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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 (3,176) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 45,950 226,536 54
Proteins 45,505 224,814 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 process0.12740.00002511Least InformativeInherited
Biological Process (BP)biosynthetic process0.24591Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.16080.9329Least InformativeInherited
Biological Process (BP)single-organism cellular process0.46661Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.23520.004556Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.28070.005487Least InformativeInherited
Biological Process (BP)cellular protein modification process0.000041450Moderately InformativeDirect
Biological Process (BP)lipid metabolic process0.0000078730.0001254Moderately InformativeDirect
Biological Process (BP)cellular localization0.00000000014250.0007647Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.000000010070.000002121Moderately InformativeDirect
Biological Process (BP)carbohydrate metabolic process0.046620.9713Moderately InformativeInherited
Biological Process (BP)anatomical structure morphogenesis0.35861Moderately InformativeInherited
Biological Process (BP)tissue development0.19831Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.000029820.171Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.026591Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process00InformativeDirect
Biological Process (BP)phospholipid metabolic process0.00000000046780.000001726InformativeDirect
Biological Process (BP)vesicle-mediated transport0.000000000064320.0002335InformativeDirect
Biological Process (BP)intracellular transport0.00000000019010.0004734InformativeDirect
Biological Process (BP)liposaccharide metabolic process0.0000000000058240.0000000000009672InformativeDirect
Biological Process (BP)epithelium development0.040781InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.00014540.03313InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.002560.2042InformativeInherited
Biological Process (BP)growth0.19760.3983InformativeInherited
Biological Process (BP)protein dephosphorylation0.0001620Highly InformativeDirect
Biological Process (BP)protein lipidation0.0000000045130.000001372Highly InformativeDirect
Biological Process (BP)glycolipid biosynthetic process00.00000000000004251Highly InformativeDirect
Biological Process (BP)oligosaccharide biosynthetic process0.000000035850.000002048Highly InformativeDirect
Biological Process (BP)phosphatidylinositol metabolic process0.000000000037680.0000001125Highly InformativeDirect
Biological Process (BP)lipid A metabolic process0.00029070.00009246Highly InformativeDirect
Biological Process (BP)morphogenesis of an epithelium0.20990.9671Highly InformativeInherited
Biological Process (BP)glycerophospholipid biosynthetic process0.11150.02231Highly InformativeInherited
Biological Process (BP)developmental growth involved in morphogenesis0.0026260.1262Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.0000000000002040Least InformativeDirect
Molecular Function (MF)binding0.37291Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.00000073280Moderately InformativeDirect
Molecular Function (MF)metal ion binding0.000000084740Moderately InformativeDirect
Molecular Function (MF)carbohydrate derivative binding0.00052010.2771Moderately InformativeInherited
Molecular Function (MF)anion binding0.54881Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.000089930.2439Moderately InformativeInherited
Molecular Function (MF)phospholipid binding0.00000074960.004046InformativeInherited
Molecular Function (MF)phosphatase activity10.002369InformativeInherited
Molecular Function (MF)manganese ion binding0.00000012380.0000000003776Highly InformativeDirect
Molecular Function (MF)glycolipid binding0.0000000000000047470.000000000000001615Highly InformativeDirect
Molecular Function (MF)iron ion binding0.034470.06336Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.046351Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.31561Least InformativeInherited
Cellular Component (CC)membrane0.08981Least InformativeInherited
Cellular Component (CC)protein complex0.036861Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.45960.9373Least InformativeInherited
Cellular Component (CC)endomembrane system0.00000000015450.06735Moderately InformativeInherited
Cellular Component (CC)membrane protein complex0.000006070.2144Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum-Golgi intermediate compartment0.00000000000030870.00000000002991Highly InformativeDirect
Cellular Component (CC)cis-Golgi network0.0000000000002210.00000000000533Highly 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 0.00002511 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9329 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.005487 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.8632 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.004556 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.0001254 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0007647 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.000002121 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.7035 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.003837 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.8328 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.9713 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.1956 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.7862 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.02516 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.171 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.07138 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 0.000001726 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.000419 Informative Direct
Biological Process (BP) lipid catabolic process 0.0000001912 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0002335 Informative Direct
Biological Process (BP) cell cycle process 0.0002468 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.000000000000114 Informative Direct
