) generation of neurons 0.8038 Informative Inherited
Biological Process (BP) epithelium development 0.102 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.2253 Informative Inherited
Biological Process (BP) protein phosphorylation 0.04186 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.4117 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.004034 Informative Inherited
Biological Process (BP) positive regulation of developmental process 1 Informative Inherited
Biological Process (BP) single-organism behavior 0.5658 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.007046 Informative Inherited
Biological Process (BP) response to oxidative stress 0.02956 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 1 Informative Inherited
Biological Process (BP) regulation of growth 1 Informative Inherited
Biological Process (BP) growth 0.411 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 1 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.5895 Informative Inherited
Biological Process (BP) response to external stimulus 0.01654 Informative Inherited
Biological Process (BP) microtubule-based process 0.7292 Informative Inherited
Biological Process (BP) cardiovascular system development 0.9703 Informative Inherited
Biological Process (BP) organ morphogenesis 1 Informative Inherited
Biological Process (BP) regulation of system process 0.06318 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.0133 Informative Inherited
Biological Process (BP) cellular component movement 0.0115 Informative Inherited
Biological Process (BP) localization of cell 0.03231 Informative Inherited
Biological Process (BP) response to hypoxia 0 Highly Informative Direct
Biological Process (BP) embryonic placenta development 5.966e-15 Highly Informative Direct
Biological Process (BP) xenobiotic metabolic process 3.322e-09 Highly Informative Direct
Biological Process (BP) monovalent inorganic cation transport 7.847e-09 Highly Informative Direct
Biological Process (BP) mammary gland epithelium development 1.295e-08 Highly Informative Direct
Biological Process (BP) regulation of proton transport 2.714e-08 Highly Informative Direct
Biological Process (BP) epithelial tube morphogenesis 7.915e-07 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.0001885 Highly Informative Direct
Biological Process (BP) morphogenesis of a branching epithelium 0.0003999 Highly Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0.000543 Highly Informative Direct
Biological Process (BP) response to toxic substance 0.0008262 Highly Informative Direct
Biological Process (BP) ion transmembrane transport 0.08978 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.001315 Highly Informative Inherited
Biological Process (BP) regulation of myeloid cell differentiation 0.005704 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 1 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.0249 Highly Informative Inherited
Biological Process (BP) positive regulation of growth 0.2177 Highly Informative Inherited
Biological Process (BP) multi-multicellular organism process 0.007291 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to growth factor stimulus 0.2401 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.02755 Highly Informative Inherited
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0.01014 Highly Informative Inherited
Biological Process (BP) chemotaxis 0.3076 Highly Informative Inherited
Biological Process (BP) microtubule-based movement 0.01109 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.06401 Highly Informative Inherited
Molecular Function (MF) binding 3.893e-10 Least Informative Direct
Molecular Function (MF) transferase activity 0.0003346 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 3.747e-11 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 1.496e-07 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 3.433e-07 Moderately Informative Direct
Molecular Function (MF) protein binding 0.01343 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.3148 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.1367 Moderately Informative Inherited
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) receptor activity 0 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 1.127e-08 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 2.605e-07 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 4.2e-06 Informative Direct
Molecular Function (MF) kinase activity 0.0005465 Informative Direct
Molecular Function (MF) enzyme binding 0.007103 Informative Inherited
Molecular Function (MF) receptor binding 0.0183 Informative Inherited
Molecular Function (MF) phosphoric ester hydrolase activity 0.004646 Informative Inherited
Molecular Function (MF) protein kinase activity 0 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding 6.744e-11 Highly Informative Direct
Molecular Function (MF) ion gated channel activity 2.477e-08 Highly Informative Direct
Molecular Function (MF) ion channel activity 2.94e-08 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 6.673e-05 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) protein complex 0.0002431 Least Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2702 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0005086 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.7378 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 2.994e-09 Informative Direct
Cellular Component (CC) integral to membrane 0.5981 Informative Inherited
Cellular Component (CC) intrinsic to plasma membrane 0.7609 Informative Inherited
Cellular Component (CC) transcription factor complex 0 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 0.651 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 hydrolases3.76e-08Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups7.319e-06Moderately 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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.1533Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3643Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.4866Least InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level3.727e-05Moderately InformativeDirect
