SUPERFAMILY 1.75 HMM library and genome assignments server


PX domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   PX domain [ 64267]
Superfamily:   PX domain [ 64268]
Families:   PX domain [ 64269] (5)


Superfamily statistics
Genomes (445) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 9,691 9,537 8
Proteins 9,618 9,464 8


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Cellular Component (CC)intracellular membrane-bounded organelle0.078530.5525Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.30151.922e-11Least InformativeInherited
Cellular Component (CC)endosome6.94e-090InformativeDirect

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) localization 2.912e-13 Least Informative Direct
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.07487 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9899 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.714 Least Informative Inherited
Biological Process (BP) cellular localization 3.435e-12 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0.0001031 Moderately Informative Direct
Biological Process (BP) immune system process 0.7877 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2821 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.7328 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.005961 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.1632 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.4704 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.01596 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.435 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.00947 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.3592 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.8503 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.5401 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.02264 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.6794 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) protein transport 2.155e-10 Informative Direct
Biological Process (BP) phospholipid metabolic process 7.363e-08 Informative Direct
Biological Process (BP) cellular membrane organization 1.541e-05 Informative Direct
Biological Process (BP) glycerolipid metabolic process 0.0001953 Informative Direct
Biological Process (BP) positive regulation of transport 0.000531 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.0006037 Informative Direct
Biological Process (BP) protein localization to organelle 1 Informative Inherited
Biological Process (BP) response to other organism 0.4691 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.05871 Informative Inherited
Biological Process (BP) cytoplasmic transport 1 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 0.158 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.008551 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.003214 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.6305 Informative Inherited
Biological Process (BP) response to light stimulus 0.3237 Informative Inherited
Biological Process (BP) response to external stimulus 0.9055 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.2995 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2729 Informative Inherited
Biological Process (BP) response to wounding 0.2227 Informative Inherited
Biological Process (BP) regulation of system process 0.00473 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.5508 Informative Inherited
Biological Process (BP) defense response 0.09668 Informative Inherited
Biological Process (BP) immune effector process 0.02161 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.3154 Informative Inherited
Biological Process (BP) endosomal transport 0 Highly Informative Direct
Biological Process (BP) defense response to Gram-positive bacterium 2.597e-10 Highly Informative Direct
Biological Process (BP) vesicle organization 4.335e-08 Highly Informative Direct
Biological Process (BP) organelle fusion 1.935e-07 Highly Informative Direct
Biological Process (BP) superoxide metabolic process 6.297e-07 Highly Informative Direct
Biological Process (BP) regulation of purine nucleotide catabolic process 5.05e-06 Highly Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 7.618e-06 Highly Informative Direct
Biological Process (BP) phototransduction 1.333e-05 Highly Informative Direct
Biological Process (BP) organelle assembly 3.424e-05 Highly Informative Direct
Biological Process (BP) regulation of muscle contraction 3.515e-05 Highly Informative Direct
Biological Process (BP) unsaturated fatty acid metabolic process 4.894e-05 Highly Informative Direct
Biological Process (BP) glycerophospholipid biosynthetic process 8.767e-05 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0.0001862 Highly Informative Direct
Biological Process (BP) response to fungus 0.0002252 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism 0.0002269 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0002813 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.0008803 Highly Informative Direct
Biological Process (BP) inflammatory response 0.0009123 Highly Informative Direct
Biological Process (BP) phagocytosis 0.004653 Highly Informative Inherited
Biological Process (BP) cellular membrane fusion 0.005815 Highly Informative Inherited
Biological Process (BP) hydrogen peroxide metabolic process 1 Highly Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.03321 Highly Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.00698 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.073 Highly Informative Inherited
Biological Process (BP) leukocyte mediated immunity 0.005192 Highly Informative Inherited
Biological Process (BP) gastrulation 0.001126 Highly Informative Inherited
Molecular Function (MF) binding 1.89e-05 Least Informative Direct
Molecular Function (MF) transferase activity 0.7813 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) anion binding 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.02471 Moderately Informative Inherited
Molecular Function (MF) protein binding 0.5429 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.09894 Moderately Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.1035 Moderately Informative Inherited
Molecular Function (MF) lipid binding 0 Informative Direct
Molecular Function (MF) enzyme activator activity 0.0007592 Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 0.0008058 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.009052 Informative Inherited
Molecular Function (MF) kinase activity 0.004464 Informative Inherited
Molecular Function (MF) enzyme binding 0.1536 Informative Inherited
Molecular Function (MF) phospholipase activity 1.146e-11 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 5.41e-11 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 6.885e-10 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1.922e-11 Least Informative Direct
Cellular Component (CC) membrane 5.714e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.9341 Least Informative Inherited
Cellular Component (CC) protein complex 0.2866 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.5525 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) organelle membrane 3.129e-15 Moderately Informative Direct
Cellular Component (CC) vesicle 2.931e-13 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.0009581 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 1 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 0.8784 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.145 Moderately Informative Inherited
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 0.7522 Informative Inherited
Cellular Component (CC) integral to membrane 1 Informative Inherited
Cellular Component (CC) actin cytoskeleton 0.2656 Informative Inherited
Cellular Component (CC) endosomal part 0 Highly Informative Direct
Cellular Component (CC) internal side of plasma membrane 2.321e-06 Highly Informative Direct
Cellular Component (CC) extrinsic to plasma membrane 5.972e-05 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 0.5862 Highly Informative Inherited

