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 (451) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,031 3,136 5
Proteins 3,026 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 3.885e-09 Least Informative Direct
Biological Process (BP) developmental process 1.349e-05 Least Informative Direct
Biological Process (BP) protein metabolic process 3.557e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0001634 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0003291 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.3245 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.002131 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.08962 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.09954 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1158 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1659 Least Informative Inherited
Biological Process (BP) organelle organization 6.593e-13 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 4.159e-11 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 9.411e-09 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 2.98e-07 Moderately Informative Direct
Biological Process (BP) organ development 6.082e-06 Moderately Informative Direct
Biological Process (BP) tissue development 8.66e-06 Moderately Informative Direct
Biological Process (BP) cell differentiation 1.066e-05 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 3.326e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 9.919e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.009537 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.01226 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.7065 Moderately Informative Inherited
Biological Process (BP) immune system process 0.003225 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.01407 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.3608 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.4182 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.9136 Moderately Informative Inherited
Biological Process (BP) reproduction 0.007286 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.000244 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.07815 Informative Inherited
Biological Process (BP) epithelium development 0.789 Informative Inherited
Biological Process (BP) reproductive system development 0.001388 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.001444 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.02296 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.006384 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.2456 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.08104 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.4407 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.02121 Informative Inherited
Biological Process (BP) sexual reproduction 0.002041 Informative Inherited
Biological Process (BP) single organism reproductive process 0.007061 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01004 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 2.627e-12 Highly Informative Direct
Biological Process (BP) protein methylation 1.14e-11 Highly Informative Direct
Biological Process (BP) myeloid cell development 5.828e-11 Highly Informative Direct
Biological Process (BP) erythrocyte differentiation 1.41e-10 Highly Informative Direct
Biological Process (BP) gonad development 8.398e-10 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 2.259e-08 Highly Informative Direct
Biological Process (BP) spermatogenesis 1.175e-07 Highly Informative Direct
Biological Process (BP) epithelial cell development 1.557e-07 Highly Informative Direct
Biological Process (BP) connective tissue development 3.496e-07 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.0006823 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 0.00153 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.1083 Highly Informative Inherited
Molecular Function (MF) binding 1.096e-05 Least Informative Direct
Molecular Function (MF) nucleic acid binding 6.574e-12 Moderately Informative Direct
Molecular Function (MF) DNA binding 7.982e-16 Informative Direct
Molecular Function (MF) chromatin binding 2.485e-10 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 1.147e-07 Informative Direct
Molecular Function (MF) protein binding transcription factor activity 3.709e-10 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 1.094e-07 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 5.233e-07 Highly Informative Direct
Molecular Function (MF) transcription factor binding 2.073e-05 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 2.281e-10 Least Informative Direct
Cellular Component (CC) protein complex 2.054e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 4.332e-05 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.2663 Least Informative Inherited
Cellular Component (CC) nuclear part 1.229e-08 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 6.94e-05 Moderately Informative Direct
Cellular Component (CC) chromosome 0.000266 Informative Direct
Cellular Component (CC) nucleoplasm part 0.1493 Informative Inherited
Cellular Component (CC) SWI/SNF superfamily-type complex 0 Highly Informative Direct
Cellular Component (CC) chromatin 5.432e-09 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.006641 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 morphology0.1535Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of head and neck0.1655Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digit0.014Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.01759Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.02044Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mouth0.0437Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the lower limbs0.0003793InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.0004302InformativeDirect
Phenotypic Abnormality (PA)Short digit0.0008341InformativeDirect
Phenotypic Abnormality (PA)Abnormality of phalanx of finger0.002374InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the distal phalanges of the hand3.32e-06Highly InformativeDirect
Phenotypic Abnormality (PA)Short finger3.978e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Short phalanx of finger6.813e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the philtrum0.000604Highly 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 phenotype0.01412Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology6.358e-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 variegation0.0001103InformativeDirect
Fly Phenotype (FP)some die during P-stage0.00616Highly 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
DomainRepeat9.409e-06Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc1.548e-06Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionIron1.237e-05Moderately InformativeDirect
Post-translational modificationDevelopmental protein4.893e-14Moderately InformativeDirect
Post-translational modificationActivator1.947e-10Moderately InformativeDirect
Post-translational modificationRepressor7.039e-09Moderately InformativeDirect
Post-translational modificationOxidoreductase8.021e-06Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationPhosphoprotein4.399e-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 ]