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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 (464) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,199 3,136 5
Proteins 3,196 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) biological regulation 0.000000000000007239 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0000002389 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000306 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.6211 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.8963 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.2264 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.05334 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.1172 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5977 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.6974 Least Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.00000000003305 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0000000004617 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.0000001666 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.000000446 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000009382 Moderately Informative Direct
Biological Process (BP) reproduction 0.00005096 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.2019 Moderately Informative Inherited
Biological Process (BP) system development 0.0516 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.003573 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.7851 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3264 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.4426 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.01419 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.8844 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.00145 Moderately Informative Inherited
Biological Process (BP) immune system process 0.0156 Moderately Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.0000002198 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.000001318 Informative Direct
Biological Process (BP) reproductive system development 0.00001666 Informative Direct
Biological Process (BP) single organism reproductive process 0.00007947 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.00009286 Informative Direct
Biological Process (BP) regulation of protein modification process 0.0001537 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.0005635 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.008368 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.04286 Informative Inherited
Biological Process (BP) epithelium development 0.7895 Informative Inherited
Biological Process (BP) cell development 0.2091 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.2052 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.7849 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) demethylation 0 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.0000000002821 Highly Informative Direct
Biological Process (BP) myeloid cell homeostasis 0.00000001682 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.000001649 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000008562 Highly Informative Direct
Biological Process (BP) sex differentiation 0.00003744 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0009301 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.005234 Highly Informative Inherited
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 0.1105 Highly Informative Inherited
Biological Process (BP) hemopoiesis 0.7224 Highly Informative Inherited
Molecular Function (MF) binding 0.00007552 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.0000000000007908 Moderately Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.0000000009091 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.002683 Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.000000000000334 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000003592 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.00000007481 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000000000311 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000001736 Least Informative Direct
Cellular Component (CC) protein complex 0.008664 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000000002071 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000002329 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.1329 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.3453 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 limbs0.09953Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.2035Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.2281Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.3678Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb bone0.004722Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving the skeleton0.0186Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the foot0.02521Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.031Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.03341Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digit0.0368Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the lower limbs0.0008358InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.001619InformativeInherited
Phenotypic Abnormality (PA)Short digit0.001912InformativeInherited
Phenotypic Abnormality (PA)Abnormality of phalanx of finger0.003508InformativeInherited
Phenotypic Abnormality (PA)Abnormal emotion/affect behavior0.003603InformativeInherited
Phenotypic Abnormality (PA)Abnormality of upper lip0.007727InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thorax0.008945InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the distal phalanx of finger0.00005564Highly InformativeDirect
Phenotypic Abnormality (PA)Short phalanx of finger0.00005743Highly InformativeDirect
Phenotypic Abnormality (PA)Aggressive behavior0.0001576Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.00601Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.009044Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology0.0002105Highly 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 variant0.0009221Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.1223Least InformativeInherited
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant0.000002302Moderately InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.00000000008755Highly 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)lethal - all die before end of P-stage0Moderately InformativeDirect
Fly Phenotype (FP)modifier of variegation0.00001933InformativeDirect
Fly Phenotype (FP)some die during P-stage0.001247Highly 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)cell0Least 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)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 rhythms0.000000000000004256InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainRepeat0.00001073Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionZinc0.000003008Least InformativeDirect
Molecular functionIron0.000003845Moderately InformativeDirect
Post-translational modificationRepressor4.502e-16Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000000000000004423Moderately InformativeDirect
Post-translational modificationActivator0.000000000001277Moderately InformativeDirect
Post-translational modificationOxidoreductase0.00001194Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond0.00000001154Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000002436Moderately InformativeDirect
Post-translational modificationMethylation0.0006262Moderately 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 ]