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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 (3,173) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 45,724 190,174 54
Proteins 45,287 185,060 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)single-organism metabolic process0.13810.9085Least InformativeInherited
Biological Process (BP)biosynthetic process0.20431Least InformativeInherited
Biological Process (BP)primary metabolic process0.14860.00004387Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.28490.008234Least InformativeInherited
Biological Process (BP)single-organism cellular process0.38881Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.32710.00466Least InformativeInherited
Biological Process (BP)cellular protein modification process0.000099080Moderately InformativeDirect
Biological Process (BP)lipid metabolic process0.0000058250.00006875Moderately InformativeDirect
Biological Process (BP)cellular localization0.00000000013730.0004223Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.0000000073050.000002036Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.000021420.1252Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.040260.9415Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.020381Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process00InformativeDirect
Biological Process (BP)phospholipid metabolic process0.00000000016550.000001018InformativeDirect
Biological Process (BP)vesicle-mediated transport0.000000000062310.0001542InformativeDirect
Biological Process (BP)liposaccharide metabolic process0.0000000000060440.000000000001028InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.00012350.03078InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.0022920.1944InformativeInherited
Biological Process (BP)dephosphorylation0.020690InformativeInherited
Biological Process (BP)protein dephosphorylation0.00089360Highly InformativeDirect
Biological Process (BP)protein lipidation0.0000000026170.000001216Highly InformativeDirect
Biological Process (BP)glycolipid biosynthetic process00.00000000000005443Highly InformativeDirect
Biological Process (BP)oligosaccharide biosynthetic process0.000000032670.000002097Highly InformativeDirect
Biological Process (BP)phosphatidylinositol metabolic process0.000000000029350.0000001038Highly InformativeDirect
Biological Process (BP)lipid A metabolic process0.00032280.0001061Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport0.018580.0003521Highly InformativeInherited
Biological Process (BP)glycerophospholipid biosynthetic process0.10650.02359Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.00000000000033120Least InformativeDirect
Molecular Function (MF)binding0.48871Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.0000013420Moderately InformativeDirect
Molecular Function (MF)metal ion binding0.000000033630Moderately InformativeDirect
Molecular Function (MF)carbohydrate derivative binding0.0004510.3421Moderately InformativeInherited
Molecular Function (MF)anion binding0.60321Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.000072720.2277Moderately InformativeInherited
Molecular Function (MF)phospholipid binding0.00000075530.003147InformativeInherited
Molecular Function (MF)phosphatase activity10.007001InformativeInherited
Molecular Function (MF)manganese ion binding0.00000015830.0000000005752Highly InformativeDirect
Molecular Function (MF)glycolipid binding0.0000000000000040630.000000000000001646Highly InformativeDirect
Molecular Function (MF)iron ion binding0.038680.05756Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.047261Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.26891Least InformativeInherited
Cellular Component (CC)membrane0.080511Least InformativeInherited
Cellular Component (CC)macromolecular complex0.30710.000819Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.50560.9245Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.0078440.135Moderately InformativeInherited
Cellular Component (CC)membrane protein complex0.0000043430.1897Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum-Golgi intermediate compartment0.0000000000002750.00000000002833Highly InformativeDirect
Cellular Component (CC)cis-Golgi network0.00000000000017650.000000000004031Highly 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 0.00004387 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.008234 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.00466 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.8736 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9085 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.00006875 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0004223 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.000002036 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.1883 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.8598 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.7521 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.04505 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.7282 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.9415 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.003879 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.1252 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 0.000001018 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0001542 Informative Direct
Biological Process (BP) dephosphorylation 0 Informative Direct
Biological Process (BP) cell cycle process 0.000455 Informative Direct
Biological Process (BP) cellular lipid catabolic process 0.00000007481 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.00000000000007228 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.0000001906 Informative Direct
Biological Process (BP) liposaccharide metabolic process 0.000000000001028 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.03078 Informative Inherited
Biological Process (BP) cell wall organization or biogenesis 0.02531 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.5299 Informative Inherited
