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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 (2,759) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,529 48,822 11
Proteins 11,452 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 process0.0000000000022970Least InformativeDirect
Biological Process (BP)single-organism cellular process0.00000018590.0003671Least InformativeDirect
Biological Process (BP)primary metabolic process0.0022620.04765Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.86670.2694Least InformativeInherited
Biological Process (BP)biosynthetic process0.082720.01951Least InformativeInherited
Biological Process (BP)lipid metabolic process00Moderately InformativeDirect
Biological Process (BP)carbohydrate metabolic process0.098960.03395Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative biosynthetic process0.026850.01919Moderately InformativeInherited
Biological Process (BP)organophosphate biosynthetic process0.47240.2779Moderately InformativeInherited
Biological Process (BP)reproduction0.08010.6504Moderately InformativeInherited
Biological Process (BP)multi-organism process0.10170.4505Moderately InformativeInherited
Biological Process (BP)membrane lipid metabolic process0.0000075530.000003237InformativeDirect
Biological Process (BP)phospholipid metabolic process0.00000000012820.0000000003908InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.0014420.0001999InformativeInherited
Biological Process (BP)glycerolipid metabolic process0.52271InformativeInherited
Biological Process (BP)liposaccharide metabolic process0.20630.02514InformativeInherited
Biological Process (BP)movement of cell or subcellular component0.15630.7033InformativeInherited
Biological Process (BP)multicellular organism reproduction0.0041110.1095InformativeInherited
Biological Process (BP)locomotion0.0095870.2547InformativeInherited
Biological Process (BP)single organism reproductive process0.17350.7297InformativeInherited
Biological Process (BP)multi-organism reproductive process0.0019040.06009InformativeInherited
Biological Process (BP)sphingolipid biosynthetic process0.00000000000017190.00000000001925Highly InformativeDirect
Biological Process (BP)oligosaccharide metabolic process0.0024630.00238Highly InformativeInherited
Biological Process (BP)lipid modification0.011410.1837Highly InformativeInherited
Biological Process (BP)glycolipid biosynthetic process0.044940.005493Highly InformativeInherited
Biological Process (BP)cell migration0.0012510.03562Highly 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)sugar-phosphatase activity0.0000000000000046620Highly InformativeDirect
Cellular Component (CC)membrane0.0000000009880.0000003621Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.38831Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.11180.8709Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.50090.6622Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.000000000028790.0000000002531Moderately InformativeDirect
Cellular Component (CC)endoplasmic reticulum membrane0.000010990.000003419InformativeDirect

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 0.0003671 Least Informative Direct
Biological Process (BP) primary metabolic process 0.04765 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.2694 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.01951 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.03395 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative biosynthetic process 0.01919 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.2779 Moderately Informative Inherited
Biological Process (BP) reproduction 0.6504 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4505 Moderately Informative Inherited
Biological Process (BP) membrane lipid metabolic process 0.000003237 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0000000003908 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.0001999 Informative Direct
Biological Process (BP) glycerolipid metabolic process 1 Informative Inherited
Biological Process (BP) liposaccharide metabolic process 0.02514 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.7033 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.1095 Informative Inherited
Biological Process (BP) locomotion 0.2547 Informative Inherited
Biological Process (BP) single organism reproductive process 0.7297 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.06009 Informative Inherited
Biological Process (BP) sphingolipid biosynthetic process 0.00000000001925 Highly Informative Direct
Biological Process (BP) lipid modification 0.1837 Highly Informative Inherited
Biological Process (BP) oligosaccharide metabolic process 0.00238 Highly Informative Inherited
Biological Process (BP) glycolipid biosynthetic process 0.005493 Highly Informative Inherited
Biological Process (BP) cell migration 0.03562 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) sugar-phosphatase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0.0000003621 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.8709 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.6622 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.0000000002531 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.000003419 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least 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)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus DEvelopment stage (XDE)embryonic stage0.1416Least InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage0.1918Least InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 200.00001343Highly InformativeDirect

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 anhydrides0.8176Moderately InformativeInherited
Enzyme Commission (EC)In phosphorus-containing anhydrides0.00000000000000434InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor0.00007939InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.0000000004518Moderately InformativeDirect
Biological processVirulence0.00003683Moderately InformativeDirect
Biological processAntibiotic resistance4.822e-16InformativeDirect
Biological processLipid biosynthesis0.9687InformativeInherited
Biological processGluconeogenesis0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis9.591e-16Highly InformativeDirect
Biological processLipid A biosynthesis0.00000000002312Highly InformativeDirect
Biological processSphingolipid metabolism0.00000003086Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentPeriplasm0.0002868InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationGlycoprotein0.0000000000000462Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0.0000000001072Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0.00001489Least InformativeDirect
UniPathway (UP)lipid metabolism0.00001931Least InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0.0000004666Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0.00007638Moderately InformativeDirect
UniPathway (UP)biopolymer biosynthesis0.01717Moderately InformativeInherited
UniPathway (UP)lipid biosynthesis0.134Moderately InformativeInherited
UniPathway (UP)gluconeogenesis0InformativeDirect
UniPathway (UP)protein glycosylation0.00000000000003136InformativeDirect
UniPathway (UP)lipopolysaccharide biosynthesis0.0000000009627InformativeDirect
UniPathway (UP)glycolipid biosynthesis1InformativeInherited
UniPathway (UP)LPS lipid A biosynthesis0.00000006087Highly 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) · 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) · 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 ]