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 0.00000001437 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00000005163 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.000006141 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00006935 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.00255 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.04075 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01316 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.4847 Least Informative Inherited
Biological Process (BP) localization 0.0118 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.004994 Least Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000000001329 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000000003098 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000007972 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.00000000881 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00000001946 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0000004465 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.00007027 Moderately Informative Direct
Biological Process (BP) immune system process 0.00008107 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.00095 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.004903 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.8238 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.5707 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.8465 Moderately Informative Inherited
Biological Process (BP) organ development 0.003371 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1261 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.07262 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.07588 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.05384 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1347 Moderately Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.000000003365 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00000001407 Informative Direct
Biological Process (BP) chromosome organization 0.000007305 Informative Direct
Biological Process (BP) locomotion 0.000009539 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.00004962 Informative Direct
Biological Process (BP) regulation of locomotion 0.0000537 Informative Direct
Biological Process (BP) muscle structure development 0.0004304 Informative Direct
Biological Process (BP) localization of cell 0.0004794 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.1315 Informative Inherited
Biological Process (BP) generation of neurons 0.9175 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.005962 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.001237 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.02945 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.004259 Informative Inherited
Biological Process (BP) cell projection organization 0.006075 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.01441 Informative Inherited
Biological Process (BP) cellular component movement 0.0197 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.01842 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.0407 Informative Inherited
Biological Process (BP) protein deacylation 0.000000000007332 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 0.00000002275 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0000002664 Highly Informative Direct
Biological Process (BP) histone modification 0.0000005332 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.000002857 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 0.000003915 Highly Informative Direct
Biological Process (BP) aging 0.0000152 Highly Informative Direct
Biological Process (BP) neuron projection development 0.00003017 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.00003557 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00005157 Highly Informative Direct
Biological Process (BP) muscle organ development 0.00007694 Highly Informative Direct
Molecular Function (MF) binding 0.002181 Least Informative Inherited
Molecular Function (MF) chromatin binding 0.00003377 Informative Direct
Molecular Function (MF) protein dimerization activity 0.006213 Informative Inherited
Molecular Function (MF) transcription factor binding transcription factor activity 0.000000000005259 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.00000002786 Highly Informative Direct
Cellular Component (CC) protein complex 0.000003073 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000003406 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0004555 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.925 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00008694 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0006744 Moderately Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.000000002504 Informative Direct
Cellular Component (CC) chromatin 0.0000000000003294 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0000003265 Highly Informative Direct

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 modificationPhosphoprotein0.00004341Least InformativeDirect
Post-translational modificationUbl conjugation0.0000009516Moderately 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 ]