SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,712) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 11,008 22,725 11
Proteins 10,946 22,658 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)biosynthetic process0.58850.4715Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.02160.0003268Least InformativeInherited
Biological Process (BP)multicellular organismal process11Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)localization0.64411Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)lipid biosynthetic process3.274e-051.025e-05Moderately InformativeDirect
Biological Process (BP)cellular lipid metabolic process00Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.068840.01774Moderately InformativeInherited
Biological Process (BP)reproduction0.16290.9591Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.0029280.003206Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process2.438e-053.056e-06InformativeDirect
Biological Process (BP)phospholipid metabolic process0.00010560.0006814InformativeDirect
Biological Process (BP)dephosphorylation00InformativeDirect
Biological Process (BP)cellular component movement0.0062880.2945InformativeInherited
Biological Process (BP)sexual reproduction0.0036040.09813InformativeInherited
Biological Process (BP)locomotion0.0032950.3201InformativeInherited
Biological Process (BP)single organism reproductive process0.0036580.1434InformativeInherited
Biological Process (BP)multicellular organismal reproductive process0.0110.1098InformativeInherited
Biological Process (BP)cellular process involved in reproduction0.012760.2078InformativeInherited
Biological Process (BP)localization of cell0.00066730.04122InformativeInherited
Biological Process (BP)sphingolipid biosynthetic process07.738e-13Highly InformativeDirect
Biological Process (BP)cellular process involved in reproduction in multicellular organism1.429e-050.00331Highly 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)transferase activity, transferring glycosyl groups0.010130.002198InformativeInherited
Molecular Function (MF)transferase activity, transferring hexosyl groups0.0020550.0004536Highly InformativeInherited
Cellular Component (CC)membrane1.37e-050.0009239Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.11540.7962Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.27361Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.50130.6626Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum3.34e-133.877e-12Moderately InformativeDirect
Cellular Component (CC)endomembrane system3.798e-082.171e-07Moderately InformativeDirect
Cellular Component (CC)organelle membrane0.00087230.0001409Moderately InformativeDirect
Cellular Component (CC)intrinsic to membrane0.026180.2097Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane6.8e-086.436e-09InformativeDirect
Cellular Component (CC)intrinsic to organelle membrane1.402e-055.056e-05Highly 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) single-organism metabolic process 0.0003268 Least Informative Direct
Biological Process (BP) biosynthetic process 0.4715 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) lipid biosynthetic process 1.025e-05 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.01774 Moderately Informative Inherited
Biological Process (BP) reproduction 0.9591 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.003206 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.01556 Moderately Informative Inherited
Biological Process (BP) membrane lipid metabolic process 3.056e-06 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0006814 Informative Direct
Biological Process (BP) dephosphorylation 0 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.06143 Informative Inherited
Biological Process (BP) cellular component movement 0.2945 Informative Inherited
Biological Process (BP) sexual reproduction 0.09813 Informative Inherited
Biological Process (BP) locomotion 0.3201 Informative Inherited
Biological Process (BP) single organism reproductive process 0.1434 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.1098 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.2078 Informative Inherited
Biological Process (BP) localization of cell 0.04122 Informative Inherited
Biological Process (BP) hexose metabolic process 0.003639 Informative Inherited
Biological Process (BP) sphingolipid biosynthetic process 7.738e-13 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 1.206e-05 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.00331 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) transferase activity, transferring glycosyl groups 0.002198 Informative Inherited
Molecular Function (MF) transferase activity, transferring hexosyl groups 0.0004536 Highly Informative Direct
Cellular Component (CC) membrane 0.0009239 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.7962 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.6626 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 3.877e-12 Moderately Informative Direct
Cellular Component (CC) endomembrane system 2.171e-07 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.0001409 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.2097 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 6.436e-09 Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 5.056e-05 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 ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides1Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides1.906e-12Moderately InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.04679Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.004612Moderately InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) 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)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.8565Moderately InformativeInherited
Enzyme Commission (EC)In phosphorous-containing anhydrides4.263e-15InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor8.294e-05InformativeDirect
Enzyme Commission (EC)Peroxidases8.029e-05Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.005036Moderately InformativeInherited
Biological processGluconeogenesis0Highly InformativeDirect
Biological processSphingolipid metabolism3.958e-12Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationGlycoprotein5.294e-15Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism1.441e-08Least InformativeDirect
UniPathway (UP)biopolymer metabolism1.403e-05Least InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0InformativeDirect
UniPathway (UP)protein glycosylation6.498e-15InformativeDirect
UniPathway (UP)gluconeogenesis0Highly InformativeDirect

Document: UP 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · 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 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]