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Homeodomain-like 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:   Homeodomain-like [ 46689] (19)
Families:   Homeodomain [ 46690] (40)
  Recombinase DNA-binding domain [ 46728] (5)
  Myb/SANT domain [ 46739] (15)
  SLIDE domain [ 100998]
  GARP response regulators [ 81683]
  DNA-binding domain of telomeric protein [ 46745] (2)
  Paired domain [ 46748] (3)
  DNA-binding domain of rap1 [ 46753]
  Centromere-binding [ 46756] (2)
  FIS-like [ 100918] (4)
  AraC type transcriptional activator [ 46759] (2)
  Tetracyclin repressor-like, N-terminal domain [ 46764] (34)
  Middle operon regulator, Mor [ 109659]
  Psq domain [ 140213]
  Alr1493-like [ 140216]
  Nanomeric phage protein-like [ 140219]
  SWIRM domain [ 140222] (3)
  Cgl2762-like [ 158260]
  RpiR-like [ 158263]


Superfamily statistics
Genomes (2,989) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 218,252 1,404,420 207
Proteins 189,461 1,198,814 197


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)Phosphotransferases with an alcohol group as accep0.0000000007689Moderately InformativeDirect
Enzyme Commission (EC)Glucokinase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)endocrine system disease0.6964Moderately InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0.000002471Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the eye0.01948Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.0407Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.04251Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.2996Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.5211Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.9449Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ear0.01286Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.08053Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.127Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.4079Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye morphology0.4185Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.4241Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.5182Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.6724Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.7888Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.8638Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.8788Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.9893Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pituitary gland0.001758InformativeInherited
Phenotypic Abnormality (PA)Abnormal lip morphology0.01433InformativeInherited
Phenotypic Abnormality (PA)Short stature0.03133InformativeInherited
Phenotypic Abnormality (PA)Abnormal palate morphology0.06989InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1648InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the calvaria0.1742InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the cerebrum0.2981InformativeInherited
Phenotypic Abnormality (PA)Abnormality of circulating hormone level0.4198InformativeInherited
Phenotypic Abnormality (PA)Abdominal symptom0.53InformativeInherited
Phenotypic Abnormality (PA)Abnormal cornea morphology0.7985InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.8343InformativeInherited
Phenotypic Abnormality (PA)Abnormal bone structure0.9424InformativeInherited
Phenotypic Abnormality (PA)Abdominal distention0.00008243Highly InformativeDirect
Phenotypic Abnormality (PA)Cleft upper lip0.0001571Highly InformativeDirect
Phenotypic Abnormality (PA)Agenesis of corpus callosum0.0009324Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of circulating adrenocorticotropin level0.001416Highly InformativeInherited
Phenotypic Abnormality (PA)Midline defect of the nose0.0153Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal anterior chamber morphology0.05106Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cheek0.2847Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the middle ear0.3546Highly InformativeInherited
Phenotypic Abnormality (PA)Cleft palate0.4177Highly InformativeInherited
Phenotypic Abnormality (PA)Reduced bone mineral density0.8304Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.0000000000005347Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00000004238Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.00000008089Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.004834Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.3511Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.7206Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype1Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype1Least InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)lethality during fetal growth through weaning0.0000000000008693Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.00000000000427Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.000000000296Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.0000002652Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.000003586Moderately InformativeDirect