Mammalian Phenotype (MP)behavior/neurological phenotype0.01497Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.06106Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular development0.106Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.1323Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.143Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.2374Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.5295Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.0002983InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland morphology0.0003208InformativeDirect
Mammalian Phenotype (MP)abnormal circulating hormone level0.001184InformativeInherited
Mammalian Phenotype (MP)abnormal heartbeat0.005516InformativeInherited
Mammalian Phenotype (MP)abnormal bone structure0.01346InformativeInherited
Mammalian Phenotype (MP)abnormal fertility/fecundity0.8095InformativeInherited
Mammalian Phenotype (MP)abnormal sleep pattern2.272e-08Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circadian period1.083e-07Highly InformativeDirect
Mammalian Phenotype (MP)increased circulating leptin level2.114e-06Highly InformativeDirect
Mammalian Phenotype (MP)decreased heart rate8.46e-05Highly InformativeDirect
Mammalian Phenotype (MP)premature aging0.0009263Highly InformativeDirect
Mammalian Phenotype (MP)decreased litter size0.0009316Highly InformativeDirect
Mammalian Phenotype (MP)abnormal catecholamine level0.001162Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.003349Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.01293Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.008651Moderately InformativeInherited
Worm Phenotype (WP)egg laying variant8.312e-06InformativeDirect
Worm Phenotype (WP)body length variant0.001979InformativeInherited
Worm Phenotype (WP)body width variant0.002389InformativeInherited
Worm Phenotype (WP)egg laying defective1.563e-07Highly InformativeDirect
Worm Phenotype (WP)carbon dioxide avoidance variant1.584e-06Highly 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)behavior defective0.003156Moderately InformativeInherited
Fly Phenotype (FP)circadian rhythm defective0.0003216InformativeDirect
Fly Phenotype (FP)locomotor behavior defective0.4979InformativeInherited
Fly Phenotype (FP)eclosion rhythm defective5.593e-07Highly InformativeDirect
Fly Phenotype (FP)semi-sterile1.466e-05Highly InformativeDirect
Fly Phenotype (FP)gravitaxis defective7.686e-05Highly InformativeDirect
Fly Phenotype (FP)locomotor rhythm defective9.871e-05Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0.9334Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.133Moderately InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.2712Moderately InformativeInherited
Xenopus ANatomical entity (XAN)sensory system0.3232Moderately InformativeInherited
Xenopus ANatomical entity (XAN)mesoderm8.84e-05InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.0002315InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0003751InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.07412InformativeInherited
Xenopus ANatomical entity (XAN)tail0.8996InformativeInherited
Xenopus ANatomical entity (XAN)lens5.325e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)trunk somite1.36e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)retina0.0001411Highly InformativeDirect
Xenopus ANatomical entity (XAN)eye primordium0.0009926Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0.2718Moderately InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.798Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases3.895e-08InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase3.618e-07InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Protein-histidine kinases0Highly 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 processIon transport1.978e-06Moderately InformativeDirect
Biological processDifferentiation2.697e-06Moderately InformativeDirect
Biological processNitrogen fixation0InformativeDirect
Biological processSensory transduction0InformativeDirect
Biological processNeurogenesis5.257e-08InformativeDirect
Biological processVirulence3.357e-07InformativeDirect
Biological processSporulation0.0002111InformativeDirect
Biological processBiological rhythms0Highly InformativeDirect
Biological processPotassium transport0Highly InformativeDirect
Biological processVoltage-gated channel0Highly InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Biological processGluconeogenesis6.759e-11Highly InformativeDirect
Biological processPhosphate transport8.299e-07Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane0.004134Least InformativeInherited
Cellular componentChromosome0.0002088InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionNucleotide-binding0.5595Least InformativeInherited
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionPotassium0InformativeDirect
Molecular functionFMN5.01e-15InformativeDirect
Molecular functionFlavoprotein9.138e-07InformativeDirect
Molecular functionCalmodulin-binding2.166e-05InformativeDirect
Molecular functionPotassium channel0Highly InformativeDirect
Post-translational modificationTransferase7.63e-08Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein1.67e-07Moderately InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation1.24e-09Moderately InformativeDirect
Post-translational modificationIsopeptide bond1.933e-06Moderately InformativeDirect
Post-translational modificationHydroxylation3.118e-12InformativeDirect
Post-translational modificationS-nitrosylation6.85e-06InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism4.854e-07Least InformativeDirect
UniPathway (UP)protein ubiquitination5.349e-12Moderately InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]