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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 (469) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,237 8,016 5
Proteins 3,234 7,986 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) biological regulation 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000002095 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0001053 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0002816 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.4597 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.5885 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.7078 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003035 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1892 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.1184 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4861 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.0000000000848 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000004025 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000001328 Moderately Informative Direct
Biological Process (BP) organelle organization 0.00000006385 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0000002533 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00001352 Moderately Informative Direct
Biological Process (BP) reproduction 0.00001431 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0003755 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.005596 Moderately Informative Inherited
Biological Process (BP) system development 0.09706 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3921 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.02856 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3112 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.52 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.9379 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.02398 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.00000002604 Informative Direct
Biological Process (BP) regulation of organelle organization 0.000003134 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.00001433 Informative Direct
Biological Process (BP) reproductive system development 0.00002291 Informative Direct
Biological Process (BP) single organism reproductive process 0.00002573 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.00004508 Informative Direct
Biological Process (BP) regulation of protein modification process 0.0001483 Informative Direct
Biological Process (BP) cell development 0.1741 Informative Inherited
Biological Process (BP) tissue development 0.002623 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.05035 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.807 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.01068 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.2103 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) demethylation 0 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.00000000001206 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.0000000002094 Highly Informative Direct
Biological Process (BP) myeloid cell homeostasis 0.00000001497 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.000002767 Highly Informative Direct
Biological Process (BP) protein alkylation 0.000005685 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.00001198 Highly Informative Direct
Biological Process (BP) myeloid cell differentiation 0.00009163 Highly Informative Direct
Biological Process (BP) sex differentiation 0.0001102 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0008564 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.01123 Highly Informative Inherited
Molecular Function (MF) binding 0.00001711 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000000000005583 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.02012 Moderately Informative Inherited
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.0000000003269 Informative Direct
Molecular Function (MF) DNA binding 0.000002542 Informative Direct
Molecular Function (MF) zinc ion binding 0.00003534 Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 0.00000000000001248 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0000000001776 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.000005926 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.00004228 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000000001545 Least Informative Direct
Cellular Component (CC) macromolecular complex 0.00000006746 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000005205 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.9488 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0000000001228 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000009812 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.1092 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.000008806 Informative Direct
Cellular Component (CC) nucleoplasm part 0.5627 Informative Inherited
Cellular Component (CC) chromatin 0.00000021 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.04006 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 limbs0.1005Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.2047Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.2267Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.3429Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb bone0.004831Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving the skeleton0.01855Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the foot0.02559Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.03146Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.03298Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digit0.03699Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the lower limbs0.0008452InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.001646InformativeInherited
Phenotypic Abnormality (PA)Short digit0.001912InformativeInherited
Phenotypic Abnormality (PA)Abnormality of phalanx of finger0.003536InformativeInherited
Phenotypic Abnormality (PA)Abnormal emotion/affect behavior0.003751InformativeInherited
Phenotypic Abnormality (PA)Abnormality of upper lip0.007736InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thorax0.008899InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the distal phalanx of finger0.00005564Highly InformativeDirect
Phenotypic Abnormality (PA)Short phalanx of finger0.00005744Highly InformativeDirect
Phenotypic Abnormality (PA)Aggressive behavior0.0001642Highly 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 phenotype0.005522Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology0.0003393Highly InformativeDirect

Document: MP 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)organism environmental stimulus response variant0.001131Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1329Least InformativeInherited
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant0.000003856Moderately InformativeDirect
Worm Phenotype (WP)protein expression variant0.0005247Moderately InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.0000000000952Highly 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 variegation0.00006888InformativeDirect
Fly Phenotype (FP)some die during P-stage0.006551Highly InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
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)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least 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
Biological processBiological rhythms0.000000000000004269InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainRepeat0.0000113Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0.000000004766Least InformativeDirect
Molecular functionIron0.00000001656Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationActivator0.000000000000001532Moderately InformativeDirect
Post-translational modificationRepressor0.000000000000005625Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00000000000004271Moderately InformativeDirect
Post-translational modificationOxidoreductase0.00008151Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond0.000000000004802Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000000063Moderately InformativeDirect
Post-translational modificationMethylation0.0006654Moderately 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 ]