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"Winged helix" DNA-binding domain 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:   "Winged helix" DNA-binding domain [ 46785] (84)
Families:   Biotin repressor-like [ 46786] (2)
  LexA repressor, N-terminal DNA-binding domain [ 46789]
  Arginine repressor (ArgR), N-terminal DNA-binding domain [ 46792]
  Transcriptional repressor Rex, N-terminal domain [ 101007]
  CAP C-terminal domain-like [ 46796] (8)
  Lrp/AsnC-like transcriptional regulator N-terminal domain [ 68967] (4)
  ArsR-like transcriptional regulators [ 46801] (4)
  Transcriptional regulator IclR, N-terminal domain [ 74676]
  MarR-like transcriptional regulators [ 63379] (19)
  DNA-binding protein Mj223 [ 81690]
  Penicillinase repressor [ 101016] (3)
  GntR-like transcriptional regulators [ 46804] (4)
  N-terminal domain of Bacillus PurR [ 101021]
  Replication terminator protein (RTP) [ 46807]
  LysR-like transcriptional regulators [ 88979] (2)
  N-terminal domain of molybdate-dependent transcriptional regulator ModE [ 46810]
  Transcription factor MotA, activation domain [ 46813]
  Transcription factor E/IIe-alpha, N-terminal domain [ 101024]
  FUR-like [ 101027]
  Replication initiation protein [ 46816] (3)
  Helicase DNA-binding domain [ 46819] (4)
  RecQ helicase DNA-binding domain-like [ 101030] (3)
  SCF ubiquitin ligase complex WHB domain [ 74679] (3)
  C-terminal fragment of elongation factor SelB [ 74683]
  Restriction endonuclease FokI, N-terminal (recognition) domain [ 46824]
  TnsA endonuclease, C-terminal domain [ 46782]
  Plant O-methyltransferase, N-terminal domain [ 63475] (5)
  Linker histone H1/H5 [ 46827] (3)
  Forkhead DNA-binding domain [ 46832] (6)
  DNA-binding domain from rap30 [ 46841]
  C-terminal domain of the rap74 subunit of TFIIF [ 63480]
  C-terminal domain of RPA32 [ 46844]
  DEP domain [ 63483] (4)
  Cell cycle transcription factor e2f-dp [ 46847] (2)
  The central core domain of TFIIE beta [ 46850]
  Z-DNA binding domain [ 46853] (4)
  P4 origin-binding domain-like [ 46856] (2)
  ets domain [ 46859] (8)
  Heat-shock transcription factor [ 46873]
  Interferon regulatory factor [ 46877] (3)
  39 kda initiator binding protein, IBP39, N-terminal domain [ 101045]
  Iron-dependent repressor protein [ 46882] (3)
  Dissimilatory sulfite reductase DsvD [ 101048]
  La domain [ 101051] (2)
  Methionine aminopeptidase, insert domain [ 46887]
  PCI domain (PINT motif) [ 109671] (2)
  F93-like [ 109674] (3)
  Archaeal DNA-binding protein [ 109677]
  TrmB-like [ 109680] (2)
  Heat-inducible transcription repressor HrcA, N-terminal domain [ 109683]
  DNA replication factor Cdt1 [ 109686]
  Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [ 109689]
  Vacuolar sorting protein domain [ 109692] (3)
  Transcriptional regulator Rrf2 [ 109699] (2)
  Rio2 serine protein kinase N-terminal domain [ 109702]
  Rad21/Rec8-like [ 116795]
  Hypothetical protein PH1932 [ 116798]
  An Obfc1 domain [ 116801]
  ScpB/YpuH-like [ 116804]
  PadR-like [ 116807] (3)
  Hypothetical protein YhgG [ 116812]
  ROK associated domain [ 140279] (3)
  PF1790-like [ 140286]
  MukF N-terminal domain-like [ 140289]
  CodY HTH domain [ 140292]
  FtsK C-terminal domain-like [ 140295]
  Nudix-associated domain [ 140299] (2)
  HxlR-like [ 140304] (5)
  Marine metagenome family WH1 [ 158296]
  ReutB4095-like [ 158299]
  PH0730 N-terminal domain-like [ 158302]
  FaeA-like [ 158305]
  STY4665 C-terminal domain-like [ 158308]
  PSPTO2686-like [ 158311]
  RHA1 ro06458-like [ 158314]
  YjcQ-like [ 158317]
  F112-like [ 158320]
  MerB N-terminal domain-like [ 158323]
  CED-4 C-terminal domain-like [ 158326]
  ELL N2 domain-like [ 158329]
  PF0610-like [ 158332]
  Rv2827c N-terminal domain-like [ 158335]
  Rps19E-like [ 158338]
  RPO3F domain-like [ 158341]


