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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 system0.06767Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1966Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.4413Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.8492Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.1607Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.2084Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.8202Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.8848Moderately InformativeInherited
Phenotypic Abnormality (PA)Short stature0.2935InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.3932InformativeInherited
Phenotypic Abnormality (PA)Abnormality of female external genitalia0.004832Highly InformativeInherited
Phenotypic Abnormality (PA)Proportionate short stature0.006269Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal pancreas morphology0.06839Highly InformativeInherited
Phenotypic Abnormality (PA)External genital hypoplasia0.2155Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mandible0.5275Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.000003988Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.005458Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.000006658Moderately InformativeDirect
Mammalian Phenotype (MP)prenatal lethality0.0007803Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0.2178Moderately 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 morphology0.53InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.6233InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.6713InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular meshwork morphology0.0003793Highly 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 variant0.0000000000002196Least InformativeDirect
Worm Phenotype (WP)cell development variant0.000000000001254Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000000000003236Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000001755Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0007448Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.01926Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.8551Least InformativeInherited
Worm Phenotype (WP)germ cell development variant0.0000000007699Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00001135Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00005899Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0004213Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.004864Moderately InformativeInherited
Worm Phenotype (WP)cell cycle variant0.00789Moderately InformativeInherited
Worm Phenotype (WP)protein interaction variant0.2505Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.4065Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.4881Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.4902Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.6966Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.8803Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant1Moderately InformativeInherited
Worm Phenotype (WP)life span variant0.000002403InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0.00004616InformativeDirect
Worm Phenotype (WP)anesthetic response variant0.00008306InformativeDirect
Worm Phenotype (WP)male gonad development variant0.0001089InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0006676InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.009508InformativeInherited
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.01638InformativeInherited
Worm Phenotype (WP)pigmentation variant0.01739InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.3292InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.7669InformativeInherited
Worm Phenotype (WP)level of protein expression variant1InformativeInherited
Worm Phenotype (WP)rachis morphology variant1InformativeInherited
Worm Phenotype (WP)mitotic spindle defective early emb0.00004062Highly InformativeDirect
Worm Phenotype (WP)passage through meiosis defective early emb0.00004792Highly InformativeDirect
Worm Phenotype (WP)spontaneous mutation rate increased0.00005401Highly InformativeDirect
Worm Phenotype (WP)X chromosome nondisjunction0.0001119Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.0002709Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0003991Highly InformativeDirect
Worm Phenotype (WP)developmental pigmentation variant0.001361Highly InformativeInherited
Worm Phenotype (WP)neuropil development variant0.0379Highly 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)embryo0.000000007781Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00004771Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.05252Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.2153Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system0.2507Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.317Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.00000000000001853Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.000000001678Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00000003411Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.00327Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.2634Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.4725Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.00000000001219InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00000003123InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0000000747InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000002177InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.000009937InformativeDirect
Xenopus ANatomical entity (XAN)neural crest0.00002384InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.00003402InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.00006235InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.0005343InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0009522InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0009907InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.0028InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.1165InformativeInherited
Xenopus ANatomical entity (XAN)tail0.3501InformativeInherited
Xenopus ANatomical entity (XAN)intersomitic region0.000001894Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.000002485Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.00005506Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.0000658Highly InformativeDirect
Xenopus ANatomical entity (XAN)preplacodal ectoderm0.00008707Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.0001512Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.0001944Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0003866Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.0005665Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.0008767Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.04242Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.3757Moderately 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 ]