SUPERFAMILY 1.75 HMM library and genome assignments server

Nucleotide cyclase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   Nucleotide cyclase [ 55073] (2)
Families:   Adenylyl and guanylyl cyclase catalytic domain [ 55074] (5)
  GGDEF domain [ 117984]


Superfamily statistics
Genomes (2,316) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 38,804 165,870 11
Proteins 36,840 162,958 11


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism cellular process0.060490.00001177Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.013930Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.0039750Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.0015020Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0022530Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.0015370Least InformativeInherited
Biological Process (BP)biosynthetic process0.0021230Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.00048930Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.000038490Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.000026780Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.000070190Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0000360Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process0.000035070Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.000085290Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000063740Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.000062140Moderately InformativeDirect
Biological Process (BP)purine ribonucleotide metabolic process0.0000026740InformativeDirect
Biological Process (BP)nucleotide biosynthetic process0.00000018680InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.000000009450InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.000000026210InformativeDirect
Molecular Function (MF)lyase activity0.0000027930Moderately InformativeDirect

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) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00001177 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.2167 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.5585 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2825 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) signal transduction 0.000005263 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.00004953 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.000009817 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.00000004969 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.02626 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4232 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.6479 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.07954 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.8141 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.4394 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.8968 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 1 Moderately Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.0004114 Informative Direct
Biological Process (BP) single-organism behavior 0.00001924 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.0001026 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.000000000000003707 Informative Direct
Biological Process (BP) regulation of cell development 0.1002 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.1446 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.2021 Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0.02259 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.002301 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.1129 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.04157 Informative Inherited
Biological Process (BP) neurological system process 0.01337 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.135 Informative Inherited
Biological Process (BP) regulation of transferase activity 1 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.6657 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1813 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.7675 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.1212 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.05117 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.01061 Informative Inherited
Biological Process (BP) energy reserve metabolic process 0.00000009017 Highly Informative Direct
Biological Process (BP) G-protein coupled receptor signaling pathway 0.000000000003555 Highly Informative Direct
Biological Process (BP) response to carbohydrate 0.0005516 Highly Informative Direct
Biological Process (BP) regulation of phospholipase activity 0.0000000002853 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.0002686 Highly Informative Direct
Biological Process (BP) positive regulation of cyclic nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.0007207 Highly Informative Direct
Biological Process (BP) cellular response to peptide 0.00008657 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.1158 Highly Informative Inherited
Biological Process (BP) regulation of reproductive process 0.00924 Highly Informative Inherited
Biological Process (BP) regulation of multi-organism process 0.01111 Highly Informative Inherited
Biological Process (BP) positive regulation of protein kinase activity 0.005593 Highly Informative Inherited
Biological Process (BP) response to alkaloid 0.001025 Highly Informative Inherited
Biological Process (BP) cellular response to growth factor stimulus 0.005361 Highly Informative Inherited
Biological Process (BP) sensory perception 0.1295 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.9859 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.5802 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.6226 Moderately Informative Inherited
Molecular Function (MF) receptor activity 0.00002033 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.000000882 Informative Direct
Molecular Function (MF) protein dimerization activity 0.01842 Informative Inherited
Molecular Function (MF) enzyme binding 0.1864 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.01596 Informative Inherited
Molecular Function (MF) manganese ion binding 0.000007184 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.000008945 Highly Informative Direct
Cellular Component (CC) membrane 0.0006926 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cell projection 0.000000000001786 Moderately Informative Direct
Cellular Component (CC) cytosol 1 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.01671Least InformativeInherited
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Adenylate cyclase0Highly InformativeDirect
Enzyme Commission (EC)Guanylate cyclase0Highly 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 phenotype0.1862Least InformativeInherited
Mammalian Phenotype (MP)muscle phenotype0.1593Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.1741Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal systemic arterial blood pressure0.03963InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.1565InformativeInherited
Mammalian Phenotype (MP)increased systemic arterial systolic blood pressure0.0004218Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.01272Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.000000006505Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant1Least InformativeInherited
Worm Phenotype (WP)chemical response variant0.2441Moderately InformativeInherited
Worm Phenotype (WP)chemotaxis variant0.00000000000008012InformativeDirect
Worm Phenotype (WP)copulation variant0.07539InformativeInherited
Worm Phenotype (WP)male behavior variant1InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.000001337Highly InformativeDirect
Worm Phenotype (WP)male mating defective0.0008141Highly InformativeDirect
Worm Phenotype (WP)aqueous positive chemotaxis defective0.03728Highly InformativeInherited
Worm Phenotype (WP)odorant positive chemotaxis variant0.5622Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)sensory perception defective0.001093InformativeInherited
Fly Phenotype (FP)stress response defective0.00002313Highly InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups0.8086Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.009964Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.0002452InformativeDirect
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Adenylate cyclase0Highly InformativeDirect

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)cardiovascular system0.002537Least InformativeInherited
Drugbank ATC_code (DB)cardiac therapy0.0001126Moderately InformativeDirect
Drugbank ATC_code (DB)vasodilators used in cardiac diseases0.000000002613InformativeDirect
Drugbank ATC_code (DB)organic nitrates0.0000000001765Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processSensory transduction0InformativeDirect
Biological processOsteogenesis0.0000000002431Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentCilium0.00000000006014Highly InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat0.0008481Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding0.0000000000007679Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functionCalmodulin-binding0.00000007058InformativeDirect
Molecular functionHeme0.0000009013InformativeDirect
Molecular functionChromophore0.0004167InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)glycan metabolism0Moderately InformativeDirect
UniPathway (UP)cellulose metabolism0InformativeDirect
UniPathway (UP)bacterial cellulose biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR001054 SSF55073 Protein matches
Abstract

Guanylate cyclases catalyse the formation of cyclic GMP (cGMP) from GTP. cGMP acts as an intracellular messenger, activating cGMP-dependent kinases and regulating cGMP-sensitive ion channels. The role of cGMP as a second messenger in vascular smooth muscle relaxation and retinal photo-transduction is well established. Guanylate cyclase is found both in the soluble and particulate fractions of eukaryotic cells. The soluble and plasma membrane-bound forms differ in structure, regulation and other properties [PubMed1349465, PubMed1356629, PubMed1680765, PubMed1982420]. Most currently known plasma membrane-bound forms are receptors for small polypeptides. The soluble forms of guanylate cyclase are cytoplasmic heterodimers having alpha and beta subunits.

In all characterised eukaryote guanylyl- and adenylyl cyclases, cyclic nucleotide synthesis is carried out by the conserved class III cyclase domain.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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 6 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 Nucleotide cyclase 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 6 hidden Markov models representing the Nucleotide cyclase 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]