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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 system0.04955Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1754Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1978Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.2926Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.1887Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.218Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.8755Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.8784Moderately InformativeInherited
Phenotypic Abnormality (PA)Short stature0.3336InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.3658InformativeInherited
Phenotypic Abnormality (PA)Abnormality of female external genitalia0.00484Highly InformativeInherited
Phenotypic Abnormality (PA)Proportionate short stature0.005449Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal pancreas morphology0.04715Highly InformativeInherited
Phenotypic Abnormality (PA)External genital hypoplasia0.1724Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mandible0.5834Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.000003959Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.00548Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.000006548Moderately InformativeDirect
Mammalian Phenotype (MP)prenatal lethality0.0007752Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0.2176Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.2422Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.3517Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.8008Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal smooth muscle morphology0.2889InformativeInherited
Mammalian Phenotype (MP)abnormal uvea morphology0.5301InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.6233InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.6713InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular meshwork morphology0.0003799Highly 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 variant0.0000000000004309Least InformativeDirect
Worm Phenotype (WP)cell development variant0.000000000001388Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00000002425Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00000006474Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.001179Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.002732Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)life span variant0.000004486Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.000008338Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.0000316Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00003944Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0006081Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.002597Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.03049Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.05958Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2503Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.4605Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.5441Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.5843Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.6557Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.7337Moderately InformativeInherited
Worm Phenotype (WP)accumulated germline cell corpses0.00003917InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0005654InformativeDirect
Worm Phenotype (WP)brood size variant0.000742InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.009288InformativeInherited
Worm Phenotype (WP)pigmentation variant0.01322InformativeInherited
Worm Phenotype (WP)pesticide response variant0.232InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.3356InformativeInherited
Worm Phenotype (WP)vulva development variant0.3401InformativeInherited
Worm Phenotype (WP)VPC competence variant0.5894InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.7926InformativeInherited
Worm Phenotype (WP)cell stress response variant0.8943InformativeInherited
Worm Phenotype (WP)level of protein expression variant1InformativeInherited
Worm Phenotype (WP)rachis morphology variant1InformativeInherited
Worm Phenotype (WP)mitotic spindle defective early emb0.00003521Highly InformativeDirect
Worm Phenotype (WP)passage through meiosis defective early emb0.00004368Highly InformativeDirect
Worm Phenotype (WP)spontaneous mutation rate increased0.00005199Highly InformativeDirect
Worm Phenotype (WP)X chromosome nondisjunction0.00007982Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.0001821Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.0002328Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0003608Highly InformativeDirect
Worm Phenotype (WP)paraquat hypersensitive0.0004997Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.0007259Highly InformativeDirect
Worm Phenotype (WP)neuropil development variant0.04276Highly InformativeInherited
Worm Phenotype (WP)transgene silencing variant0.1418Highly 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 Phenotype (FP)

(show details) Document: FP 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)embryo0.000000002226Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.0001234Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.03425Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.233Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.2557Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00000000000001081Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.00000000226Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.000000008643Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.001412Moderately InformativeInherited
Xenopus ANatomical entity (XAN)tail region0.0531Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.3679Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3992Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.00000000003347InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.000000003838InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00000006125InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000004105InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0000006304InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.00002645InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0001851InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.0004205InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0007359InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.003482InformativeInherited
Xenopus ANatomical entity (XAN)tail0.3714InformativeInherited
Xenopus ANatomical entity (XAN)cranial neural crest0.00003697Highly InformativeDirect
Xenopus ANatomical entity (XAN)intersomitic region0.0000462Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.00006052Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.0001188Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0006217Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior placodal area0.0007215Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordoneural hinge0.0009888Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.0009967Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.153Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.3012Moderately 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 groups0.5223Moderately 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 acetyltransferase0.0001774InformativeDirect
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 ligase0.0000005233Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.0001183Highly 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 Phenotype (FP) · 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 Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]