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 (2,758) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,537 48,822 11
Proteins 11,460 48,729 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 process0.000031730.00000001709Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.58590.4502Least InformativeInherited
Biological Process (BP)multicellular organismal process11Least InformativeInherited
Biological Process (BP)localization0.70031Least InformativeInherited
Biological Process (BP)single-organism cellular process0.13070.4058Least InformativeInherited
Biological Process (BP)lipid metabolic process00Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.071690.01778Moderately InformativeInherited
Biological Process (BP)reproductive process0.082350.8176Moderately InformativeInherited
Biological Process (BP)multi-organism process0.47981Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.0051020.004142Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process0.000035940.000003229InformativeDirect
Biological Process (BP)phospholipid metabolic process0.000047540.0002974InformativeDirect
Biological Process (BP)dephosphorylation00InformativeDirect
Biological Process (BP)cellular component movement0.053070.4979InformativeInherited
Biological Process (BP)sexual reproduction0.029030.1257InformativeInherited
Biological Process (BP)cellular process involved in reproduction in multicellular organism0.00037350.01642InformativeInherited
Biological Process (BP)locomotion0.0036650.3367InformativeInherited
Biological Process (BP)single organism reproductive process0.11550.615InformativeInherited
Biological Process (BP)multicellular organismal reproductive process0.0064450.1023InformativeInherited
Biological Process (BP)localization of cell0.0005860.04457InformativeInherited
Biological Process (BP)germ cell migration0.000000000069960.0000000002031Highly InformativeDirect
Biological Process (BP)sphingolipid biosynthetic process00.0000000000006378Highly InformativeDirect
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)transferase activity11Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)phosphatase activity00InformativeDirect
Molecular Function (MF)transferase activity, transferring glycosyl groups0.012390.002348InformativeInherited
Molecular Function (MF)transferase activity, transferring hexosyl groups0.0025480.0004684Highly InformativeInherited
Cellular Component (CC)intracellular organelle part0.16870.8874Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.52480.7136Least InformativeInherited
Cellular Component (CC)membrane0.000054960.003016Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.30981Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.00000000000047160.000000000005106Moderately InformativeDirect
Cellular Component (CC)bounding membrane of organelle0.00000025750.000001837Moderately InformativeDirect
Cellular Component (CC)intrinsic component of membrane0.03530.1892Moderately InformativeInherited
Cellular Component (CC)membrane region0.00063110.001144Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane0.000000075350.000000005603InformativeDirect
Cellular Component (CC)integral component of membrane0.017230.1091InformativeInherited
Cellular Component (CC)integral component of organelle membrane0.0000052430.00003446Highly 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 0.00000001709 Least Informative Direct
Biological Process (BP) biosynthetic process 0.4502 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) localization 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.4058 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.01778 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.01454 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.8176 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.004142 Moderately Informative Inherited
Biological Process (BP) membrane lipid metabolic process 0.000003229 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0002974 Informative Direct
Biological Process (BP) dephosphorylation 0 Informative Direct
Biological Process (BP) hexose metabolic process 0.001642 Informative Inherited
Biological Process (BP) cellular component movement 0.4979 Informative Inherited
Biological Process (BP) sexual reproduction 0.1257 Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.01642 Informative Inherited
Biological Process (BP) locomotion 0.3367 Informative Inherited
Biological Process (BP) single organism reproductive process 0.615 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.1023 Informative Inherited
Biological Process (BP) localization of cell 0.04457 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.04912 Informative Inherited
Biological Process (BP) glucose metabolic process 0.0006697 Highly Informative Direct
Biological Process (BP) germ cell migration 0.0000000002031 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.0000000000006378 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.00001158 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
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 0.002348 Informative Inherited
Molecular Function (MF) transferase activity, transferring hexosyl groups 0.0004684 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.8874 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7136 Least Informative Inherited
Cellular Component (CC) membrane 0.003016 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.000000000005106 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.000001837 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.1892 Moderately Informative Inherited
Cellular Component (CC) membrane region 0.001144 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.000000005603 Informative Direct
Cellular Component (CC) integral component of membrane 0.1091 Informative Inherited
Cellular Component (CC) integral component of organelle membrane 0.00003446 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 anhydrides0.000000000001906Moderately InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.04876Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.004555Moderately 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 anhydrides0.8504Moderately InformativeInherited
Enzyme Commission (EC)In phosphorous-containing anhydrides0.000000000000003574InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor0.00007816InformativeDirect
Enzyme Commission (EC)Peroxidases0.00007566Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.005093Moderately InformativeInherited
Biological processGluconeogenesis0Highly InformativeDirect
Biological processSphingolipid metabolism0.000000000004518Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationGlycoprotein0.000000000000005297Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism0.00000003312Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.00126Least InformativeInherited
UniPathway (UP)carbohydrate biosynthesis0Moderately InformativeDirect
UniPathway (UP)gluconeogenesis0InformativeDirect
UniPathway (UP)protein glycosylation2.278e-16InformativeDirect

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 ]