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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 system0.06349Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1902Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.4327Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.8546Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.1586Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.1913Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.7854Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.8796Moderately InformativeInherited
Phenotypic Abnormality (PA)Short stature0.2725InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.3985InformativeInherited
Phenotypic Abnormality (PA)Abnormality of female external genitalia0.005095Highly InformativeInherited
Phenotypic Abnormality (PA)Proportionate short stature0.006928Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal pancreas morphology0.06797Highly InformativeInherited
Phenotypic Abnormality (PA)External genital hypoplasia0.2098Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mandible0.5129Highly 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 development variant0.000000000006427Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.00000000002151Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00000000002189Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00000003664Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000001039Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0005474Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.003093Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)germ cell development variant0.0000000001992Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.000000001487Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.0000473Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.00009793Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0005602Moderately InformativeDirect
Worm Phenotype (WP)body region morphology variant0.000584Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.000584Moderately InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.000591Moderately InformativeDirect
Worm Phenotype (WP)adult body morphology variant0.0005976Moderately InformativeDirect
Worm Phenotype (WP)body morphology variant0.0007878Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.002194Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.03041Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2412Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.497Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.5002Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.5113Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant0.9971Moderately InformativeInherited
Worm Phenotype (WP)drug response variant1Moderately InformativeInherited
Worm Phenotype (WP)life span variant0.00000351InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0.00004231InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0008319InformativeDirect
Worm Phenotype (WP)brood size variant0.0009152InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.008723InformativeInherited
Worm Phenotype (WP)pigmentation variant0.01434InformativeInherited
Worm Phenotype (WP)non apoptotic cell death variant0.01668InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.04472InformativeInherited
Worm Phenotype (WP)pesticide response variant0.1451InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.3247InformativeInherited
Worm Phenotype (WP)vulva development variant0.3981InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.6756InformativeInherited
Worm Phenotype (WP)cell stress response variant0.8981InformativeInherited
Worm Phenotype (WP)level of protein expression variant1InformativeInherited
Worm Phenotype (WP)rachis morphology variant1InformativeInherited
Worm Phenotype (WP)spontaneous mutation rate increased0.00005054Highly InformativeDirect
Worm Phenotype (WP)X chromosome nondisjunction0.00009903Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.0001925Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.0002711Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0003944Highly InformativeDirect
Worm Phenotype (WP)paraquat hypersensitive0.0005341Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.000729Highly InformativeDirect
Worm Phenotype (WP)neuropil development variant0.04054Highly InformativeInherited
Worm Phenotype (WP)transgene silencing variant0.1518Highly InformativeInherited
Worm Phenotype (WP)spindle position orientation defective early emb0.7803Highly 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)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)cell0.1441Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.5902Moderately InformativeInherited
Zebrafish Anatomy (ZA)epithelial cell0.09649Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.000000007792Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.0001227Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.05009Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.2933Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.3201Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00000000000001806Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.000000003062Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0000001228Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.003528Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.3439Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.423Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.000000000033InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00000002009InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0000002492InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000003179InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.000008743InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.00003674InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.00026InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0008419InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.004196InformativeInherited
Xenopus ANatomical entity (XAN)neural tube0.000002071Highly InformativeDirect
Xenopus ANatomical entity (XAN)intersomitic region0.000008121Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.00005097Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.00006941Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.0001587Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.0001828Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.0003771Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0003896Highly InformativeDirect
Xenopus ANatomical entity (XAN)ventral blood island0.0004105Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior placodal area0.0008805Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0691Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.368Moderately 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 groups0.3964Moderately 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)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 acetyltransferase0.0001013InformativeDirect
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 ligase0.0000005422Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.0001088Highly InformativeDirect
Enzyme Commission (EC)Other lyases1Highly InformativeInherited

Document: EC 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) ]

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) · Internal database links ]