Biological Process (BP) intracellular transport 0.0004734 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.0000002915 Informative Direct
Biological Process (BP) liposaccharide metabolic process 0.0000000000009672 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00165 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.572 Informative Inherited
Biological Process (BP) response to radiation 0.1584 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.1499 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.952 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.03313 Informative Inherited
Biological Process (BP) glycerolipid metabolic process 0.2042 Informative Inherited
Biological Process (BP) growth 0.3983 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.2682 Informative Inherited
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) protein lipidation 0.000001372 Highly Informative Direct
Biological Process (BP) ceramide metabolic process 0.00000000000235 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0001906 Highly Informative Direct
Biological Process (BP) nucleotide catabolic process 0.0004585 Highly Informative Direct
Biological Process (BP) glycolipid biosynthetic process 0.00000000000004251 Highly Informative Direct
Biological Process (BP) oligosaccharide biosynthetic process 0.000002048 Highly Informative Direct
Biological Process (BP) phospholipid catabolic process 0.0000001425 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.0000000004653 Highly Informative Direct
Biological Process (BP) response to drug 0 Highly Informative Direct
Biological Process (BP) phosphatidylinositol metabolic process 0.0000001125 Highly Informative Direct
Biological Process (BP) lipid A metabolic process 0.00009246 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0003689 Highly Informative Direct
Biological Process (BP) morphogenesis of an epithelium 0.9671 Highly Informative Inherited
Biological Process (BP) regulation of circadian rhythm 0.03126 Highly Informative Inherited
Biological Process (BP) photoperiodism 0.001009 Highly Informative Inherited
Biological Process (BP) regulation of chromosome segregation 0.006376 Highly Informative Inherited
Biological Process (BP) regulation of chromosome organization 0.129 Highly Informative Inherited
Biological Process (BP) regulation of mitotic nuclear division 0.07557 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle 0.006364 Highly Informative Inherited
Biological Process (BP) circadian rhythm 0.08225 Highly Informative Inherited
Biological Process (BP) glycerophospholipid biosynthetic process 0.02231 Highly Informative Inherited
Biological Process (BP) developmental growth involved in morphogenesis 0.1262 Highly Informative Inherited
Biological Process (BP) mitotic cell cycle phase transition 0.232 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 0.2771 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 0.2439 Moderately Informative Inherited
Molecular Function (MF) enzyme binding 0.00000007459 Informative Direct
Molecular Function (MF) protein dimerization activity 0.2533 Informative Inherited
Molecular Function (MF) phospholipid binding 0.004046 Informative Inherited
Molecular Function (MF) nuclease activity 1 Informative Inherited
Molecular Function (MF) phosphatase activity 0.002369 Informative Inherited
Molecular Function (MF) endoribonuclease activity 0.00005186 Highly Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 0.000001251 Highly Informative Direct
Molecular Function (MF) calcium ion binding 0.0003367 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 0.00008483 Highly Informative Direct
Molecular Function (MF) protein phosphatase binding 0 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.0000000003776 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.00002669 Highly Informative Direct
Molecular Function (MF) glycolipid binding 0.000000000000001615 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 1 Highly Informative Inherited
Molecular Function (MF) iron ion binding 0.06336 Highly Informative Inherited
Molecular Function (MF) lipase activity 1 Highly Informative Inherited
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) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9373 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.06735 Moderately Informative Inherited
Cellular Component (CC) membrane protein complex 0.2144 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum-Golgi intermediate compartment 0.00000000002991 Highly Informative Direct
Cellular Component (CC) cis-Golgi network 0.00000000000533 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

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 cycle0.05218Moderately InformativeInherited
Biological processMeiosis0.000000000000001442InformativeDirect
Biological processLipid biosynthesis0.0000000000004713InformativeDirect
Biological processMitosis0.000001935InformativeDirect
Biological processmRNA processing0.0003786InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processER-Golgi transport0.0000005843Highly InformativeDirect
Cellular componentMembrane0.0000000131Least InformativeDirect
Cellular componentCell membrane0.0000000001023Moderately InformativeDirect
Cellular componentSecreted0.0004872Moderately InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
Cellular componentVacuole0.0000007874InformativeDirect
Cellular componentChromosome0.000001124InformativeDirect
Cellular componentGPI-anchor0.00007467InformativeDirect
Cellular componentCentromere0.00000000005401Highly InformativeDirect
Cellular componentKinetochore0.00005453Highly InformativeDirect
DomainSignal0.00000002855Least InformativeDirect
DomainKelch repeat0.0003047Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNickel0.00000000000001023InformativeDirect
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-binding0.0000000000001134InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0.0007324Highly InformativeDirect
Post-translational modificationGlycoprotein0.000001726Least InformativeDirect
Post-translational modificationMethylation0.000003624Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]