SUPERFAMILY 1.75 HMM library and genome assignments server


Composite domain of metallo-dependent hydrolases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Composite domain of metallo-dependent hydrolases [ 51337]
Superfamily:   Composite domain of metallo-dependent hydrolases [ 51338] (11)
Families:   Cytosine deaminase [ 69373]
  alpha-Subunit of urease [ 51339]
  Hydantoinase (dihydropyrimidinase) [ 75044] (5)
  SAH/MTA deaminase-like [ 82224] (3)
  Isoaspartyl dipeptidase [ 89438]
  N-acetylglucosamine-6-phosphate deacetylase, NagA [ 82227]
  D-aminoacylase [ 82230]
  Adenine deaminase [ 141689]
  Zn-dependent arginine carboxypeptidase-like [ 159340] (3)
  Imidazolonepropionase-like [ 159347] (3)
  DR0824-like [ 159355]


Superfamily statistics
Genomes (2,921) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,797 0 88
Proteins 20,810 0 58


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) nitrogen compound metabolic process 0.0002166 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0002784 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0005939 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.001583 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.005404 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.5302 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.7049 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.5127 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.5695 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 5.853e-13 Moderately Informative Direct
Biological Process (BP) nervous system development 1.452e-05 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 3.206e-05 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 8.009e-05 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0001406 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0002385 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0003127 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0007737 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.1508 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.07332 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2512 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.7442 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5853 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.04978 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.0323 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.001237 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.6244 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.5161 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.2474 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.08758 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.141 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) system process 0.8062 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.005589 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.06838 Moderately Informative Inherited
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) protein complex assembly 7.143e-07 Informative Direct
Biological Process (BP) response to cytokine stimulus 1.711e-06 Informative Direct
Biological Process (BP) generation of neurons 3.948e-06 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 4.544e-06 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 1.563e-05 Informative Direct
Biological Process (BP) regulation of cellular component movement 1.563e-05 Informative Direct
Biological Process (BP) regulation of locomotion 3.936e-05 Informative Direct
Biological Process (BP) regulation of nervous system development 4.728e-05 Informative Direct
Biological Process (BP) response to wounding 5.125e-05 Informative Direct
Biological Process (BP) actin filament-based process 8.728e-05 Informative Direct
Biological Process (BP) cytoskeleton organization 9.742e-05 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0001334 Informative Direct
Biological Process (BP) regulation of cell development 0.0001823 Informative Direct
Biological Process (BP) organelle localization 0.001505 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.201 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.2193 Informative Inherited
Biological Process (BP) cellular amide metabolic process 0.001302 Informative Inherited
Biological Process (BP) single-organism behavior 0.04014 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.3043 Informative Inherited
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0 Highly Informative Direct
Biological Process (BP) response to axon injury 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) protein homooligomerization 1.077e-14 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 3.516e-11 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 1.102e-10 Highly Informative Direct
Biological Process (BP) amino sugar metabolic process 3.395e-10 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 8.473e-09 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 1.662e-06 Highly Informative Direct
Biological Process (BP) actin filament organization 3.974e-06 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0.0001651 Highly Informative Direct
Biological Process (BP) learning or memory 0.0002964 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) cation binding 0.2103 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.7452 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0 Informative Direct
Molecular Function (MF) sulfur compound binding 1.724e-11 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 1.738e-10 Informative Direct
Molecular Function (MF) transition metal ion binding 1.62e-09 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0008553 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0.008539 Informative Inherited
Molecular Function (MF) deacetylase activity 3.262e-09 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 4.087e-08 Highly Informative Direct
Molecular Function (MF) deaminase activity 2.752e-06 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.8915 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.6973 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.936 Least Informative Inherited
Cellular Component (CC) cell projection 4.811e-07 Moderately Informative Direct
Cellular Component (CC) cytosol 3.848e-06 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.006983 Moderately Informative Inherited
Cellular Component (CC) vesicle 0.008739 Moderately Informative Inherited
Cellular Component (CC) neuron projection 5.774e-12 Informative Direct
Cellular Component (CC) cell leading edge 1.557e-08 Informative Direct
Cellular Component (CC) actin cytoskeleton 0.0001141 Informative Direct
Cellular Component (CC) cell body 0 Highly Informative Direct
Cellular Component (CC) actin filament 1.426e-13 Highly Informative Direct
Cellular Component (CC) transport vesicle 6.006e-13 Highly Informative Direct
Cellular Component (CC) growth cone 3.168e-09 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)In linear amides1Moderately InformativeInherited
Enzyme Commission (EC)In cyclic amides0InformativeDirect
Enzyme Commission (EC)In cyclic amidines1InformativeInherited
Enzyme Commission (EC)Urease0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)syndrome0Moderately InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal brain morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal neuron morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system physiology0.2508Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cerebrum morphology0.0006345InformativeDirect
Mammalian Phenotype (MP)abnormal neurite morphology0.02684Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)In linear amides1InformativeInherited
Enzyme Commission (EC)In cyclic amidines1InformativeInherited
Enzyme Commission (EC)In cyclic amides0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHistidine metabolism0Highly InformativeDirect
Biological processPurine metabolism0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNickel0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism1.597e-13Least InformativeDirect
UniPathway (UP)aromatic compound metabolism0.0007374Least InformativeDirect
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)nitrogen metabolism0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism0.7796Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)purine metabolism1Moderately InformativeInherited
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)purine degradation2.763e-05InformativeDirect
UniPathway (UP)amino-sugar metabolism0.001284InformativeInherited
UniPathway (UP)amine and polyamine degradation0.005081InformativeInherited
UniPathway (UP)purine base metabolism0.5057InformativeInherited
UniPathway (UP)xenobiotic degradation1InformativeInherited
UniPathway (UP)ureide metabolism1InformativeInherited
UniPathway (UP)purine biosynthesis via salvage pathway1InformativeInherited
UniPathway (UP)urea degradation0Highly InformativeDirect
UniPathway (UP)(S)-allantoin degradation0Highly InformativeDirect
UniPathway (UP)L-histidine degradation0Highly InformativeDirect
UniPathway (UP)N-acetylneuraminate degradation0.000128Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011059 SSF51338 Protein matches
Abstract

The composite domain of metal-dependent hydrolases has a pseudo-barrel fold that is interrupted by the catalytic beta/alpha barrel domain. This domain is found in a variety of bacterial and fungal enzymes, including: cytosine deaminase, an enzyme that is important in the pyrimidine salvage pathway [PubMed11812140]; the alpha-subunit of urease, a virulence factor of gastric pathogens such as Helicobacter pylori [PubMed12127484]; D- and L-hydantoinases (dihydropyrimidinase), which catalyse the production of D- and L-amino acids, respectively [PubMed12837777]; isoaspartyl dipeptidase from Escherichia coli, which functions in protein degradation [PubMed12718528]; N-acetylglucosamine-6-phosphate deacetylase, which is an enzyme from the biosynthetic pathway to amino-sugar-nucleotides [PubMed14557261]; and N-acyl-D-amino acid amidohydrolase (D-aminoacylase), involved in the synthesis of D-amino acids [PubMed12454005].


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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · 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 33 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 Composite domain of metallo-dependent hydrolases 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 33 hidden Markov models representing the Composite domain of metallo-dependent hydrolases 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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]