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 bonds5.668e-07Least InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases9.895e-05Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0.008197Moderately InformativeInherited
Enzyme Commission (EC)Phosphatidylinositol-4-phosphate 3-kinase0Highly InformativeDirect
Enzyme Commission (EC)Phospholipase D0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of head and neck0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the integument0.1086Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdomen0.1097Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.1507Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mouth0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skull0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.03111Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.03328Moderately InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.04228Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.06307Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the oral cavity0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of facial skeleton0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the lymph nodes3.588e-05InformativeDirect
Phenotypic Abnormality (PA)Respiratory tract infection0.0008869InformativeDirect
Phenotypic Abnormality (PA)Vascular skin abnormality0.0009018InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the spleen0.001532InformativeInherited
Phenotypic Abnormality (PA)Visceromegaly0.004005InformativeInherited
Phenotypic Abnormality (PA)Sinusitis4.658e-06Highly InformativeDirect
Phenotypic Abnormality (PA)Lymphadenopathy2.713e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of temperature regulation0.0001982Highly InformativeDirect
Phenotypic Abnormality (PA)Recurrent respiratory infections0.0007526Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)cell death variant0Moderately InformativeDirect
Worm Phenotype (WP)sensillum morphology variant0.0004604InformativeDirect
Worm Phenotype (WP)cell corpse number variant0.0004672InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.03916InformativeInherited
Yeast Phenotype (YP)protein/peptide modification0.0006656Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups4.042e-07Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.009982Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.0001005Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.008107Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase9.904e-10InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol-4-phosphate 3-kinase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processLipid metabolism0.146Moderately InformativeInherited
Biological processEndocytosis2.431e-13InformativeDirect
Biological processAutophagy0Highly InformativeDirect
Biological processLipid degradation1.765e-08Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCell projection4.018e-10Moderately InformativeDirect
Cellular componentCell junction0.0006965Moderately InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainSH3 domain0InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Post-translational modificationGTPase activation3.825e-08InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001683 SSF64268 Protein matches
Abstract

The PX (phox) domain [PubMed8931154] occurs in a variety of eukaryotic proteins and have been implicated in highly diverse functions such as cell signalling, vesicular trafficking, protein sorting and lipid modification [PubMed10782093, PubMed11736640, PubMed12461558]. PX domains are important phosphoinositide-binding modules that have varying lipid-binding specificities [PubMed11884510]. The PX domain is approximately 120 residues long [PubMed11373621], and folds into a three-stranded beta-sheet followed by three -helices and a proline-rich region that immediately preceeds a membrane-interaction loop and spans approximately eight hydrophobic and polar residues. The PX domain of p47phox binds to the SH3 domain in the same protein [PubMed11373621]. Phosphorylation of p47(phox), a cytoplasmic activator of the microbicidal phagocyte oxidase (phox), elicits interaction of p47(phox) with phoinositides. The protein phosphorylation-driven conformational change of p47(phox) enables its PX domain to bind to phosphoinositides, the interaction of which plays a crucial role in recruitment of p47(phox) from the cytoplasm to membranes and subsequent activation of the phagocyte oxidase. The lipid-binding activity of this protein is normally suppressed by intramolecular interaction of the PX domain with the C-terminal Src homology 3 (SH3) domain [PubMed12356722].

The PX domain is conserved from yeast to human. A recent multiple alignment of representative PX domain sequences can be found in [PubMed9687503], although showing relatively little sequence conservation, their structure appears to be highly conserved. Although phosphatidylinositol-3-phosphate (PtdIns(3)P) is the primary target of PX domains, binding to phosphatidic acid, phosphatidylinositol-3,4-bisphosphate (PtdIns(3,4)P2), phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2), phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2), and phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P3) has been reported as well. The PX-domain is also a protein-protein interaction domain [PubMed15263065].


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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 PX domain 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 PX domain 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]