SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 limbs0.04356Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.125Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1375Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1566Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.163Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1759Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.2762Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.2889Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.01016Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.01248Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.01332Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.01403Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.01465Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.01586Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.01628Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.01831Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.02657Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.03737Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.04149Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.04602Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.07702Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.08722Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.1084Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.2141Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.7373Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.7389Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the palm0.00004988InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.000526InformativeDirect
Phenotypic Abnormality (PA)Abnormal hair quantity0.0006121InformativeDirect
Phenotypic Abnormality (PA)Abnormality of lower limb bone0.0006329InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the testis0.002486InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the spinal cord0.003048InformativeInherited
Phenotypic Abnormality (PA)Abnormal lip morphology0.003223InformativeInherited
Phenotypic Abnormality (PA)Abnormality of finger0.003659InformativeInherited
Phenotypic Abnormality (PA)Abnormal eyelid morphology0.005796InformativeInherited
Phenotypic Abnormality (PA)Vascular skin abnormality0.0058InformativeInherited
Phenotypic Abnormality (PA)Abnormality of joint mobility0.005994InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the cerebrum0.007728InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.0131InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.02882InformativeInherited
Phenotypic Abnormality (PA)Joint dislocation0.03387InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.04248InformativeInherited
Phenotypic Abnormality (PA)Abnormal facial shape0.06258InformativeInherited
Phenotypic Abnormality (PA)Hernia0.0704InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.07049InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the metencephalon1InformativeInherited
Phenotypic Abnormality (PA)Slow-growing hair0.000001489Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the phalanges of the hand0.000005006Highly InformativeDirect
Phenotypic Abnormality (PA)Absent toe0.000007522Highly InformativeDirect
Phenotypic Abnormality (PA)Spina bifida occulta0.000008834Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the patella0.00001107Highly InformativeDirect
Phenotypic Abnormality (PA)Congenital diaphragmatic hernia0.0000157Highly InformativeDirect
Phenotypic Abnormality (PA)Elbow dislocation0.00002289Highly InformativeDirect
Phenotypic Abnormality (PA)Long eyelashes0.00002432Highly InformativeDirect
Phenotypic Abnormality (PA)Widened posterior fossa0.0000323Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the phalanges of the toes0.0000399Highly InformativeDirect
Phenotypic Abnormality (PA)Generalized hirsutism0.00004844Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the femoral neck0.00007296Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.00013Highly InformativeDirect
Phenotypic Abnormality (PA)Wide mouth0.0001396Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the phalanges of the 5th finger0.0001685Highly InformativeDirect
Phenotypic Abnormality (PA)Cerebellar vermis hypoplasia0.0001701Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.0001878Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the philtrum0.0002988Highly InformativeDirect
Phenotypic Abnormality (PA)Coarse facial features0.0003818Highly InformativeDirect
Phenotypic Abnormality (PA)Delayed speech and language development0.0004306Highly InformativeDirect
Phenotypic Abnormality (PA)Joint hyperflexibility0.0004436Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasal dorsum0.0004436Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal dermatoglyphics0.0004885Highly InformativeDirect
Phenotypic Abnormality (PA)Agenesis of corpus callosum0.0006921Highly InformativeDirect
Phenotypic Abnormality (PA)Cryptorchidism0.0008482Highly InformativeDirect
Phenotypic Abnormality (PA)Ventriculomegaly0.005322Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower lip0.03123Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal eyebrow morphology0.04672Highly 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 variant0.001738Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1417Least InformativeInherited
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant0.000004361Moderately InformativeDirect
Worm Phenotype (WP)protein expression variant0.0006167Moderately InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.00000000009493Highly 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 variegation0.00006572InformativeDirect
Fly Phenotype (FP)some die during P-stage0.007187Highly 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 ]