Biological Process (BP) response to radiation 0.1135 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.9234 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.1343 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.003833 Informative Inherited
Biological Process (BP) glycerolipid metabolic process 0.1944 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.306 Informative Inherited
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) protein lipidation 0.000001216 Highly Informative Direct
Biological Process (BP) ceramide metabolic process 0.000000000001425 Highly Informative Direct
Biological Process (BP) RNA splicing 0.000151 Highly Informative Direct
Biological Process (BP) nucleotide catabolic process 0.0004682 Highly Informative Direct
Biological Process (BP) glycolipid biosynthetic process 0.00000000000005443 Highly Informative Direct
Biological Process (BP) oligosaccharide biosynthetic process 0.000002097 Highly Informative Direct
Biological Process (BP) phospholipid catabolic process 0.0000001184 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.000000000461 Highly Informative Direct
Biological Process (BP) response to drug 0.000000000000001945 Highly Informative Direct
Biological Process (BP) phosphatidylinositol metabolic process 0.0000001038 Highly Informative Direct
Biological Process (BP) lipid A metabolic process 0.0001061 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0003521 Highly Informative Direct
Biological Process (BP) regulation of chromosome segregation 0.006071 Highly Informative Inherited
Biological Process (BP) photoperiodism 0.001287 Highly Informative Inherited
Biological Process (BP) regulation of nuclear division 0.008657 Highly Informative Inherited
Biological Process (BP) regulation of chromosome organization 0.1174 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle 0.006693 Highly Informative Inherited
Biological Process (BP) circadian rhythm 0.07429 Highly Informative Inherited
Biological Process (BP) regulation of circadian rhythm 0.02711 Highly Informative Inherited
Biological Process (BP) glycerophospholipid biosynthetic process 0.02359 Highly Informative Inherited
Biological Process (BP) mitotic cell cycle phase transition 0.186 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 0.3421 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.2277 Moderately Informative Inherited
Molecular Function (MF) enzyme binding 0.00000004455 Informative Direct
Molecular Function (MF) protein dimerization activity 0.3184 Informative Inherited
Molecular Function (MF) phospholipid binding 0.003147 Informative Inherited
Molecular Function (MF) nuclease activity 1 Informative Inherited
Molecular Function (MF) phosphatase activity 0.007001 Informative Inherited
Molecular Function (MF) endoribonuclease activity 0.00004066 Highly Informative Direct
Molecular Function (MF) phospholipase activity 0.000000000004859 Highly Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 0.000001829 Highly Informative Direct
Molecular Function (MF) calcium ion binding 0.000327 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 0.0000000005752 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0001489 Highly Informative Direct
Molecular Function (MF) glycolipid binding 0.000000000000001646 Highly Informative Direct
Molecular Function (MF) iron ion binding 0.05756 Highly Informative Inherited
Molecular Function (MF) phosphoric diester hydrolase activity 1 Highly Informative Inherited
Cellular Component (CC) macromolecular complex 0.000819 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9245 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.135 Moderately Informative Inherited
Cellular Component (CC) membrane protein complex 0.1897 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum-Golgi intermediate compartment 0.00000000002833 Highly Informative Direct
Cellular Component (CC) cis-Golgi network 0.000000000004031 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 variant0.9498Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.3181Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.8906Moderately InformativeInherited
Worm Phenotype (WP)electrophysiology variant0.0000005539InformativeDirect
Worm Phenotype (WP)cell stress response variant0.2839InformativeInherited
Worm Phenotype (WP)mutagen induced apoptosis variant0.0005658Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.02778Highly 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 hydrolases0.00002571InformativeDirect
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 cycle0.05167Moderately InformativeInherited
Biological processMeiosis0.000000000000001439InformativeDirect
Biological processLipid biosynthesis0.0000000000005975InformativeDirect
Biological processMitosis0.000001448InformativeDirect
Biological processmRNA processing0.0003797InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processER-Golgi transport0.0000006019Highly InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentSecreted0.0003274Moderately InformativeDirect
Cellular componentVacuole0.0000007744InformativeDirect
Cellular componentChromosome0.000001115InformativeDirect
Cellular componentGPI-anchor0.000002495InformativeDirect
Cellular componentCentromere0.00000000005289Highly InformativeDirect
Cellular componentKinetochore0.00005534Highly InformativeDirect
DomainSignal0.0000000028Least InformativeDirect
DomainKelch repeat0.0003079Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0.00006271Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNickel0InformativeDirect
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 modificationCalmodulin-binding0.0000000000001194InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0.0007334Highly InformativeDirect
Post-translational modificationGlycoprotein0.000002097Least InformativeDirect
Post-translational modificationMethylation0.000004099Moderately 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 metabolism0.0000000001843Least 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 biosynthesis0.000000000000367Moderately 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 ]