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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 the musculature0.09646Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1175Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.1257Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1262Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.1445Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1531Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.2456Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.253Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.2553Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal ocular adnexa morphology0.005169Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.01005Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.0164Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.03301Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.034Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.0416Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.05024Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.05256Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.05425Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.05619Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.07701Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal physiology0.09506Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.1158Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.2392Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.3758Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.3809Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.4315Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.6632Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the palm0.0002429InformativeDirect
Phenotypic Abnormality (PA)Abnormal testis morphology0.0006704InformativeDirect
Phenotypic Abnormality (PA)Abnormal lip morphology0.0009727InformativeDirect
Phenotypic Abnormality (PA)Abnormal eyelid morphology0.002571InformativeInherited
Phenotypic Abnormality (PA)Abnormal finger phalanx morphology0.002667InformativeInherited
Phenotypic Abnormality (PA)Abnormal hair quantity0.002667InformativeInherited
Phenotypic Abnormality (PA)Abnormal lower limb bone morphology0.002816InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.002865InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral white matter0.007295InformativeInherited
Phenotypic Abnormality (PA)Abnormality of eye movement0.009392InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.01075InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.01262InformativeInherited
Phenotypic Abnormality (PA)Joint hypermobility0.03412InformativeInherited
Phenotypic Abnormality (PA)Abnormal cerebellum morphology0.04094InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.05612InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.06157InformativeInherited
Phenotypic Abnormality (PA)Joint dislocation0.06901InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nail0.07262InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.07433InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.1753InformativeInherited
Phenotypic Abnormality (PA)Hypoplastic fifth fingernail0.00000003008Highly InformativeDirect
Phenotypic Abnormality (PA)Hypoplastic fifth toenail0.00000004564Highly InformativeDirect
Phenotypic Abnormality (PA)Slow-growing hair0.00000468Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the distal phalanges of the hand0.000004796Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the 5th toe0.00001487Highly InformativeDirect
Phenotypic Abnormality (PA)Short phalanx of finger0.00002738Highly InformativeDirect
Phenotypic Abnormality (PA)Cutis marmorata0.00002901Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal patella morphology0.00004025Highly InformativeDirect
Phenotypic Abnormality (PA)Long eyelashes0.000083Highly InformativeDirect
Phenotypic Abnormality (PA)Thick eyebrow0.0001156Highly InformativeDirect
Phenotypic Abnormality (PA)Generalized hirsutism0.0001156Highly InformativeDirect
Phenotypic Abnormality (PA)Cerebellar cyst0.0001206Highly InformativeDirect
Phenotypic Abnormality (PA)Lacrimation abnormality0.0001361Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the phalanges of the toes0.000196Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal 5th finger phalanx morphology0.0002217Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal hand morphology0.0002891Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the diaphragm0.0003664Highly InformativeDirect
Phenotypic Abnormality (PA)Wide mouth0.0003977Highly InformativeDirect
Phenotypic Abnormality (PA)Hypoplasia of the corpus callosum0.0004851Highly InformativeDirect
Phenotypic Abnormality (PA)Spinal dysraphism0.0004879Highly InformativeDirect
Phenotypic Abnormality (PA)Dilatation of the renal pelvis0.0005604Highly InformativeDirect
Phenotypic Abnormality (PA)Strabismus0.0006977Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasal bridge0.0008771Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the cerebellar vermis0.0008787Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving bones of the hand0.0009022Highly InformativeDirect
Phenotypic Abnormality (PA)Joint hyperflexibility0.0009383Highly InformativeDirect
Phenotypic Abnormality (PA)Short digit0.001513Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of toe0.01446Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of femur morphology0.09006Highly InformativeInherited
Phenotypic Abnormality (PA)Agenesis of corpus callosum0.1062Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral ventricles0.1189Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the elbow0.1728Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skin of the palm0.2478Highly 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 phenotype0.005472Least InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology0.0003407Highly 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 behavior variant0.003208Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.004107Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1688Least InformativeInherited
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant0.0002054Moderately InformativeDirect
Worm Phenotype (WP)protein expression variant0.0006893Moderately InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.00000000009842Highly 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)lethal0Moderately InformativeDirect
Fly Phenotype (FP)modifier of variegation0.00006137InformativeDirect
Fly Phenotype (FP)some die during P-stage0.008105Highly 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)organism subdivision0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)adult tagma0Moderately InformativeDirect
Fly Anatomy (FA)adult segment0Moderately InformativeDirect
Fly Anatomy (FA)region of integument0Moderately 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
Xenopus ANatomical entity (XAN)embryo0.09156Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.1027Least InformativeInherited
Xenopus ANatomical entity (XAN)urogenital system0.1891Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.3113Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.01072Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.01215InformativeInherited
Xenopus ANatomical entity (XAN)urinary system0.0241InformativeInherited
Xenopus ANatomical entity (XAN)pronephric tubule0.0007177Highly 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 ]