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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 variant0.000000000006473Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.00000000002188Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00000000002226Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00000003829Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000001089Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0005643Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.003154Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)germ cell development variant0.0000000002033Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.000000001512Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00004747Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.0001004Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0005616Moderately InformativeDirect
Worm Phenotype (WP)body region morphology variant0.0005997Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.0005997Moderately InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.0006063Moderately InformativeDirect
Worm Phenotype (WP)adult body morphology variant0.0006134Moderately InformativeDirect
Worm Phenotype (WP)body morphology variant0.0008086Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.002209Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.03014Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2425Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.4979Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.5003Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.5113Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant0.998Moderately InformativeInherited
Worm Phenotype (WP)drug response variant1Moderately InformativeInherited
Worm Phenotype (WP)life span variant0.000003597InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0.0000415InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.000844InformativeDirect
Worm Phenotype (WP)brood size variant0.0009364InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.008793InformativeInherited
Worm Phenotype (WP)pigmentation variant0.01449InformativeInherited
Worm Phenotype (WP)non apoptotic cell death variant0.01688InformativeInherited
Worm Phenotype (WP)cell fate specification variant0.04526InformativeInherited
Worm Phenotype (WP)pesticide response variant0.1454InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.3221InformativeInherited
Worm Phenotype (WP)vulva development variant0.3985InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.6723InformativeInherited
Worm Phenotype (WP)cell stress response variant0.8992InformativeInherited
Worm Phenotype (WP)level of protein expression variant1InformativeInherited
Worm Phenotype (WP)rachis morphology variant1InformativeInherited
Worm Phenotype (WP)spontaneous mutation rate increased0.00005112Highly InformativeDirect
Worm Phenotype (WP)X chromosome nondisjunction0.00009494Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.000194Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.0002717Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0003999Highly InformativeDirect
Worm Phenotype (WP)paraquat hypersensitive0.0005389Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.0007378Highly InformativeDirect
Worm Phenotype (WP)neuropil development variant0.04059Highly InformativeInherited
Worm Phenotype (WP)transgene silencing variant0.1519Highly InformativeInherited
Worm Phenotype (WP)spindle position orientation defective early emb0.7805Highly 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)cell0.1424Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.588Moderately InformativeInherited
Zebrafish Anatomy (ZA)epithelial cell0.09606Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.000000008246Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00004967Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.04946Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.222Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system0.2336Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.3223Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00000000000002141Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.000000002836Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0000000245Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.003418Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.2675Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.4729Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.0000000000136InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00000003128InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0000000777InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000003022InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.000009401InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0000374InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.00006956InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.0005117InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0009663InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.002721InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.1246InformativeInherited
Xenopus ANatomical entity (XAN)tail0.3471InformativeInherited
Xenopus ANatomical entity (XAN)intersomitic region0.000001889Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.000002337Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.00005622Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.00006786Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.0001552Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.0001787Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0003796Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.0005237Highly InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.0007092Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.0008808Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior placodal area0.0009309Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.04092Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.3682Moderately 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 groups0.3947Moderately 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 acetyltransferase0.000101InformativeDirect
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 ligase0.000000537Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.0000751Highly 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 ]