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Metallo-dependent phosphatases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Metallo-dependent phosphatases [ 56299]
Superfamily:   Metallo-dependent phosphatases [ 56300] (12)
Families:   Purple acid phosphatase-like [ 56301] (2)
  DNA double-strand break repair nuclease [ 64427]
  5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain [ 56307]
  Protein serine/threonine phosphatase [ 56310] (5)
  Phosphoesterase-related [ 82803]
  TT1561-like [ 103320] (2)
  YfcE-like [ 111233] (4)
  Hypothetical protein aq 1666 [ 118152]
  DR1281-like [ 118155] (2)
  TTHA0625-like [ 143938]
  GpdQ-like [ 160875] (2)
  ADPRibase-Mn-like [ 160880]


Superfamily statistics
Genomes (3,169) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 45,437 190,174 54
Proteins 45,003 185,060 54


Functional annotation
General category Processes_IC
Detailed category Proteases

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)primary metabolic process0.16050.00001608Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.21230.002095Least InformativeInherited
Biological Process (BP)biosynthetic process0.3021Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.1740.9473Least InformativeInherited
Biological Process (BP)single-organism cellular process0.74341Least InformativeInherited
Biological Process (BP)cellular protein modification process0.000068010Moderately InformativeDirect
Biological Process (BP)lipid metabolic process0.000018940.0004425Moderately InformativeDirect
Biological Process (BP)cellular localization0.00000001690.0009075Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.000000048610.00001596Moderately InformativeDirect
Biological Process (BP)carbohydrate metabolic process0.095281Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative biosynthetic process0.00000041520.005196Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.016071Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process00InformativeDirect
Biological Process (BP)phospholipid metabolic process0.0000000008920.00000569InformativeDirect
Biological Process (BP)vesicle-mediated transport0.00000078240.00001883InformativeDirect
Biological Process (BP)liposaccharide metabolic process0.000000000071580.00000000006183InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.00068360.1485InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.00095240.1035InformativeInherited
Biological Process (BP)glycolipid biosynthetic process00.000000000001666Highly InformativeDirect
Biological Process (BP)endosomal transport0.0000000000035720.000008864Highly InformativeDirect
Biological Process (BP)lipoprotein metabolic process0.000000000014780.000000006216Highly InformativeDirect
Biological Process (BP)phosphatidylinositol metabolic process0.000000000022870.00000006574Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport0.0005010.0005504Highly InformativeDirect
Biological Process (BP)vesicle-mediated transport to the plasma membrane0.00014210.01434Highly InformativeInherited
Biological Process (BP)oligosaccharide metabolic process0.0000032240.006071Highly InformativeInherited
Biological Process (BP)glycerophospholipid biosynthetic process0.047790.003384Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.0000000000055460Least InformativeDirect
Molecular Function (MF)binding0.56161Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.00000018240Moderately InformativeDirect
Molecular Function (MF)metal ion binding0.00000055740Moderately InformativeDirect
Molecular Function (MF)carbohydrate derivative binding0.0015510.4223Moderately InformativeInherited
Molecular Function (MF)anion binding0.39661Moderately InformativeInherited
Molecular Function (MF)phosphoric ester hydrolase activity00InformativeDirect
Molecular Function (MF)phospholipid binding0.00000013010.002777InformativeInherited
Molecular Function (MF)manganese ion binding0.0000018840.00000003222Highly InformativeDirect
Molecular Function (MF)glycolipid binding0.00000000000025690.00000000000001399Highly InformativeDirect
Molecular Function (MF)iron ion binding0.019290.03547Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.87010.8042Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.16351Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.32461Least InformativeInherited
Cellular Component (CC)membrane0.075041Least InformativeInherited
Cellular Component (CC)protein complex0.017361Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.0055210.1378Moderately InformativeInherited
Cellular Component (CC)membrane protein complex0.0000032410.1598Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum-Golgi intermediate compartment0.00000000000025930.00000000001999Highly InformativeDirect
Cellular Component (CC)cis-Golgi network0.000000000000090680.000000000004241Highly 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) primary metabolic process 0.00001608 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.002095 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9473 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.0004425 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0009075 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.00001596 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.001482 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative biosynthetic process 0.005196 Moderately Informative Inherited
Biological Process (BP) reproduction 0.7997 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.9723 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.1756 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.8674 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.687 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.007385 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6292 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) membrane lipid metabolic process 0 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.00000569 Informative Direct
Biological Process (BP) lipid catabolic process 0.00000006747 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.00001883 Informative Direct
Biological Process (BP) cell cycle process 0.000199 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.00000000000002741 Informative Direct
Biological Process (BP) organelle fission 0.0005267 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 0.0000881 Informative Direct
Biological Process (BP) liposaccharide metabolic process 0.00000000006183 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.003498 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.1485 Informative Inherited
Biological Process (BP) single organism reproductive process 0.8282 Informative Inherited
Biological Process (BP) response to radiation 0.1558 Informative Inherited
Biological Process (BP) glycerolipid metabolic process 0.1035 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.424 Informative Inherited
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) ceramide metabolic process 0.000000000001248 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0001136 Highly Informative Direct
Biological Process (BP) nucleotide catabolic process 0.000456 Highly Informative Direct
Biological Process (BP) glycolipid biosynthetic process 0.000000000001666 Highly Informative Direct
Biological Process (BP) phospholipid catabolic process 0.00000006724 Highly Informative Direct
Biological Process (BP) endosomal transport 0.000008864 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.0000000007266 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0.000000006216 Highly Informative Direct
Biological Process (BP) response to drug 0 Highly Informative Direct
Biological Process (BP) phosphatidylinositol metabolic process 0.00000006574 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0005504 Highly Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.000000001034 Highly Informative Direct
Biological Process (BP) vesicle-mediated transport to the plasma membrane 0.01434 Highly Informative Inherited
Biological Process (BP) photoperiodism 0.001268 Highly Informative Inherited
Biological Process (BP) circadian rhythm 0.073 Highly Informative Inherited
Biological Process (BP) regulation of circadian rhythm 0.02413 Highly Informative Inherited
Biological Process (BP) oligosaccharide metabolic process 0.006071 Highly Informative Inherited
Biological Process (BP) glycerophospholipid biosynthetic process 0.003384 Highly Informative Inherited
Biological Process (BP) cell cycle phase transition 0.1893 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.4223 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) protein binding 0.5848 Moderately Informative Inherited
Molecular Function (MF) enzyme binding 0.00000002159 Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.1863 Informative Inherited
Molecular Function (MF) phospholipid binding 0.002777 Informative Inherited
Molecular Function (MF) nuclease activity 1 Informative Inherited
Molecular Function (MF) endoribonuclease activity 0.000006867 Highly Informative Direct
Molecular Function (MF) phospholipase activity 0.000000000005292 Highly Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 0.000001337 Highly Informative Direct
Molecular Function (MF) calcium ion binding 0.00007021 Highly Informative Direct
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) protein phosphatase binding 0 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.00000003222 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0001128 Highly Informative Direct
Molecular Function (MF) glycolipid binding 0.00000000000001399 Highly Informative Direct
Molecular Function (MF) iron ion binding 0.03547 Highly Informative Inherited
Molecular Function (MF) phosphoric diester hydrolase activity 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.8042 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.1378 Moderately Informative Inherited
Cellular Component (CC) membrane protein complex 0.1598 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum-Golgi intermediate compartment 0.00000000001999 Highly Informative Direct
Cellular Component (CC) cis-Golgi network 0.000000000004241 Highly Informative Direct
Cellular Component (CC) protein serine/threonine phosphatase complex 0 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)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.00005707Moderately InformativeDirect
Enzyme Commission (EC)Phosphoprotein phosphatase0InformativeDirect
Enzyme Commission (EC)3',5'-cyclic-nucleotide phosphodiesterase0.000000000002986Highly InformativeDirect
Enzyme Commission (EC)Acid phosphatase0.00000001228Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the vasculature0Moderately InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.9743Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.2362Moderately InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.5145Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.9099Moderately InformativeInherited
Worm Phenotype (WP)electrophysiology variant0.0000004327InformativeDirect
Worm Phenotype (WP)cell stress response variant0.2073InformativeInherited
Worm Phenotype (WP)mutagen induced apoptosis variant0.0003496Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.02577Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA 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)fruit0.00000000001045InformativeDirect

