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.


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 (2,789) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 71,199 577,810 30
Proteins 45,948 381,012 30


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 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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.1232Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.1887Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.6402Least InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.00001927Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood vessel morphology0.06152Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.1201Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.192Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.2005Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.5063Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0007147InformativeDirect
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.0008212InformativeDirect
Mammalian Phenotype (MP)abnormal heartbeat0.009148InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.04532InformativeInherited
Mammalian Phenotype (MP)abnormal circulating leptin level0.1027InformativeInherited
Mammalian Phenotype (MP)decreased heart rate0.0002507Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circadian rhythm0.0003489Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating estradiol level0.0005882Highly InformativeDirect
Mammalian Phenotype (MP)abnormal catecholamine level0.001712Highly InformativeInherited
Mammalian Phenotype (MP)abnormal osteoblast cell number0.002863Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organ system morphology variant0.000005299Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0003181Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.001389Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.008579Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.04265Least InformativeInherited
Worm Phenotype (WP)protein protein interaction variant0.0009156Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.01688Moderately InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.2506Moderately InformativeInherited
Worm Phenotype (WP)egg laying variant0.00001824InformativeDirect
Worm Phenotype (WP)oxygen response variant0.000131InformativeDirect
Worm Phenotype (WP)body length variant0.003701InformativeInherited
Worm Phenotype (WP)body width variant0.004721InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.1988InformativeInherited
Worm Phenotype (WP)carbon dioxide avoidance variant0.000001231Highly InformativeDirect
Worm Phenotype (WP)neuronal cell fate specification variant0.000003999Highly InformativeDirect
Worm Phenotype (WP)gene expression level reduced0.00001572Highly InformativeDirect
Worm Phenotype (WP)dumpy0.0002096Highly InformativeDirect
Worm Phenotype (WP)transgene expression reduced0.0003186Highly InformativeDirect
Worm Phenotype (WP)exploded through vulva0.0004417Highly 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 defective0.03827Moderately InformativeInherited
Fly Phenotype (FP)circadian rhythm defective0.001574InformativeInherited
Fly Phenotype (FP)locomotor behavior defective0.5127InformativeInherited
Fly Phenotype (FP)sleep defective0.00002139Highly InformativeDirect
Fly Phenotype (FP)locomotor rhythm defective0.000893Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)trunk0.07052Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.1526Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.4063Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.4768Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.9729Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.0007132Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.0009543Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.291Moderately InformativeInherited
Xenopus ANatomical entity (XAN)spinal cord0.00004062InformativeDirect
Xenopus ANatomical entity (XAN)eye0.000118InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.002582InformativeInherited
Xenopus ANatomical entity (XAN)muscle0.1298InformativeInherited
Xenopus ANatomical entity (XAN)tail0.9656InformativeInherited
Xenopus ANatomical entity (XAN)somite0.0002128Highly 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 phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.0001059Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.9745Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.0000000002905InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0.000001264InformativeDirect
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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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 43 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 43 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 · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]