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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 system0.07177Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.1963Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.2419Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.2984Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.1896Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.388Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.8497Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.8765Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.3692InformativeInherited
Phenotypic Abnormality (PA)Short stature0.37InformativeInherited
Phenotypic Abnormality (PA)Hypoplastic labia majora0.000008514Highly InformativeDirect
Phenotypic Abnormality (PA)Retrognathia0.00006183Highly InformativeDirect
Phenotypic Abnormality (PA)Proportionate short stature0.004174Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal pancreas morphology0.0489Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.000003936Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.005554Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.000006679Moderately InformativeDirect
Mammalian Phenotype (MP)prenatal lethality0.0007979Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0.2175Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.2415Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.3514Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.8007Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal smooth muscle morphology0.2897InformativeInherited
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 morphology0.0003799Highly 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 variant0.0000000000004228Least InformativeDirect
Worm Phenotype (WP)cell development variant0.000000000001307Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00000002424Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000000637Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.001133Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.002707Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)life span variant0.000004034Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.000008333Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.00003158Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00003942Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0006166Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.00256Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.03059Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.05913Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2487Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.4689Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.5454Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.5826Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.6539Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.742Moderately InformativeInherited
Worm Phenotype (WP)accumulated germline cell corpses0.00003915InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.000565InformativeDirect
Worm Phenotype (WP)brood size variant0.0007416InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.009286InformativeInherited
Worm Phenotype (WP)pigmentation variant0.01321InformativeInherited
Worm Phenotype (WP)pesticide response variant0.2323InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.3326InformativeInherited
Worm Phenotype (WP)vulva development variant0.3368InformativeInherited
Worm Phenotype (WP)VPC competence variant0.5893InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.7901InformativeInherited
Worm Phenotype (WP)cell stress response variant0.8956InformativeInherited
Worm Phenotype (WP)level of protein expression variant1InformativeInherited
Worm Phenotype (WP)rachis morphology variant1InformativeInherited
Worm Phenotype (WP)mitotic spindle defective early emb0.00003519Highly InformativeDirect
Worm Phenotype (WP)passage through meiosis defective early emb0.00004367Highly InformativeDirect
Worm Phenotype (WP)spontaneous mutation rate increased0.00005196Highly InformativeDirect
Worm Phenotype (WP)X chromosome nondisjunction0.0000753Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.0001819Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.0002326Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0003605Highly InformativeDirect
Worm Phenotype (WP)paraquat hypersensitive0.0004996Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.0007825Highly InformativeDirect
Worm Phenotype (WP)neuropil development variant0.04274Highly 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)embryo0.000000001318Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.0001017Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.03397Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system0.2181Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.229Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.2535Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.000000000000002936Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0.0000000008431Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.000000003196Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.001463Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.3607Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.3973Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.00000000003561InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.00000004927InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00000005018InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000001765InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.00002218InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0001273InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.0002992InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.000698InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.003552InformativeInherited
Xenopus ANatomical entity (XAN)tail0.3548InformativeInherited
Xenopus ANatomical entity (XAN)intersomitic region0.00003055Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.00003508Highly InformativeDirect
Xenopus ANatomical entity (XAN)non-neural ectoderm0.00004364Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.00005776Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.0001136Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.0002403Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.0005645Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.0009699Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail bud0.002832Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.2977Moderately 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 groups0.5763Moderately 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 acetyltransferase0.0001602InformativeDirect
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 ligase0.0000005437Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.000126Highly 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 ]