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Acid phosphatase/Vanadium-dependent haloperoxidase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Acid phosphatase/Vanadium-dependent haloperoxidase [ 48316]
Superfamily:   Acid phosphatase/Vanadium-dependent haloperoxidase [ 48317] (3)
Families:   Type 2 phosphatidic acid phosphatase, PAP2 [ 48318]
  Haloperoxidase (bromoperoxidase) [ 48321]
  Chloroperoxidase [ 48325]


Superfamily statistics
Genomes (2,764) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 11,590 58,844 11
Proteins 11,512 58,534 11


Functional annotation
General category Metabolism
Detailed category Redox

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 process0.00000000000021520Least InformativeDirect
Biological Process (BP)single-organism cellular process0.000000064750.00001247Least InformativeDirect
Biological Process (BP)response to stimulus0.56861Least InformativeInherited
Biological Process (BP)primary metabolic process0.0039540.07811Least InformativeInherited
Biological Process (BP)biosynthetic process0.031890.008076Least InformativeInherited
Biological Process (BP)multicellular organismal process0.54831Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)lipid metabolic process00Moderately InformativeDirect
Biological Process (BP)carbohydrate metabolic process0.028630.007949Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.022420.002837Moderately InformativeInherited
Biological Process (BP)cellular response to chemical stimulus0.5780.6784Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.85630.67Moderately InformativeInherited
Biological Process (BP)response to external stimulus0.0078670.08495Moderately InformativeInherited
Biological Process (BP)reproduction0.038950.4927Moderately InformativeInherited
Biological Process (BP)cell differentiation0.030380.8951Moderately InformativeInherited
Biological Process (BP)organophosphate biosynthetic process0.55620.3606Moderately InformativeInherited
Biological Process (BP)multi-organism process0.095520.4309Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process0.000014840.000005664InformativeDirect
Biological Process (BP)phospholipid metabolic process0.00000000028050.000000001191InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.00020450.00001681InformativeDirect
Biological Process (BP)cell death0.013410.07114InformativeInherited
Biological Process (BP)single organism reproductive process0.051760.4339InformativeInherited
Biological Process (BP)developmental process involved in reproduction0.011730.181InformativeInherited
Biological Process (BP)localization of cell0.0023270.02966InformativeInherited
Biological Process (BP)movement of cell or subcellular component0.23210.7661InformativeInherited
Biological Process (BP)multicellular organism reproduction0.0010960.05602InformativeInherited
Biological Process (BP)cell development0.075760.7805InformativeInherited
Biological Process (BP)liposaccharide metabolic process0.19370.02576InformativeInherited
Biological Process (BP)locomotion0.0094410.1856InformativeInherited
Biological Process (BP)multi-organism reproductive process0.0027530.05932InformativeInherited
Biological Process (BP)monosaccharide metabolic process0.0014170.001168InformativeInherited
Biological Process (BP)glucose metabolic process0.000011990.000005836Highly InformativeDirect
Biological Process (BP)programmed cell death involved in cell development0.00000011680.0000004713Highly InformativeDirect
Biological Process (BP)hexose biosynthetic process0.0000015510.0000001964Highly InformativeDirect
Biological Process (BP)sphingolipid biosynthetic process0.0000000000013610.0000000000658Highly InformativeDirect
Biological Process (BP)cell chemotaxis0.0000087960.00001384Highly InformativeDirect
Biological Process (BP)oligosaccharide biosynthetic process0.028080.007354Highly InformativeInherited
Biological Process (BP)lipid modification0.011670.1887Highly InformativeInherited
Biological Process (BP)glycolipid biosynthetic process0.053320.006494Highly InformativeInherited
Biological Process (BP)lipid A metabolic process0.027840.0007245Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)phosphatase activity00InformativeDirect
Molecular Function (MF)sugar-phosphatase activity0.0000000000000060550Highly InformativeDirect
Cellular Component (CC)membrane0.000000000025340.00000002967Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.094670.8548Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.6630.8588Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.2360.9605Least InformativeInherited
Cellular Component (CC)endomembrane system0.00000008920.000002059Moderately InformativeDirect
Cellular Component (CC)endoplasmic reticulum membrane0.000019160.00000882InformativeDirect

