SUPERFAMILY 1.75 HMM library and genome assignments server


ARID-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA/RNA-binding 3-helical bundle [ 46688] (14)
Superfamily:   ARID-like [ 46774]
Families:   ARID domain [ 46775] (4)


Superfamily statistics
Genomes (463) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,191 3,136 5
Proteins 3,186 3,130 5


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) regulation of metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1.049e-08 Least Informative Direct
Biological Process (BP) developmental process 9.232e-06 Least Informative Direct
Biological Process (BP) protein metabolic process 9.736e-06 Least Informative Direct
Biological Process (BP) multicellular organismal process 1.761e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 5.282e-05 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.5627 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.002982 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.02951 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.03117 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.03777 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.06098 Least Informative Inherited
Biological Process (BP) organelle organization 2.268e-13 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 1.373e-09 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 4.663e-09 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 4.864e-08 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 3.834e-07 Moderately Informative Direct
Biological Process (BP) cell differentiation 8.305e-07 Moderately Informative Direct
Biological Process (BP) tissue development 1.904e-06 Moderately Informative Direct
Biological Process (BP) organ development 2.403e-06 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 8.279e-06 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0003496 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.02696 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.158 Moderately Informative Inherited
Biological Process (BP) immune system process 0.005399 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.2791 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.2366 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.684 Moderately Informative Inherited
Biological Process (BP) reproduction 0.00185 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) cellular process involved in reproduction 9.12e-05 Informative Direct
Biological Process (BP) reproductive system development 0.0002009 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0004689 Informative Direct
Biological Process (BP) sexual reproduction 0.0005214 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.1152 Informative Inherited
Biological Process (BP) epithelium development 0.605 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.005807 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.002323 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1742 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.6701 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.003468 Informative Inherited
Biological Process (BP) single organism reproductive process 0.001175 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.003365 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 3.755e-15 Highly Informative Direct
Biological Process (BP) protein methylation 1.435e-14 Highly Informative Direct
Biological Process (BP) gonad development 7.305e-12 Highly Informative Direct
Biological Process (BP) erythrocyte differentiation 1.686e-10 Highly Informative Direct
Biological Process (BP) myeloid cell development 3.792e-10 Highly Informative Direct
Biological Process (BP) spermatogenesis 7.679e-10 Highly Informative Direct
Biological Process (BP) epithelial cell development 3.801e-09 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 2.14e-08 Highly Informative Direct
Biological Process (BP) connective tissue development 1.322e-06 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.0002676 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 0.002698 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.2047 Highly Informative Inherited
Molecular Function (MF) binding 3.848e-06 Least Informative Direct
Molecular Function (MF) nucleic acid binding 1.013e-12 Moderately Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) chromatin binding 4.092e-10 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 7.888e-08 Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 7.566e-13 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 7.541e-08 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 9.063e-08 Highly Informative Direct
Molecular Function (MF) transcription factor binding 2.548e-05 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 3.432e-10 Least Informative Direct
Cellular Component (CC) protein complex 1.537e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 6.275e-05 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.3405 Least Informative Inherited
Cellular Component (CC) nuclear part 1.92e-08 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0001001 Moderately Informative Direct
Cellular Component (CC) chromosome 0.000145 Informative Direct
Cellular Component (CC) nucleoplasm part 0.1317 Informative Inherited
Cellular Component (CC) chromatin 5.112e-09 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.006001 Highly Informative Inherited

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.151Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of head and neck0.1622Least InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving the skeleton0.009054Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digit0.01331Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.01683Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.01983Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mouth0.04235Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.0004338InformativeDirect
Phenotypic Abnormality (PA)Short digit0.0008197InformativeDirect
Phenotypic Abnormality (PA)Abnormality of phalanx of finger0.002221InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the distal phalanges of the hand3.282e-06Highly InformativeDirect
Phenotypic Abnormality (PA)Short finger4.128e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Short phalanx of finger6.786e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the philtrum0.0005494Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.01459Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology6.257e-05Highly InformativeDirect

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)larval development variant0Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.0004423Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant5.68e-07InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive4.677e-11Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)modifier of variegation8.648e-05InformativeDirect
Fly Phenotype (FP)some die during P-stage0.004957Highly InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon 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
DomainRepeat9.477e-06Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionZinc2.302e-06Least InformativeDirect
Molecular functionIron3.688e-06Moderately InformativeDirect
Post-translational modificationDevelopmental protein5.93e-14Moderately InformativeDirect
Post-translational modificationActivator2.33e-10Moderately InformativeDirect
Post-translational modificationRepressor9.263e-09Moderately InformativeDirect
Post-translational modificationOxidoreductase1.034e-05Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationPhosphoprotein4.412e-08Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001606 SSF46774 Protein matches
Abstract

Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure [PubMed10838570]. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.

The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 [PubMed10757798]. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [PubMed10757798].


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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 4 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 ARID-like 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 4 hidden Markov models representing the ARID-like 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]