SUPERFAMILY 1.75 HMM library and genome assignments server


PAH2 domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   PAH2 domain [ 47761]
Superfamily:   PAH2 domain [ 47762]
Families:   PAH2 domain [ 47763] (2)


Superfamily statistics
Genomes (452) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,462 3,199 3
Proteins 1,538 1,401 3


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 1.379e-08 Least Informative Direct
Biological Process (BP) multicellular organismal process 1.039e-07 Least Informative Direct
Biological Process (BP) regulation of metabolic process 3.819e-06 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 4.839e-05 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.002173 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.03958 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01283 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.004935 Least Informative Inherited
Biological Process (BP) localization 0.009653 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 9.654e-10 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1.155e-09 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 2.712e-09 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 6.249e-09 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 6.744e-09 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 2.77e-07 Moderately Informative Direct
Biological Process (BP) immune system process 8.013e-05 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.0004486 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0009244 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.004335 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.5691 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.8218 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.07073 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.07317 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2971 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1575 Moderately Informative Inherited
Biological Process (BP) organ development 0.00398 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.8241 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.001506 Moderately Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 2.824e-09 Informative Direct
Biological Process (BP) negative regulation of gene expression 1.844e-08 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 2.857e-08 Informative Direct
Biological Process (BP) chromosome organization 7.173e-06 Informative Direct
Biological Process (BP) locomotion 9.473e-06 Informative Direct
Biological Process (BP) regulation of cellular component movement 5.183e-05 Informative Direct
Biological Process (BP) regulation of locomotion 5.375e-05 Informative Direct
Biological Process (BP) localization of cell 0.0005475 Informative Direct
Biological Process (BP) generation of neurons 0.9113 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.1626 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.006013 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.001897 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.01432 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.02308 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.03125 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.00396 Informative Inherited
Biological Process (BP) cell projection organization 0.00987 Informative Inherited
Biological Process (BP) muscle structure development 0.001298 Informative Inherited
Biological Process (BP) cellular component movement 0.02938 Informative Inherited
Biological Process (BP) protein deacylation 7.433e-12 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 4.494e-08 Highly Informative Direct
Biological Process (BP) regulation of protein stability 1.238e-07 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 3.585e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 3.993e-06 Highly Informative Direct
Biological Process (BP) aging 1.446e-05 Highly Informative Direct
Biological Process (BP) neuron projection development 2.969e-05 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 3.886e-05 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 5.086e-05 Highly Informative Direct
Biological Process (BP) histone modification 0.0003209 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0005998 Highly Informative Direct
Molecular Function (MF) binding 0.001903 Least Informative Inherited
Molecular Function (MF) chromatin binding 2.951e-05 Informative Direct
Molecular Function (MF) protein dimerization activity 0.006245 Informative Inherited
Molecular Function (MF) protein heterodimerization activity 2.675e-08 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 3.165e-06 Least Informative Direct
Cellular Component (CC) protein complex 3.392e-06 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0005406 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8047 Least Informative Inherited
Cellular Component (CC) nuclear part 4.327e-06 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 2.983e-05 Moderately Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 1.72e-08 Informative Direct
Cellular Component (CC) nuclear chromosome part 1.441e-07 Highly Informative Direct
Cellular Component (CC) chromatin 0.008901 Highly Informative Inherited

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainRepeat0Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationPhosphoprotein4.279e-05Least InformativeDirect
Post-translational modificationUbl conjugation9.128e-07Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR003822 SSF47762 Protein matches
Abstract

This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 [PubMed11101889]. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin [PubMed14705930]. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [PubMed15235594].


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-coverage) · Arabidopsis Plant Ontology (AP) · 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 2 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 PAH2 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 2 hidden Markov models representing the PAH2 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-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]