Mammalian Phenotype (MP)respiratory system phenotype0.00001101Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal digestive system morphology0.0007245Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal muscle morphology0.006625Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.01347Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.01778Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.04323Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.04829Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.05195Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1888Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.2995Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.339Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.4431Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.7029Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.8063Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)perinatal lethality0.0000000003228InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.0000004023InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.000006725InformativeDirect
Mammalian Phenotype (MP)abnormal cell differentiation0.00006035InformativeDirect
Mammalian Phenotype (MP)abnormal gas homeostasis0.00006286InformativeDirect
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.0001058InformativeDirect
Mammalian Phenotype (MP)abnormal spinal cord morphology0.0002994InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.001038InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.001091InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.002028InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.002372InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.002891InformativeInherited
Mammalian Phenotype (MP)abnormal consumption behavior0.002964InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.02428InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.03243InformativeInherited
Mammalian Phenotype (MP)abnormal hypaxial muscle morphology0.06346InformativeInherited
Mammalian Phenotype (MP)abnormal hearing physiology0.06392InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.09492InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.1172InformativeInherited
Mammalian Phenotype (MP)abnormal uvea morphology0.1305InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.162InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.2028InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.2345InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.2775InformativeInherited
Mammalian Phenotype (MP)abnormal pancreas morphology0.3482InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5328InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.5363InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.6511InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.6803InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.7614InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.8221InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.8395InformativeInherited
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.8531InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.9613InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.9765InformativeInherited
Mammalian Phenotype (MP)cyanosis0.000000002727Highly InformativeDirect
Mammalian Phenotype (MP)abnormal middle ear morphology0.000000004079Highly InformativeDirect
Mammalian Phenotype (MP)abnormal joint morphology0.0000002161Highly InformativeDirect
Mammalian Phenotype (MP)taste/olfaction phenotype0.000000641Highly InformativeDirect
Mammalian Phenotype (MP)abnormal brain ventricle morphology0.000001292Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.000001441Highly InformativeDirect
Mammalian Phenotype (MP)abnormal forelimb morphology0.000005175Highly InformativeDirect
Mammalian Phenotype (MP)abnormal secondary palate development0.000005409Highly InformativeDirect
Mammalian Phenotype (MP)postnatal lethality0.00002345Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neurocranium morphology0.00003577Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vas deferens morphology0.000039Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circumventricular organ morphology0.00005668Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.0001829Highly InformativeDirect
Mammalian Phenotype (MP)abnormal nose morphology0.0003125Highly InformativeDirect
Mammalian Phenotype (MP)abnormal telencephalon development0.0003449Highly InformativeDirect
Mammalian Phenotype (MP)abnormal kidney development0.0004247Highly InformativeDirect
Mammalian Phenotype (MP)abnormal right subclavian artery morphology0.0006029Highly InformativeDirect
Mammalian Phenotype (MP)impaired branching involved in ureteric bud morphogenesis0.0006345Highly InformativeDirect
Mammalian Phenotype (MP)abnormal tongue morphology0.001191Highly InformativeInherited
