SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,126) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 43,073 85,034 54
Proteins 42,698 84,316 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)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)protein metabolic process0.0052178.443e-05Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.019120.4587Least InformativeInherited
Biological Process (BP)localization0.056131Least InformativeInherited
Biological Process (BP)single-organism cellular process0.42911Least InformativeInherited
Biological Process (BP)biosynthetic process0.95561Least InformativeInherited
Biological Process (BP)single-organism metabolic process11Least InformativeInherited
Biological Process (BP)lipid biosynthetic process0.00011395.982e-06Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.84051Moderately InformativeInherited
Biological Process (BP)cellular localization1.275e-070.01877Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process8.743e-080.01598Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.0019240.2654Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.012180.6004Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.01120.9081Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.048591Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.083071.252e-09Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process3.07e-120InformativeDirect
Biological Process (BP)vesicle-mediated transport8.17e-060.0005389InformativeDirect
Biological Process (BP)dephosphorylation0.00026890InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis0.01182.79e-11InformativeInherited
Biological Process (BP)cytoplasmic transport0.0094250.00137InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.00061390.05674InformativeInherited
Biological Process (BP)phospholipid metabolic process7.958e-060.3511InformativeInherited
Biological Process (BP)glycolipid biosynthetic process2.133e-126.326e-12Highly InformativeDirect
Biological Process (BP)lipoprotein metabolic process5.95e-081.186e-07Highly InformativeDirect
Biological Process (BP)phosphatidylinositol metabolic process1.183e-095.865e-06Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport2.322e-113.745e-08Highly InformativeDirect
Biological Process (BP)RNA phosphodiester bond hydrolysis, endonucleolytic9.039e-050Highly InformativeDirect
Biological Process (BP)glycerophospholipid biosynthetic process0.013740.0003468Highly InformativeInherited
Molecular Function (MF)hydrolase activity2.981e-100Least InformativeDirect
Molecular Function (MF)binding0.69721Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds3.716e-110Moderately InformativeDirect
Molecular Function (MF)cation binding1.563e-070Moderately InformativeDirect
Molecular Function (MF)anion binding0.61711Moderately InformativeInherited
Molecular Function (MF)lipid binding1.786e-050.03563InformativeInherited
Molecular Function (MF)transition metal ion binding3.755e-111InformativeInherited
Molecular Function (MF)nuclease activity0.84471InformativeInherited
Molecular Function (MF)phosphatase activity10.002617InformativeInherited
Molecular Function (MF)endoribonuclease activity4.486e-054.277e-07Highly InformativeDirect
Molecular Function (MF)endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo3.374e-061.055e-06Highly InformativeDirect
Molecular Function (MF)manganese ion binding4.858e-068.65e-10Highly InformativeDirect
Molecular Function (MF)phosphatidylinositol binding2.647e-111.432e-05Highly InformativeDirect
Molecular Function (MF)glycolipid binding2.5e-139.294e-14Highly InformativeDirect
Molecular Function (MF)iron ion binding0.045070.01355Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.50191Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.76841Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.82891Least InformativeInherited
Cellular Component (CC)protein complex0.40354.073e-08Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.0016120.1249Moderately InformativeInherited
Cellular Component (CC)cis-Golgi network5.272e-151.959e-14Highly InformativeDirect
Cellular Component (CC)protein serine/threonine phosphatase complex3.099e-050Highly 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) protein metabolic process 8.443e-05 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.4587 Least Informative Inherited
Biological Process (BP) response to stimulus 0.972 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 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) 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 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 1.252e-09 Moderately Informative Direct
Biological Process (BP) lipid biosynthetic process 5.982e-06 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.01877 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.01395 Moderately Informative Inherited
Biological Process (BP) reproduction 0.4695 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.758 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.8331 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.6727 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.2654 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.6004 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.01598 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.9081 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.01107 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.002738 Moderately Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 5.567e-05 Informative Direct
Biological Process (BP) membrane lipid metabolic process 0 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0005389 Informative Direct
Biological Process (BP) dephosphorylation 0 Informative Direct
Biological Process (BP) cell cycle process 1.022e-06 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 2.79e-11 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0.08917 Informative Inherited
Biological Process (BP) locomotion 1 Informative Inherited
Biological Process (BP) single-organism behavior 0.1518 Informative Inherited
Biological Process (BP) response to nutrient levels 0.1305 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.01005 Informative Inherited
Biological Process (BP) lipid catabolic process 0.007787 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.09352 Informative Inherited
Biological Process (BP) RNA processing 0.04839 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.00137 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.04838 Informative Inherited
Biological Process (BP) cellular amide metabolic process 0.005429 Informative Inherited
Biological Process (BP) phospholipid metabolic process 0.3511 Informative Inherited
Biological Process (BP) glycerolipid metabolic process 0.05674 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.8504 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.283 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.3235 Informative Inherited
