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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 system0.02659Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1967Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.2763Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.4354Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.1412Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.1797Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.8189Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.8623Moderately InformativeInherited
Phenotypic Abnormality (PA)Short stature0.297InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.3938InformativeInherited
Phenotypic Abnormality (PA)Abnormality of female external genitalia0.005653Highly InformativeInherited
Phenotypic Abnormality (PA)Proportionate short stature0.006765Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal pancreas morphology0.06566Highly InformativeInherited
Phenotypic Abnormality (PA)External genital hypoplasia0.2096Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the mandible0.5626Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.000004032Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.005453Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.000006602Moderately InformativeDirect
Mammalian Phenotype (MP)prenatal lethality0.0007739Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0.2176Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.2425Moderately 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 morphology0.6233InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.6724InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular meshwork morphology0.0003796Highly InformativeDirect
Mammalian Phenotype (MP)abnormal esophagus morphology0.1119Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)blast cell physiology variant0.000000000002588Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.000000000002634Least InformativeDirect
Worm Phenotype (WP)cell development variant0.000000000004721Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0000000111Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00000006896Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0006216Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.002964Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)germ cell development variant0.0000000001443Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.000000001037Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.00003275Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.000615Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.003232Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.02986Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2613Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.3745Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.4594Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.5456Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.5776Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.6508Moderately InformativeInherited
Worm Phenotype (WP)drug response variant1Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant1Moderately InformativeInherited
Worm Phenotype (WP)life span variant0.000008918InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0.00003936InformativeDirect
Worm Phenotype (WP)brood size variant0.0007653InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0007802InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.009174InformativeInherited
Worm Phenotype (WP)pigmentation variant0.01323InformativeInherited
Worm Phenotype (WP)non apoptotic cell death variant0.02339InformativeInherited
Worm Phenotype (WP)pesticide response variant0.143InformativeInherited
Worm Phenotype (WP)vulva development variant0.3371InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.3399InformativeInherited
Worm Phenotype (WP)VPC competence variant0.5848InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.6839InformativeInherited
Worm Phenotype (WP)cell stress response variant0.886InformativeInherited
Worm Phenotype (WP)level of protein expression variant1InformativeInherited
Worm Phenotype (WP)rachis morphology variant1InformativeInherited
Worm Phenotype (WP)spontaneous mutation rate increased0.00005368Highly InformativeDirect
Worm Phenotype (WP)X chromosome nondisjunction0.0000828Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.000188Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.0002625Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0003867Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.0004002Highly InformativeDirect
Worm Phenotype (WP)paraquat hypersensitive0.0005141Highly InformativeDirect
Worm Phenotype (WP)neuropil development variant0.04279Highly InformativeInherited
Worm Phenotype (WP)transgene silencing variant0.1378Highly InformativeInherited
Worm Phenotype (WP)spindle position orientation defective early emb0.7839Highly 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)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)multi-tissue structure0.0009927Least InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)cell0.201Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.6722Moderately InformativeInherited
Zebrafish Anatomy (ZA)epithelial cell0.08871Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.000000001359Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.0000676Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.03573Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.2396Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.2572Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.000000000000003915Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.000000001269Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.00000004039Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.0008348Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.003487Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.2718Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3794Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.00000000003992InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.0000000112InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0000001971InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000002239InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.000005693InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.00003322InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.000533InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.0006871InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0007277InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.003368InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.09635InformativeInherited
Xenopus ANatomical entity (XAN)neural tube0.000001274Highly InformativeDirect
Xenopus ANatomical entity (XAN)intersomitic region0.000005819Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.00004524Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.00006662Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.000139Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.0001593Highly InformativeDirect
Xenopus ANatomical entity (XAN)ventral blood island0.0001957Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0002583Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.0003392Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior placodal area0.0008332Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.04812Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.4142Moderately 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 groups0.3921Moderately 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 acetyltransferase0.0001858InformativeDirect
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 ligase0.0000005343Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.0001163Highly 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 ]