Mammalian Phenotype (MP)abnormal aortic arch morphology0.001518Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary gland morphology0.00771Highly InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.01073Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.01151Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.01396Highly InformativeInherited
Mammalian Phenotype (MP)abnormal limb long bone morphology0.02087Highly InformativeInherited
Mammalian Phenotype (MP)impaired hearing0.02658Highly InformativeInherited
Mammalian Phenotype (MP)abnormal rib morphology0.03427Highly InformativeInherited
Mammalian Phenotype (MP)abnormal alveolar process morphology0.264Highly InformativeInherited
Mammalian Phenotype (MP)abnormal olfactory bulb layer morphology0.2678Highly InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular meshwork morphology0.2767Highly InformativeInherited
Mammalian Phenotype (MP)abnormal mesonephros morphology0.2914Highly InformativeInherited
Mammalian Phenotype (MP)abnormal food intake0.4945Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.614Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pancreatic islet morphology0.9793Highly 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 variant0.00000004038Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0000002549Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000002986Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0679Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.07444Least InformativeInherited
Worm Phenotype (WP)larval lethal0.353Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.7737Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.0000000002985Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.00000001401Moderately InformativeDirect
Worm Phenotype (WP)nervous system morphology variant0.00001328Moderately InformativeDirect
Worm Phenotype (WP)metabolic pathway variant0.6235Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.7969Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.8075Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.8681Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.8854Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.9189Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant1Moderately InformativeInherited
Worm Phenotype (WP)male morphology variant0.00000000007223InformativeDirect
Worm Phenotype (WP)tail morphology variant0.0000688InformativeDirect
Worm Phenotype (WP)growth rate variant0.0001112InformativeDirect
Worm Phenotype (WP)protein degradation variant0.0007292InformativeDirect
Worm Phenotype (WP)locomotor coordination variant0.05202InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.05621InformativeInherited
Worm Phenotype (WP)foraging behavior variant0.1531InformativeInherited
Worm Phenotype (WP)body posture variant0.202InformativeInherited
Worm Phenotype (WP)vulva development variant0.2326InformativeInherited
Worm Phenotype (WP)egg laying variant0.3136InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.4498InformativeInherited
Worm Phenotype (WP)locomotion reduced0.6045InformativeInherited
Worm Phenotype (WP)drug resistant0.6837InformativeInherited
Worm Phenotype (WP)VPC competence variant1InformativeInherited
Worm Phenotype (WP)cell number increased1InformativeInherited
Worm Phenotype (WP)lineage variant0.00000006402Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00000006984Highly InformativeDirect
Worm Phenotype (WP)body axis morphology variant0.0000007131Highly InformativeDirect
Worm Phenotype (WP)forward locomotion decreased0.00001406Highly InformativeDirect
Worm Phenotype (WP)carbon dioxide avoidance variant0.00005458Highly InformativeDirect
Worm Phenotype (WP)cell number decreased0.00006199Highly InformativeDirect
Worm Phenotype (WP)neuronal cell fate specification variant0.0001399Highly InformativeDirect
Worm Phenotype (WP)vulvaless0.0003269Highly InformativeDirect
Worm Phenotype (WP)male tail development variant0.0003486Highly InformativeDirect
Worm Phenotype (WP)coiling frequency0.0003704Highly InformativeDirect
Worm Phenotype (WP)multiple anchor cells0.0004407Highly InformativeDirect
Worm Phenotype (WP)male nervous system development variant0.0006778Highly InformativeDirect
Worm Phenotype (WP)early larval lethal0.0008451Highly InformativeDirect
Worm Phenotype (WP)cell fusion variant0.0008779Highly InformativeDirect
Worm Phenotype (WP)body posture amplitude variant0.0009534Highly InformativeDirect
Worm Phenotype (WP)roaming variant0.01961Highly InformativeInherited
Worm Phenotype (WP)egg retention0.417Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.07052Least InformativeInherited
Fly Phenotype (FP)lethal - all die before end of P-stage0.03618Moderately InformativeInherited
Fly Phenotype (FP)visible0InformativeDirect
Fly Phenotype (FP)lethal - all die before end of larval stage0.0000004831InformativeDirect
Fly Phenotype (FP)wild-type0.0006577InformativeDirect
Fly Phenotype (FP)lethal - all die before end of embryonic stage0.00000000001816Highly InformativeDirect
Fly Phenotype (FP)homeotic0.00000006903Highly InformativeDirect
