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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 system0.1577Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.2955Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.3068Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.3366Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.2149Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.3982Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.811Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.8941Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.3582InformativeInherited
Phenotypic Abnormality (PA)Short stature0.3658InformativeInherited
Phenotypic Abnormality (PA)Hypoplastic labia majora0.000007964Highly InformativeDirect
Phenotypic Abnormality (PA)Retrognathia0.00008434Highly InformativeDirect
Phenotypic Abnormality (PA)Proportionate short stature0.003161Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of pancreas morphology0.04863Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.000003933Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.005553Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.000006674Moderately InformativeDirect
Mammalian Phenotype (MP)prenatal lethality0.0007975Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0.2176Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.2416Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.3515Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.8007Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal smooth muscle morphology0.2898InformativeInherited
Mammalian Phenotype (MP)abnormal uvea morphology0.5299InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.623InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.6711InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular meshwork morphology0.0003797Highly 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 variant0.000000000006971Least InformativeDirect
Worm Phenotype (WP)cell development variant0.000000000008144Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00000007246Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0000002295Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.000585Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.002663Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.000006759Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.000021Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00008976Moderately InformativeDirect
Worm Phenotype (WP)life span variant0.00009867Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.0007658Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.001212Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.03914Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.05871Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.1671Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.4557Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.4955Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.5115Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.7113Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.7161Moderately InformativeInherited
Worm Phenotype (WP)accumulated germline cell corpses0.00003045InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0005058InformativeDirect
Worm Phenotype (WP)growth rate variant0.0008581InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.008053InformativeInherited
Worm Phenotype (WP)pesticide response variant0.2164InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.244InformativeInherited
Worm Phenotype (WP)vulva development variant0.3626InformativeInherited
Worm Phenotype (WP)VPC competence variant0.6164InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.7988InformativeInherited
Worm Phenotype (WP)cell stress response variant0.9179InformativeInherited
Worm Phenotype (WP)level of protein expression variant1InformativeInherited
Worm Phenotype (WP)rachis morphology variant1InformativeInherited
Worm Phenotype (WP)mitotic spindle defective early emb0.00003157Highly InformativeDirect
Worm Phenotype (WP)passage through meiosis defective early emb0.00004568Highly InformativeDirect
Worm Phenotype (WP)spontaneous mutation rate increased0.00004812Highly InformativeDirect
Worm Phenotype (WP)X chromosome nondisjunction0.00006152Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.0001364Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.0002054Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.000215Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0003365Highly InformativeDirect
Worm Phenotype (WP)paraquat hypersensitive0.0004027Highly InformativeDirect
Worm Phenotype (WP)neuropil development variant0.04277Highly InformativeInherited
Worm Phenotype (WP)transgene silencing variant0.1463Highly 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 progression0.0002701InformativeDirect

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)embryo0.000000002369Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00007055Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.03327Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.2131Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.245Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system0.2656Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.000000000000003667Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00000001002Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00000001102Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.001694Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.3486Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.4028Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.0000000001921InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00000003403InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00000008828InformativeDirect
Xenopus ANatomical entity (XAN)eye0.000001571InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.0003645InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0007287InformativeDirect
Xenopus ANatomical entity (XAN)tail0.4063InformativeInherited
Xenopus ANatomical entity (XAN)intersomitic region0.00001994Highly InformativeDirect
Xenopus ANatomical entity (XAN)non-neural ectoderm0.00002161Highly InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0000347Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.00004977Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.00005894Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.0001049Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0003239Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordoneural hinge0.0003904Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.2445Moderately 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 groups0.5795Moderately 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 acetyltransferase0.000161InformativeDirect
Enzyme Commission (EC)In cyclic amidines1InformativeInherited
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds1InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Phenylalanine--tRNA ligase0.0000005777Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.0001389Highly 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 208 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 208 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 ]