SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (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 0.000000009068 Least Informative Direct
Biological Process (BP) developmental process 0.000009172 Least Informative Direct
Biological Process (BP) protein metabolic process 0.000009288 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00001731 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00005172 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.5684 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.002895 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.02942 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.03112 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.03766 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.06078 Least Informative Inherited
Biological Process (BP) organelle organization 0.0000000000002259 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.000000001329 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000000005607 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00000006025 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000004451 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000008129 Moderately Informative Direct
Biological Process (BP) tissue development 0.000001853 Moderately Informative Direct
Biological Process (BP) organ development 0.000002404 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000007706 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0003163 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.02405 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.1694 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.6032 Moderately Informative Inherited
Biological Process (BP) immune system process 0.005382 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.2736 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.2241 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.7709 Moderately Informative Inherited
Biological Process (BP) reproduction 0.001819 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 0.00009049 Informative Direct
Biological Process (BP) reproductive system development 0.0002013 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0004693 Informative Direct
Biological Process (BP) sexual reproduction 0.0004897 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.1146 Informative Inherited
Biological Process (BP) epithelium development 0.6 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.005607 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.002321 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.5443 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1562 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.6836 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.003452 Informative Inherited
Biological Process (BP) single organism reproductive process 0.001132 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.003361 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.000000000000003741 Highly Informative Direct
Biological Process (BP) protein methylation 0.00000000000001429 Highly Informative Direct
Biological Process (BP) gonad development 0.000000000007386 Highly Informative Direct
Biological Process (BP) erythrocyte differentiation 0.0000000001703 Highly Informative Direct
Biological Process (BP) myeloid cell development 0.0000000003906 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.000000000707 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.000000003619 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.00000002109 Highly Informative Direct
Biological Process (BP) connective tissue development 0.000001268 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.0002871 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 0.002831 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.1971 Highly Informative Inherited
Molecular Function (MF) binding 0.00000347 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.0000000000009703 Moderately Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) chromatin binding 0.0000000003271 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0.00000007641 Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.000000000001354 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.00000007297 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00000007391 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.00002672 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000000003154 Least Informative Direct
Cellular Component (CC) protein complex 0.000000001603 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00006329 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.3439 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000002046 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0001032 Moderately Informative Direct
Cellular Component (CC) chromosome 0.0001433 Informative Direct
Cellular Component (CC) nucleoplasm part 0.1324 Informative Inherited
Cellular Component (CC) chromatin 0.000000005349 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.005612 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 neck0.1624Least InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving the skeleton0.009082Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digit0.01337Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.0169Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.01991Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mouth0.04252Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the lower limbs0.0003595InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.0004375InformativeDirect
Phenotypic Abnormality (PA)Short digit0.0008266InformativeDirect
Phenotypic Abnormality (PA)Abnormality of phalanx of finger0.002236InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the distal phalanges of the hand0.000003339Highly InformativeDirect
Phenotypic Abnormality (PA)Short finger0.00004187Highly InformativeDirect
Phenotypic Abnormality (PA)Short phalanx of finger0.0000688Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the philtrum0.0005416Highly 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 phenotype0.0143Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology0.00006564Highly 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 variant0.000000568InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.00000000004677Highly 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 variegation0.00008661InformativeDirect
Fly Phenotype (FP)some die during P-stage0.0049Highly 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
DomainRepeat0.000009318Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0.000001532Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionIron0.0000124Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00000000000004784Moderately InformativeDirect
Post-translational modificationActivator0.0000000001946Moderately InformativeDirect
Post-translational modificationRepressor0.000000007076Moderately InformativeDirect
Post-translational modificationOxidoreductase0.000008214Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.0000000429Least 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 ]