Fly Phenotype (FP)some die during embryonic stage0.00001071Highly InformativeDirect
Fly Phenotype (FP)some die during P-stage0.3543Highly InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.00000000003309Least InformativeDirect
Fly Anatomy (FA)adult0.0000000007793Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0.0006278Least InformativeDirect
Fly Anatomy (FA)larva0.01388Least InformativeInherited
Fly Anatomy (FA)nervous system0.3022Least InformativeInherited
Fly Anatomy (FA)somatic cell0.3502Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)adult integumentary system0.0000003978Moderately InformativeDirect
Fly Anatomy (FA)appendage0.0000148Moderately InformativeDirect
Fly Anatomy (FA)multi-cell-component structure0.00002597Moderately InformativeDirect
Fly Anatomy (FA)adult thorax0.0001374Moderately InformativeDirect
Fly Anatomy (FA)acellular anatomical structure0.0001465Moderately InformativeDirect
Fly Anatomy (FA)cell cluster organ0.0002631Moderately InformativeDirect
Fly Anatomy (FA)sense organ0.001098Moderately InformativeInherited
Fly Anatomy (FA)ganglion0.001591Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.00208Moderately InformativeInherited
Fly Anatomy (FA)portion of tissue0.01793Moderately InformativeInherited
Fly Anatomy (FA)neuron0.0567Moderately InformativeInherited
Fly Anatomy (FA)tagmatic subdivision of integument0.08457Moderately InformativeInherited
Fly Anatomy (FA)late embryo0.1182Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.1836Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.3259Moderately InformativeInherited
Fly Anatomy (FA)stem cell0.3411Moderately InformativeInherited
Fly Anatomy (FA)thoracic segment0.3629Moderately InformativeInherited
Fly Anatomy (FA)somatic precursor cell0.4723Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.8194Moderately InformativeInherited
Fly Anatomy (FA)head0.8991Moderately InformativeInherited
Fly Anatomy (FA)larval abdomen0.00000000006689InformativeDirect
Fly Anatomy (FA)interneuron0.000008539InformativeDirect
Fly Anatomy (FA)adult external head0.00001291InformativeDirect
Fly Anatomy (FA)syncytium0.0002185InformativeDirect
Fly Anatomy (FA)gland0.0002289InformativeDirect
Fly Anatomy (FA)abdominal segment0.000347InformativeDirect
Fly Anatomy (FA)mechanosensory system0.0004643InformativeDirect
Fly Anatomy (FA)extended germ band embryo0.0006846InformativeDirect
Fly Anatomy (FA)adult procephalic segment0.001071InformativeInherited
Fly Anatomy (FA)primordium0.001114InformativeInherited
Fly Anatomy (FA)muscle system0.003029InformativeInherited
Fly Anatomy (FA)presumptive embryonic/larval system0.006089InformativeInherited
Fly Anatomy (FA)dorsal closure embryo0.0119InformativeInherited
Fly Anatomy (FA)nerve0.01392InformativeInherited
Fly Anatomy (FA)chemosensory system0.01881InformativeInherited
Fly Anatomy (FA)neuromere0.02377InformativeInherited
Fly Anatomy (FA)embryonic/larval integumentary system0.03881InformativeInherited
Fly Anatomy (FA)cuticular specialization0.03905InformativeInherited
Fly Anatomy (FA)leg0.06111InformativeInherited
Fly Anatomy (FA)supraesophageal ganglion0.1653InformativeInherited
Fly Anatomy (FA)tract0.2219InformativeInherited
Fly Anatomy (FA)adult brain0.2299InformativeInherited
Fly Anatomy (FA)larval thoracic segment0.2671InformativeInherited
Fly Anatomy (FA)eye photoreceptor cell0.3736InformativeInherited
Fly Anatomy (FA)embryonic/larval peripheral nervous system0.6308InformativeInherited
Fly Anatomy (FA)chaeta0.6617InformativeInherited
Fly Anatomy (FA)neuroblast0.8165InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.9325InformativeInherited
Fly Anatomy (FA)ventral nerve cord primordium0.00000001202Highly InformativeDirect
Fly Anatomy (FA)embryonic neuroblast0.000001767Highly InformativeDirect
Fly Anatomy (FA)trunk mesoderm derivative0.000006485Highly InformativeDirect
Fly Anatomy (FA)commissure0.00001425Highly InformativeDirect
Fly Anatomy (FA)embryonic head0.00004294Highly InformativeDirect
Fly Anatomy (FA)mesothoracic tergum0.00005233Highly InformativeDirect
Fly Anatomy (FA)antennal lobe glomerulus VA1v0.00006595Highly InformativeDirect
Fly Anatomy (FA)segment of leg0.0001075Highly InformativeDirect
Fly Anatomy (FA)presumptive embryonic/larval central nervous system0.0001197Highly InformativeDirect
Fly Anatomy (FA)ventral nervous system0.0002448Highly InformativeDirect
Fly Anatomy (FA)adult metathoracic segment0.0003335Highly InformativeDirect
Fly Anatomy (FA)head bristle0.0003638Highly InformativeDirect
Fly Anatomy (FA)larval abdominal segment 20.0005786Highly InformativeDirect
Fly Anatomy (FA)maxillary palp sense organ0.0009805Highly InformativeDirect
Fly Anatomy (FA)denticle belt0.001101Highly InformativeInherited
Fly Anatomy (FA)subesophageal ganglion0.001365Highly InformativeInherited
Fly Anatomy (FA)sensillum basiconicum0.04029Highly InformativeInherited
Fly Anatomy (FA)third segment of antenna0.0475Highly InformativeInherited
Fly Anatomy (FA)olfactory sensory organ0.2735Highly InformativeInherited