Biological Process (BP) regulation of immune response 0.7513 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.2284 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.07335 Informative Inherited
Biological Process (BP) leukocyte homeostasis 0.0006347 Highly Informative Direct
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) meiosis 0.0001877 Highly Informative Direct
Biological Process (BP) RNA splicing 2.266e-05 Highly Informative Direct
Biological Process (BP) glycolipid biosynthetic process 6.326e-12 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 5.794e-07 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 1.186e-07 Highly Informative Direct
Biological Process (BP) ethanolamine-containing compound metabolic process 1.427e-08 Highly Informative Direct
Biological Process (BP) response to drug 0 Highly Informative Direct
Biological Process (BP) alcohol catabolic process 1.322e-05 Highly Informative Direct
Biological Process (BP) glycerophospholipid biosynthetic process 0.0003468 Highly Informative Direct
Biological Process (BP) phosphatidylinositol metabolic process 5.865e-06 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 3.745e-08 Highly Informative Direct
Biological Process (BP) RNA phosphodiester bond hydrolysis, endonucleolytic 0 Highly Informative Direct
Biological Process (BP) ceramide metabolic process 0.001356 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.3167 Highly Informative Inherited
Biological Process (BP) external encapsulating structure organization 0.002352 Highly Informative Inherited
Biological Process (BP) cellular response to starvation 0.1194 Highly Informative Inherited
Biological Process (BP) energy reserve metabolic process 0.002019 Highly Informative Inherited
Biological Process (BP) regulation of cell killing 0.001179 Highly Informative Inherited
Biological Process (BP) negative regulation of immune system process 0.1312 Highly Informative Inherited
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 0.006148 Highly Informative Inherited
Biological Process (BP) regulation of lymphocyte mediated immunity 0.008298 Highly Informative Inherited
Biological Process (BP) cell cycle phase 0.00418 Highly Informative Inherited
Biological Process (BP) mitotic cell cycle phase transition 0.05509 Highly Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.1873 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) cation binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) enzyme binding 5.417e-10 Informative Direct
Molecular Function (MF) lipid binding 0.03563 Informative Inherited
Molecular Function (MF) transition metal ion binding 1 Informative Inherited
Molecular Function (MF) phosphatase activity 0.002617 Informative Inherited
Molecular Function (MF) nuclease activity 1 Informative Inherited
Molecular Function (MF) endoribonuclease activity 4.277e-07 Highly Informative Direct
Molecular Function (MF) phospholipase activity 7.574e-09 Highly Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 2.233e-06 Highly Informative Direct
Molecular Function (MF) calcium ion binding 1.063e-08 Highly Informative Direct
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo 1.055e-06 Highly Informative Direct
Molecular Function (MF) manganese ion binding 8.65e-10 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 1.432e-05 Highly Informative Direct
Molecular Function (MF) glycolipid binding 9.294e-14 Highly Informative Direct
Molecular Function (MF) iron ion binding 0.01355 Highly Informative Inherited
Molecular Function (MF) phosphoric diester hydrolase activity 1 Highly Informative Inherited
Cellular Component (CC) protein complex 4.073e-08 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.1249 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.9835 Moderately Informative Inherited
Cellular Component (CC) cis-Golgi network 1.959e-14 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 hydrolases5.707e-05Moderately InformativeDirect
Enzyme Commission (EC)Phosphoprotein phosphatase0InformativeDirect
Enzyme Commission (EC)3',5'-cyclic-nucleotide phosphodiesterase2.986e-12Highly InformativeDirect
Enzyme Commission (EC)Acid phosphatase1.228e-08Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details) Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.4837Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant1Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.09125Moderately InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.3017Moderately InformativeInherited
Worm Phenotype (WP)cell death variant0.3847Moderately InformativeInherited
Worm Phenotype (WP)electrophysiology variant9.147e-08InformativeDirect
Worm Phenotype (WP)cell stress response variant0.2254InformativeInherited
Worm Phenotype (WP)protein expression variant0.3253InformativeInherited
Worm Phenotype (WP)genotoxic induced apoptosis variant7.183e-06Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.0004906Highly InformativeDirect
Worm Phenotype (WP)cell ionizing radiation response variant0.0006182Highly InformativeDirect
Worm Phenotype (WP)antibody staining variant0.0006806Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)sleep defective0.0002272Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)fruit1.005e-11InformativeDirect

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 phosphorous-containing anhydrides0InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases8.528e-05InformativeDirect
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 cycle0.04708Moderately InformativeInherited
Biological processMeiosis1.166e-15InformativeDirect
Biological processLipid biosynthesis9.015e-14InformativeDirect
Biological processMitosis8.566e-07InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processER-Golgi transport5.515e-07Highly InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentSecreted0.0005543Moderately InformativeDirect
Cellular componentVacuole2.074e-07InformativeDirect
Cellular componentGPI-anchor5.833e-05InformativeDirect
Cellular componentLysosome0.0009373InformativeDirect
Cellular componentChromosome0.0009718InformativeDirect
Cellular componentCentromere1.249e-11Highly InformativeDirect
Cellular componentKinetochore2.418e-05Highly InformativeDirect
DomainSignal1.637e-09Least InformativeDirect
DomainKelch repeat0.0002906Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNickel0InformativeDirect
Molecular functionCalmodulin-binding3.885e-15InformativeDirect
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 polymerase0.0006694InformativeDirect
Post-translational modificationGlycoprotein3.068e-07Least InformativeDirect
Post-translational modificationMethylation4.765e-05Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)membrane lipid metabolism0.2532Moderately InformativeInherited
UniPathway (UP)carbohydrate biosynthesis0InformativeDirect
UniPathway (UP)gluconeogenesis0Highly 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 Phenotype (FP) · Fly Anatomy (FA) · 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 Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]