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)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)In phosphorus-containing anhydrides0InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.00008827InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine phosphatase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processLipid metabolism0Moderately InformativeDirect
Biological processCell cycle0.04955Moderately InformativeInherited
Biological processMeiosis9.591e-16InformativeDirect
Biological processLipid biosynthesis0.0000000000006647InformativeDirect
Biological processMitosis0.000001272InformativeDirect
Biological processmRNA processing0.0003382InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processER-Golgi transport0.00000059Highly InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentSecreted0.0002668Moderately InformativeDirect
Cellular componentVacuole0.0000007236InformativeDirect
Cellular componentChromosome0.0000007334InformativeDirect
Cellular componentGPI-anchor0.000002169InformativeDirect
Cellular componentCentromere0.00000000004034Highly InformativeDirect
Cellular componentKinetochore0.00004904Highly InformativeDirect
DomainSignal0.000000001986Least InformativeDirect
DomainKelch repeat0.0003003Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0.000002326Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNickel0InformativeDirect
Molecular functionCalmodulin-binding0.000000000000005756InformativeDirect
Molecular functioncAMP0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease1Moderately InformativeInherited
Post-translational modificationNucleotidyltransferase1Moderately InformativeInherited
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationProtein phosphatase0InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0.0007344InformativeDirect
Post-translational modificationGlycoprotein0.000001688Least InformativeDirect
Post-translational modificationMethylation0.000003411Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0.0000000002032Least InformativeDirect
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0.0000000000003816Moderately InformativeDirect
UniPathway (UP)lipopolysaccharide biosynthesis0InformativeDirect
UniPathway (UP)gluconeogenesis0InformativeDirect
UniPathway (UP)glycolipid biosynthesis1InformativeInherited
UniPathway (UP)lipid IV(A) biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · 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 29 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 Metallo-dependent phosphatases 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 29 hidden Markov models representing the Metallo-dependent phosphatases 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]