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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 (471) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 3,267 9,686 5
Proteins 3,264 9,654 5


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limbs0.04348Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1249Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1374Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1565Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.1629Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1758Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.276Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.2888Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.01013Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.01246Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.01329Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.014Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.01462Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.01585Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.01625Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.01828Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.02651Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.0373Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.04141Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.04592Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.07696Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.08713Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.1083Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.214Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.7372Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.7388Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the palm0.0000499InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.0005263InformativeDirect
Phenotypic Abnormality (PA)Abnormal hair quantity0.0006127InformativeDirect
Phenotypic Abnormality (PA)Abnormality of lower limb bone0.0006337InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the testis0.002485InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the spinal cord0.003046InformativeInherited
Phenotypic Abnormality (PA)Abnormal lip morphology0.003221InformativeInherited
Phenotypic Abnormality (PA)Abnormality of finger0.003654InformativeInherited
Phenotypic Abnormality (PA)Abnormal eyelid morphology0.005781InformativeInherited
Phenotypic Abnormality (PA)Vascular skin abnormality0.005785InformativeInherited
Phenotypic Abnormality (PA)Abnormality of joint mobility0.005978InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the cerebrum0.007703InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.01307InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.02877InformativeInherited
Phenotypic Abnormality (PA)Joint dislocation0.03381InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.04239InformativeInherited
Phenotypic Abnormality (PA)Abnormal facial shape0.06254InformativeInherited
Phenotypic Abnormality (PA)Hernia0.07035InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.07044InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the metencephalon1InformativeInherited
Phenotypic Abnormality (PA)Slow-growing hair0.000001491Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the phalanges of the hand0.000005011Highly InformativeDirect
Phenotypic Abnormality (PA)Absent toe0.000007536Highly InformativeDirect
Phenotypic Abnormality (PA)Spina bifida occulta0.000008851Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the patella0.0000111Highly InformativeDirect
Phenotypic Abnormality (PA)Congenital diaphragmatic hernia0.00001573Highly InformativeDirect
Phenotypic Abnormality (PA)Elbow dislocation0.00002157Highly InformativeDirect
Phenotypic Abnormality (PA)Long eyelashes0.00002435Highly InformativeDirect
Phenotypic Abnormality (PA)Widened posterior fossa0.00003233Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the phalanges of the toes0.00003994Highly InformativeDirect
Phenotypic Abnormality (PA)Generalized hirsutism0.00004848Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the femoral neck0.00007303Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.0001301Highly InformativeDirect
Phenotypic Abnormality (PA)Wide mouth0.0001398Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal 5th finger phalanx morphology0.0001684Highly InformativeDirect
Phenotypic Abnormality (PA)Cerebellar vermis hypoplasia0.0001701Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.0001877Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the philtrum0.0002988Highly InformativeDirect
Phenotypic Abnormality (PA)Coarse facial features0.000382Highly InformativeDirect
Phenotypic Abnormality (PA)Delayed speech and language development0.0004308Highly InformativeDirect
Phenotypic Abnormality (PA)Joint hyperflexibility0.0004437Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasal dorsum0.0004437Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal dermatoglyphics0.0004888Highly InformativeDirect
Phenotypic Abnormality (PA)Agenesis of corpus callosum0.0006927Highly InformativeDirect
Phenotypic Abnormality (PA)Cryptorchidism0.0008487Highly InformativeDirect
Phenotypic Abnormality (PA)Ventriculomegaly0.005307Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower lip0.03116Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal eyebrow morphology0.04662Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.00549Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology0.0003409Highly 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 variant0.001843Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1425Least InformativeInherited
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant0.000004707Moderately InformativeDirect
Worm Phenotype (WP)protein expression variant0.0006267Moderately InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.00000000009521Highly 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 variegation0.00006709InformativeDirect
Fly Phenotype (FP)some die during P-stage0.007409Highly InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)adult segment0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least 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

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 · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) ]

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 10 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 10 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 · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Internal database links ]