Fly Anatomy (FA)antennal lobe projection neuron iPN0.2752Highly InformativeInherited
Fly Anatomy (FA)antennal lobe projection neuron adPN0.4157Highly InformativeInherited
Fly Anatomy (FA)adult antennal sense organ0.4437Highly InformativeInherited
Fly Anatomy (FA)unilateral ACT relay interneuron0.7497Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)multi-tissue structure0.008686Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.08343Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.1592Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.1776Least InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.2721Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.8939Moderately InformativeInherited
Zebrafish Anatomy (ZA)forebrain0.0001995InformativeDirect
Zebrafish Anatomy (ZA)embryonic structure0.2199InformativeInherited
Zebrafish Anatomy (ZA)digestive system0.3123InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.9228InformativeInherited
Zebrafish Anatomy (ZA)endocrine system0.004469Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.0000000000001496Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00001062Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.02272Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.3129Least InformativeInherited
Xenopus ANatomical entity (XAN)cell1Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk1Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ1Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.002084Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.2094Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.2955Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)forebrain0InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.000000000000002943InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.00000000000002204InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000000000002096InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0000000000006194InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.000000000007555InformativeDirect
Xenopus ANatomical entity (XAN)peripheral nervous system0.00000000005944InformativeDirect
Xenopus ANatomical entity (XAN)epithelium0.000000005044InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.00002761InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.0000401InformativeDirect
Xenopus ANatomical entity (XAN)vestibuloauditory system0.00205InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.02935InformativeInherited
Xenopus ANatomical entity (XAN)tail0.7511InformativeInherited
Xenopus ANatomical entity (XAN)intestine1InformativeInherited
Xenopus ANatomical entity (XAN)endocrine system1InformativeInherited
Xenopus ANatomical entity (XAN)connective tissue1InformativeInherited
Xenopus ANatomical entity (XAN)limb1InformativeInherited
Xenopus ANatomical entity (XAN)solid compound organ1InformativeInherited
Xenopus ANatomical entity (XAN)midbrain0Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0Highly InformativeDirect
Xenopus ANatomical entity (XAN)presumptive midbrain-hindbrain boundary0Highly InformativeDirect
Xenopus ANatomical entity (XAN)non-neural ectoderm0Highly InformativeDirect
Xenopus ANatomical entity (XAN)neuromere0Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.000000000000001473Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.000000000000002943Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesenchyme0.00000000000001323Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0000000000003362Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural plate border0.000000000002048Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.000000000002949Highly InformativeDirect
Xenopus ANatomical entity (XAN)neuron0.000000000003683Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.000000000007186Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural ridge0.0000000002885Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000000004338Highly InformativeDirect
Xenopus ANatomical entity (XAN)proliferative region0.000000005559Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.00000006029Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindgut0.0000001359Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.0000002324Highly InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.0000004562Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.0000008077Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural nucleus0.000002475Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail bud0.000002943Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial nerve0.000003284Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.000009914Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00001453Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.00002346Highly InformativeDirect
Xenopus ANatomical entity (XAN)ganglion0.00002947Highly InformativeDirect
Xenopus ANatomical entity (XAN)retinal ganglion cell layer0.00003093Highly InformativeDirect
