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 (2,749) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,344 48,822 11
Proteins 11,268 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)biosynthetic process0.60490.478Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.020150.0002904Least InformativeInherited
Biological Process (BP)multicellular organismal process11Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)localization0.68651Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)lipid biosynthetic process0.000030240.000008638Moderately InformativeDirect
Biological Process (BP)cellular lipid metabolic process00Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.069560.01743Moderately InformativeInherited
Biological Process (BP)reproduction0.17850.9785Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.0029970.00321Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process0.000030150.000003599InformativeDirect
Biological Process (BP)phospholipid metabolic process0.00010780.0005821InformativeDirect
Biological Process (BP)dephosphorylation00InformativeDirect
Biological Process (BP)cellular component movement0.0075940.3289InformativeInherited
Biological Process (BP)sexual reproduction0.0035480.1076InformativeInherited
Biological Process (BP)locomotion0.0042750.3555InformativeInherited
Biological Process (BP)single organism reproductive process0.0044380.1603InformativeInherited
Biological Process (BP)multicellular organismal reproductive process0.010840.1221InformativeInherited
Biological Process (BP)cellular process involved in reproduction0.012420.2064InformativeInherited
Biological Process (BP)localization of cell0.00075330.04778InformativeInherited
Biological Process (BP)sphingolipid biosynthetic process0.0000000000000017070.0000000000009291Highly InformativeDirect
Biological Process (BP)cellular process involved in reproduction in multicellular organism0.000018110.003938Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)phosphoric ester hydrolase activity00InformativeDirect
Molecular Function (MF)transferase activity, transferring glycosyl groups0.011860.002368InformativeInherited
Molecular Function (MF)transferase activity, transferring hexosyl groups0.0025340.0004908Highly InformativeInherited
Cellular Component (CC)intracellular organelle part0.20870.9676Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.45681Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.61130.7539Least InformativeInherited
Cellular Component (CC)membrane0.000040960.002943Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.00000000000069340.000000000007885Moderately InformativeDirect
Cellular Component (CC)endomembrane system0.000000081390.000000479Moderately InformativeDirect
Cellular Component (CC)organelle membrane0.00061610.0002203Moderately InformativeDirect
Cellular Component (CC)intrinsic to membrane0.029620.2122Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane0.000000072670.000000006835InformativeDirect
Cellular Component (CC)intrinsic to organelle membrane0.0000096740.00005861Highly 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 0.0002904 Least Informative Direct
Biological Process (BP) biosynthetic process 0.478 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 0.000008638 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.01743 Moderately Informative Inherited
Biological Process (BP) reproduction 0.9785 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.00321 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.0152 Moderately Informative Inherited
Biological Process (BP) membrane lipid metabolic process 0.000003599 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0005821 Informative Direct
Biological Process (BP) dephosphorylation 0 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.05869 Informative Inherited
Biological Process (BP) cellular component movement 0.3289 Informative Inherited
Biological Process (BP) sexual reproduction 0.1076 Informative Inherited
Biological Process (BP) locomotion 0.3555 Informative Inherited
Biological Process (BP) single organism reproductive process 0.1603 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.1221 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.2064 Informative Inherited
Biological Process (BP) localization of cell 0.04778 Informative Inherited
Biological Process (BP) hexose metabolic process 0.003816 Informative Inherited
Biological Process (BP) sphingolipid biosynthetic process 0.0000000000009291 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.00001312 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.003938 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) phosphoric ester hydrolase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring glycosyl groups 0.002368 Informative Inherited
Molecular Function (MF) transferase activity, transferring hexosyl groups 0.0004908 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.9676 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7539 Least Informative Inherited
Cellular Component (CC) membrane 0.002943 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.000000000007885 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.000000479 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.0002203 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.2122 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.000000006835 Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 0.00005861 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 homeostasis0.04815Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.004595Moderately 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 anhydrides0.8605Moderately InformativeInherited
Enzyme Commission (EC)In phosphorous-containing anhydrides0.00000000000000379InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor0.00007722InformativeDirect
Enzyme Commission (EC)Peroxidases0.00007471Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.004731Moderately InformativeInherited
Biological processGluconeogenesis0Highly InformativeDirect
Biological processSphingolipid metabolism0.00000000000427Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationGlycoprotein0.00000000000000528Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism0.0000000164Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.0009173Least InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0Moderately InformativeDirect
UniPathway (UP)gluconeogenesis0InformativeDirect
UniPathway (UP)protein glycosylation0InformativeDirect

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 ]