Superfamily statistics
Genomes (3,229) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 270,271 2,080,509 304
Proteins 262,297 2,029,236 284


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Ligases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep1Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Methyltransferases0.6492Moderately InformativeInherited
Enzyme Commission (EC)Phenylalanine--tRNA ligase0.0000008665InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0.00009867InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.0003545InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for lyases that do not belong in1InformativeInherited

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.06789Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1959Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.4409Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.8492Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.1615Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.2089Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.82Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.884Moderately InformativeInherited
Phenotypic Abnormality (PA)Short stature0.2934InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.3933InformativeInherited
Phenotypic Abnormality (PA)Abnormality of female external genitalia0.004829Highly InformativeInherited
Phenotypic Abnormality (PA)Proportionate short stature0.006262Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal pancreas morphology0.06839Highly InformativeInherited
Phenotypic Abnormality (PA)External genital hypoplasia0.2154Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mandible0.5274Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.00000403Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.005415Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.00000669Moderately InformativeDirect
Mammalian Phenotype (MP)prenatal lethality0.0007805Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0.2177Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.2422Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.3516Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.8001Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal smooth muscle morphology0.2888InformativeInherited
Mammalian Phenotype (MP)abnormal uvea morphology0.53InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.6234InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.6725InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular meshwork morphology0.0003794Highly InformativeDirect
Mammalian Phenotype (MP)abnormal esophagus morphology0.1118Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.0000000000002117Least InformativeDirect
Worm Phenotype (WP)cell development variant0.00000000000122Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000000000002999Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000001727Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0007298Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.01879Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.8552Least InformativeInherited
Worm Phenotype (WP)germ cell development variant0.0000000007565Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00001108Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00006001Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0004295Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.004888Moderately InformativeInherited
Worm Phenotype (WP)cell cycle variant0.007964Moderately InformativeInherited
Worm Phenotype (WP)protein interaction variant0.25Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.406Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.4901Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.4919Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.6942Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.8803Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant1Moderately InformativeInherited
Worm Phenotype (WP)life span variant0.000002501InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0.00004712InformativeDirect
Worm Phenotype (WP)anesthetic response variant0.00008308InformativeDirect
Worm Phenotype (WP)male gonad development variant0.0001076InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0006589InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.009439InformativeInherited
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.01613InformativeInherited
Worm Phenotype (WP)pigmentation variant0.01752InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.3292InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.7697InformativeInherited
Worm Phenotype (WP)level of protein expression variant1InformativeInherited
Worm Phenotype (WP)rachis morphology variant1InformativeInherited
Worm Phenotype (WP)mitotic spindle defective early emb0.0000401Highly InformativeDirect
Worm Phenotype (WP)passage through meiosis defective early emb0.0000475Highly InformativeDirect
Worm Phenotype (WP)spontaneous mutation rate increased0.00005351Highly InformativeDirect
Worm Phenotype (WP)X chromosome nondisjunction0.0001107Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.0002693Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0003944Highly InformativeDirect
Worm Phenotype (WP)developmental pigmentation variant0.001351Highly InformativeInherited
Worm Phenotype (WP)neuropil development variant0.03792Highly InformativeInherited
Worm Phenotype (WP)transgene silencing variant0.1394Highly InformativeInherited
Worm Phenotype (WP)spindle position variant0.1614Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)cell cycle progression0.0007695InformativeDirect
Yeast Phenotype (YP)chromosome/plasmid maintenance0.0009782InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.000000007879Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00004817Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.05245Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.2151Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system0.2507Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.3168Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00000000000001845Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.000000001709Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0000000333Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.003221Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.2623Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.4716Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.00000000001295InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00000002997InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00000007984InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000002168InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.000008753InformativeDirect
Xenopus ANatomical entity (XAN)neural crest0.00002367InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.00003391InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.00006116InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.0005015InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0009172InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0009877InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.002736InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.1171InformativeInherited
Xenopus ANatomical entity (XAN)tail0.3487InformativeInherited
Xenopus ANatomical entity (XAN)intersomitic region0.000001886Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.000002194Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.00005473Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.00006557Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.0001507Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.0001936Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0003853Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.0005055Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.0008413Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior placodal area0.0009686Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.04166Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.3758Moderately InformativeInherited

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.3415Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor1Moderately InformativeInherited
Enzyme Commission (EC)Glycosylases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds1Moderately InformativeInherited
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0.0001028InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0.9744InformativeInherited
Enzyme Commission (EC)In cyclic amidines1InformativeInherited
Enzyme Commission (EC)Forming carbon-oxygen bonds1InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Phenylalanine--tRNA ligase0.0000005603Highly InformativeDirect
Enzyme Commission (EC)ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase0.000001906Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.0000768Highly InformativeDirect
Enzyme Commission (EC)Other lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationAcetylation0Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · 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 301 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 "Winged helix" DNA-binding domain 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 301 hidden Markov models representing the "Winged helix" DNA-binding domain 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 · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]