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 (2,282) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 19,106 57,176 88
Proteins 16,620 50,931 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) heterocycle metabolic process 5.038e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000342 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0005297 Least Informative Direct
Biological Process (BP) response to stimulus 0.7785 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.001609 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.001908 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1217 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.1953 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.08608 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8377 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 4.735e-14 Moderately Informative Direct
Biological Process (BP) nervous system development 6.475e-07 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 6.789e-06 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 8.691e-05 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0002093 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.09414 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.01133 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8026 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.002513 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.006974 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.8004 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1426 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.001052 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.001217 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.001763 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.004092 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.03866 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.008788 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.01429 Moderately Informative Inherited
Biological Process (BP) system process 0.7872 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.05332 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00218 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.02141 Moderately Informative Inherited
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) protein oligomerization 6.458e-14 Informative Direct
Biological Process (BP) generation of neurons 4.771e-08 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 6.382e-08 Informative Direct
Biological Process (BP) response to cytokine stimulus 8.543e-08 Informative Direct
Biological Process (BP) regulation of cellular component movement 1.448e-07 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 1.847e-07 Informative Direct
Biological Process (BP) regulation of nervous system development 4.36e-07 Informative Direct
Biological Process (BP) regulation of locomotion 4.633e-07 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 1.981e-06 Informative Direct
Biological Process (BP) response to wounding 2.576e-06 Informative Direct
Biological Process (BP) cytoskeleton organization 5.53e-06 Informative Direct
Biological Process (BP) actin filament-based process 6.283e-06 Informative Direct
Biological Process (BP) regulation of cell development 1.485e-05 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.0001196 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.04004 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.004283 Informative Inherited
Biological Process (BP) single-organism behavior 0.01607 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2011 Informative Inherited
Biological Process (BP) protein homooligomerization 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) pyrimidine-containing compound biosynthetic process 4.382e-14 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 1.679e-13 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 4.176e-13 Highly Informative Direct
Biological Process (BP) regulation of cell projection organization 2.346e-10 Highly Informative Direct
Biological Process (BP) amino sugar metabolic process 8.382e-10 Highly Informative Direct
Biological Process (BP) regulation of neuron differentiation 3.745e-09 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 9.629e-08 Highly Informative Direct
Biological Process (BP) actin filament organization 2.047e-06 Highly Informative Direct
Biological Process (BP) learning or memory 8.929e-05 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0.0001102 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.8894 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) cation binding 0.6656 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.5984 Moderately Informative Inherited
Molecular Function (MF) protein binding 0.8778 Moderately Informative Inherited
Molecular Function (MF) transition metal ion binding 1.177e-07 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0003767 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0.004474 Informative Inherited
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 1 Informative Inherited
Molecular Function (MF) glycosaminoglycan binding 5.469e-14 Highly Informative Direct
Molecular Function (MF) sulfur compound binding 1.037e-13 Highly Informative Direct
Molecular Function (MF) deacetylase activity 4.122e-10 Highly Informative Direct
Molecular Function (MF) deaminase activity 9.589e-07 Highly Informative Direct
Cellular Component (CC) protein complex 0.4359 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.5264 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.7728 Least Informative Inherited
Cellular Component (CC) cell projection 4.375e-09 Moderately Informative Direct
Cellular Component (CC) cytosol 3.68e-07 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0003292 Moderately Informative Direct
Cellular Component (CC) extracellular region 0.009597 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.01152 Moderately Informative Inherited
Cellular Component (CC) neuron part 4.43e-13 Informative Direct
Cellular Component (CC) cell leading edge 4.856e-10 Informative Direct
Cellular Component (CC) cell projection part 1.408e-08 Informative Direct
Cellular Component (CC) actin cytoskeleton 2.121e-07 Informative Direct
Cellular Component (CC) extracellular space 3.796e-06 Informative Direct
Cellular Component (CC) cell body 0 Highly Informative Direct
Cellular Component (CC) actin filament 0 Highly Informative Direct
Cellular Component (CC) transport vesicle 2.632e-14 Highly Informative Direct
Cellular Component (CC) growth cone 3.349e-09 Highly Informative Direct
Cellular Component (CC) lamellipodium 9.135e-08 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 physiology0.295Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cerebrum morphology0.00064InformativeDirect
Mammalian Phenotype (MP)abnormal neurite morphology0.02347Highly 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)fertile0Least 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)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least 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 amides0Highly InformativeDirect
Enzyme Commission (EC)In cyclic amidines1Highly InformativeInherited

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 metabolism9.594e-14Least InformativeDirect
UniPathway (UP)aromatic compound metabolism0.0005315Least InformativeDirect
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)nitrogen metabolism0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism0.7774Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)purine metabolism1Moderately InformativeInherited
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)histidine metabolism0InformativeDirect
UniPathway (UP)purine degradation2.743e-05InformativeDirect
UniPathway (UP)amino-sugar metabolism0.001275InformativeInherited
UniPathway (UP)amine and polyamine degradation0.005307InformativeInherited
UniPathway (UP)purine base metabolism0.5059InformativeInherited
UniPathway (UP)xenobiotic degradation1InformativeInherited
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 degradation0.0001272Highly 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 ]