Xenopus ANatomical entity (XAN)somite0.0001445Highly InformativeDirect
Xenopus ANatomical entity (XAN)intersomitic region0.0002566Highly InformativeDirect
Xenopus ANatomical entity (XAN)pronephric kidney0.1368Highly InformativeInherited
Xenopus ANatomical entity (XAN)neurogenic placode0.4262Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone1Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage1Least InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.0000000001335Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage1Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)tailbud stage0.9945InformativeInherited
Xenopus DEvelopment stage (XDE)adult frog stage0.00000003145Highly InformativeDirect
Xenopus DEvelopment stage (XDE)premetamorphosis stage0.07432Highly InformativeInherited
Xenopus DEvelopment stage (XDE)gastrula stage0.1106Highly InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0.6371Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.8211Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.8878Least InformativeInherited
Plant ANatomical entity (PAN)whole plant1Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue1Least InformativeInherited
Plant ANatomical entity (PAN)megasporophyll1Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll1Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure1Least InformativeInherited
Plant ANatomical entity (PAN)root system1Least InformativeInherited
Plant ANatomical entity (PAN)leaf1Least InformativeInherited
Plant ANatomical entity (PAN)sporangium1Least InformativeInherited
Plant ANatomical entity (PAN)root tip0.000000003833InformativeDirect
Plant ANatomical entity (PAN)portion of vascular tissue0.000000004857InformativeDirect
Plant ANatomical entity (PAN)primordium0.0000000417InformativeDirect
Plant ANatomical entity (PAN)portion of ground tissue0.00000009866InformativeDirect
Plant ANatomical entity (PAN)fruit0.0005262InformativeDirect
Plant ANatomical entity (PAN)root epidermis0.046InformativeInherited
Plant ANatomical entity (PAN)shoot apical meristem0.00000000000009716Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex0.0000000001167Highly InformativeDirect
Plant ANatomical entity (PAN)primary root0.000000005827Highly InformativeDirect
Plant ANatomical entity (PAN)vegetative shoot apex0.000000008143Highly InformativeDirect
Plant ANatomical entity (PAN)plant ovule0.00000003744Highly InformativeDirect
Plant ANatomical entity (PAN)phyllome primordium0.00000009138Highly InformativeDirect
Plant ANatomical entity (PAN)trichome0.000001882Highly InformativeDirect
Plant ANatomical entity (PAN)plant axis elongation zone0.000008875Highly InformativeDirect
Plant ANatomical entity (PAN)anther0.00001195Highly InformativeDirect
Plant ANatomical entity (PAN)juvenile vascular leaf0.00002125Highly InformativeDirect
Plant ANatomical entity (PAN)phyllome vascular system0.00006884Highly InformativeDirect
Plant ANatomical entity (PAN)style0.0001112Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.0002813Highly InformativeDirect
Plant ANatomical entity (PAN)lateral root0.0003888Highly InformativeDirect
Plant ANatomical entity (PAN)root meristem0.006502Highly InformativeInherited
Plant structure DEvelopment stage (PDE)seedling development stage0.0005921InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0.3413Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.00000006816Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.1714Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.2552Moderately InformativeInherited

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR009057 SSF46689 Protein matches
Abstract

Homeodomain proteins are transcription factors that share a related DNA binding homeodomain [PubMed10377888]. The homeodomain was first identified in a number of Drosophila homeotic and segmentation proteins, but is now known to be well conserved in many other animals, including vertebrates. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. The first helix helps to stabilise the structure. Many proteins contain homeodomains, including Drosophila Engrailed, yeast mating type proteins, hepatocyte nuclear factor 1a and HOX proteins.

The homeodomain motif is very similar in sequence and structure to domains in a wide range of DNA-binding proteins, including recombinases, Myb proteins, GARP response regulators, human telomeric proteins (hTRF1), paired domain proteins (PAX), yeast RAP1, centromere-binding proteins CENP-B and ABP-1, transcriptional regulators (TyrR), AraC-type transcriptional activators, and tetracycline repressor-like proteins (TetR, QacR, YcdC) [PubMed12215502, PubMed9739097, PubMed7707374].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 187 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 Homeodomain-like 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 187 hidden Markov models representing the Homeodomain-like 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 · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]