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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00001247 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.07811 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.008076 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.007949 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.6784 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.002837 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.67 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.08495 Moderately Informative Inherited
Biological Process (BP) reproduction 0.4927 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.8951 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.3606 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4309 Moderately Informative Inherited
Biological Process (BP) membrane lipid metabolic process 0.000005664 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.000000001191 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00001681 Informative Direct
Biological Process (BP) liposaccharide metabolic process 0.02576 Informative Inherited
Biological Process (BP) cell death 0.07114 Informative Inherited
Biological Process (BP) single organism reproductive process 0.4339 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.181 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.05602 Informative Inherited
Biological Process (BP) cell development 0.7805 Informative Inherited
Biological Process (BP) localization of cell 0.02966 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.7661 Informative Inherited
Biological Process (BP) locomotion 0.1856 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.05932 Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.001168 Informative Inherited
Biological Process (BP) glucose metabolic process 0.000005836 Highly Informative Direct
Biological Process (BP) programmed cell death involved in cell development 0.0000004713 Highly Informative Direct
Biological Process (BP) hexose biosynthetic process 0.0000001964 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.0000000000658 Highly Informative Direct
Biological Process (BP) lipid A metabolic process 0.0007245 Highly Informative Direct
Biological Process (BP) cell chemotaxis 0.00001384 Highly Informative Direct
Biological Process (BP) oligosaccharide biosynthetic process 0.007354 Highly Informative Inherited
Biological Process (BP) lipid modification 0.1887 Highly Informative Inherited
Biological Process (BP) glycolipid biosynthetic process 0.006494 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) phosphatase activity 0 Informative Direct
Molecular Function (MF) sugar-phosphatase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0.00000002967 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8548 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.8588 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9605 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.000002059 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.00000882 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 ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides1Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0.000000000001906Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.0000000004456Moderately InformativeDirect
Biological processVirulence0.00004117Moderately InformativeDirect
Biological processAntibiotic resistance7.259e-16InformativeDirect
Biological processLipid biosynthesis0.9639InformativeInherited
Biological processGluconeogenesis0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis9.645e-16Highly InformativeDirect
Biological processLipid A biosynthesis0.00000000002192Highly InformativeDirect
Biological processSphingolipid metabolism0.00000003371Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentPeriplasm0.0002794InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationGlycoprotein0.00000000000004687Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000326 SSF48317 Protein matches
Abstract

This entry represents type 2 phosphatidic acid phosphatase (PAP2) enzymes, such as phosphatidylglycerophosphatase B from Escherichia coli. PAP2 enzymes have a core structure consisting of a 5-helical bundle, where the beginning of the third helix binds the cofactor [PubMed10835340]. PAP2 enzymes catalyse the dephosphorylation of phosphatidate, yielding diacylglycerol and inorganic phosphate. In eukaryotic cells, PAP activity has a central role in the synthesis of phospholipids and triacylglycerol through its product diacylglycerol, and it also generates and/or degrades lipid-signaling molecules that are related to phosphatidate.

Other related enzymes have a similar core structure, including haloperoxidases such as bromoperoxidase (contains one core bundle, but forms a dimer), chloroperoxidases (contains two core bundles arranged as in other family dimers), bacitracin transport permease from Bacillus licheniformis, glucose-6-phosphatase from rat. The vanadium-dependent haloperoxidases exclusively catalyse the oxidation of halides, and act as histidine phosphatases, using histidine for the nucleophilic attack in the first step of the reaction [PubMed12447906]. Amino acid residues involved in binding phosphate/vanadate are conserved between the two families, supporting a proposal that vanadium passes through a tetrahedral intermediate during the reaction mechanism.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-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 5 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 Acid phosphatase/Vanadium-dependent haloperoxidase 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 5 hidden Markov models representing the Acid phosphatase/Vanadium-dependent haloperoxidase superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


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