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 (2,315) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 38,746 165,870 11
Proteins 36,790 162,958 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)
Molecular Function (MF)lyase activity2.503e-060Moderately 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) single-organism metabolic process 0 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) biosynthetic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.1723 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9384 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.263 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 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) system process 5.741e-11 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 1.073e-09 Moderately Informative Direct
Biological Process (BP) signal transduction 4.461e-06 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 9.301e-06 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 5.637e-05 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.8571 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.003738 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2148 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) response to abiotic stimulus 0.4154 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.9898 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.04423 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.6393 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular 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 0.79 Moderately Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 3.741e-15 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 3.084e-11 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.0003938 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.2929 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.001206 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.001845 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.5511 Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0.0209 Informative Inherited
Biological Process (BP) regulation of cell development 0.145 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.8475 Informative Inherited
Biological Process (BP) single-organism behavior 0.02619 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.04992 Informative Inherited
Biological Process (BP) regulation of kinase activity 0.04336 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.1193 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.1211 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.4643 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1303 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.1163 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.002001 Informative Inherited
Biological Process (BP) purine ribonucleotide biosynthetic process 0 Highly Informative Direct
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) G-protein coupled receptor signaling pathway 3.499e-12 Highly Informative Direct
Biological Process (BP) regulation of phospholipase activity 2.954e-10 Highly Informative Direct
Biological Process (BP) energy reserve metabolic process 9.577e-08 Highly Informative Direct
Biological Process (BP) cellular response to peptide 7.725e-05 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.0002836 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 0.0006579 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 0.0511 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle 0.03653 Highly Informative Inherited
Biological Process (BP) sensory perception 0.0147 Highly Informative Inherited
Biological Process (BP) cellular response to growth factor stimulus 0.004924 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.9876 Highly Informative Inherited
Biological Process (BP) response to carbohydrate stimulus 0.0022 Highly Informative Inherited
Biological Process (BP) positive regulation of protein kinase activity 0.005034 Highly Informative Inherited
Biological Process (BP) response to alkaloid 0.001075 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) cation binding 0.6243 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.5822 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 8.764e-07 Informative Direct
Molecular Function (MF) receptor activity 3.372e-05 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0178 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.0208 Informative Inherited
Molecular Function (MF) enzyme binding 0.176 Informative Inherited
Molecular Function (MF) manganese ion binding 6.813e-06 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 8.795e-06 Highly Informative Direct
Cellular Component (CC) membrane 0.0005907 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cell projection 6.287e-12 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1.61e-07 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 phenotype0.1817Least InformativeInherited
Mammalian Phenotype (MP)muscle phenotype0.1554Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.1709Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal systemic arterial blood pressure0.0403InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.1492InformativeInherited
Mammalian Phenotype (MP)increased systemic arterial systolic blood pressure0.0004424Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.01108Highly 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 variant6.505e-09Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant1Least InformativeInherited
Worm Phenotype (WP)chemical response variant0.2441Moderately InformativeInherited
Worm Phenotype (WP)chemotaxis variant8.012e-14InformativeDirect
Worm Phenotype (WP)copulation variant0.07539InformativeInherited
Worm Phenotype (WP)male behavior variant1InformativeInherited
Worm Phenotype (WP)metabolic pathway variant1.337e-06Highly 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 defective0.001094InformativeInherited
Fly Phenotype (FP)stress response defective2.316e-05Highly 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 groups0.8119Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.01013Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.0002469InformativeDirect
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Adenylate cyclase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processSensory transduction0InformativeDirect
Biological processOsteogenesis2.436e-10Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentCilium6.963e-11Highly InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRepeat0.0008187Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding4.434e-13Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functionCalmodulin-binding7.23e-08InformativeDirect
Molecular functionHeme1.062e-06InformativeDirect
Molecular functionChromophore0.0004238InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect

Document: KW 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) · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]