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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 disease0.6969Moderately 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 inheritance0.000005623Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the eye0.038Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.04269Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.08529Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.2947Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.696Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.9346Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.1724Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.249Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.3841Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye morphology0.3947Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.407Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.4661Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.5875Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.8225Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.8291Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal lip morphology0.01901InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.02374InformativeInherited
Phenotypic Abnormality (PA)Short stature0.04197InformativeInherited
Phenotypic Abnormality (PA)Abnormal palate morphology0.1008InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the calvaria0.1603InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1862InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating hormone level0.4845InformativeInherited
Phenotypic Abnormality (PA)Abdominal symptom0.565InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.7895InformativeInherited
Phenotypic Abnormality (PA)Abnormal cornea morphology0.8051InformativeInherited
Phenotypic Abnormality (PA)Abdominal distention0.0001289Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of circulating adrenocorticotropin level0.0009952Highly InformativeDirect
Phenotypic Abnormality (PA)Oral cleft0.006147Highly InformativeInherited
Phenotypic Abnormality (PA)Midline defect of the nose0.014Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal hard palate morphology0.02282Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cervical spine0.2435Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cheek0.3644Highly InformativeInherited
Phenotypic Abnormality (PA)Reduced bone mineral density0.8432Highly InformativeInherited
Phenotypic Abnormality (PA)Anterior hypopituitarism0.9504Highly 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 phenotype0.0000000000008791Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00000002897Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.00000006067Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.005565Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.363Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.7365Least 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 weaning0.0000000000005872Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.00000000000559Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000000003852Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.0000003128Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.000003855Moderately InformativeDirect
Mammalian Phenotype (MP)respiratory system phenotype0.00001267Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal digestive system morphology0.0007273Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal muscle morphology0.006691Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.013Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.01745Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.0418Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.04679Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.04835Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1888Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.3079Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.3384Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.4516Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.6989Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.814Moderately 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 lethality0.0000000004904InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.0000005381InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.000007937InformativeDirect
Mammalian Phenotype (MP)abnormal cell differentiation0.00006043InformativeDirect
Mammalian Phenotype (MP)abnormal gas homeostasis0.00006751InformativeDirect
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.0001005InformativeDirect
Mammalian Phenotype (MP)abnormal spinal cord morphology0.0002944InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.001039InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.001279InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.002033InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.00242InformativeInherited
Mammalian Phenotype (MP)abnormal consumption behavior0.002929InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.002962InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.01898InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.03243InformativeInherited
Mammalian Phenotype (MP)abnormal hypaxial muscle morphology0.06244InformativeInherited
Mammalian Phenotype (MP)abnormal hearing physiology0.06663InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.09497InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.1173InformativeInherited
Mammalian Phenotype (MP)abnormal uvea morphology0.1306InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.1731InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.2029InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.2346InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.2776InformativeInherited
Mammalian Phenotype (MP)abnormal pancreas morphology0.3484InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5329InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.6038InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.6484InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.6804InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.7616InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.8223InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.8395InformativeInherited
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.8531InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.9636InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.9767InformativeInherited
Mammalian Phenotype (MP)cyanosis0.000000002987Highly InformativeDirect
Mammalian Phenotype (MP)abnormal middle ear morphology0.000000003814Highly InformativeDirect
Mammalian Phenotype (MP)abnormal joint morphology0.00000009722Highly InformativeDirect
Mammalian Phenotype (MP)taste/olfaction phenotype0.0000006822Highly InformativeDirect
Mammalian Phenotype (MP)abnormal brain ventricle morphology0.00000139Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.000001584Highly InformativeDirect
Mammalian Phenotype (MP)abnormal forelimb morphology0.00000518Highly InformativeDirect
Mammalian Phenotype (MP)abnormal secondary palate development0.000005623Highly InformativeDirect
Mammalian Phenotype (MP)postnatal lethality0.0000154Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neurocranium morphology0.0000212Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vas deferens morphology0.00003902Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circumventricular organ morphology0.00005671Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.0001871Highly InformativeDirect
Mammalian Phenotype (MP)abnormal nose morphology0.000313Highly InformativeDirect
Mammalian Phenotype (MP)abnormal telencephalon development0.0003457Highly InformativeDirect
Mammalian Phenotype (MP)abnormal kidney development0.0004399Highly InformativeDirect
Mammalian Phenotype (MP)abnormal right subclavian artery morphology0.0006175Highly InformativeDirect
Mammalian Phenotype (MP)impaired branching involved in ureteric bud morphogenesis0.0006489Highly InformativeDirect
Mammalian Phenotype (MP)abnormal basicranium morphology0.0008001Highly InformativeDirect
Mammalian Phenotype (MP)abnormal tongue morphology0.001194Highly InformativeInherited
Mammalian Phenotype (MP)abnormal aortic arch morphology0.001562Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary gland morphology0.007719Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.01152Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.01399Highly InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.015Highly InformativeInherited
Mammalian Phenotype (MP)abnormal limb long bone morphology0.02088Highly InformativeInherited
Mammalian Phenotype (MP)impaired hearing0.02597Highly InformativeInherited
Mammalian Phenotype (MP)abnormal rib morphology0.03011Highly InformativeInherited
Mammalian Phenotype (MP)abnormal alveolar process morphology0.2641Highly InformativeInherited
Mammalian Phenotype (MP)abnormal olfactory bulb layer morphology0.2679Highly InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular meshwork morphology0.2768Highly InformativeInherited
Mammalian Phenotype (MP)abnormal mesonephros morphology0.2914Highly InformativeInherited
Mammalian Phenotype (MP)abnormal food intake0.4946Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.6141Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pancreatic islet morphology0.9794Highly 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 variant0.00000002479Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000002078Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0000002316Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.08936Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.1565Least InformativeInherited
Worm Phenotype (WP)larval lethal0.2744Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.7692Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.0000000008243Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.00000001534Moderately InformativeDirect
Worm Phenotype (WP)nervous system morphology variant0.00001691Moderately InformativeDirect
Worm Phenotype (WP)metabolic pathway variant0.6535Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.782Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.8152Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.8419Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.9287Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.9388Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant1Moderately InformativeInherited
Worm Phenotype (WP)male morphology variant0.00000000005552InformativeDirect
Worm Phenotype (WP)tail morphology variant0.00004737InformativeDirect
Worm Phenotype (WP)protein degradation variant0.0007329InformativeDirect
Worm Phenotype (WP)locomotor coordination variant0.05538InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.06359InformativeInherited
Worm Phenotype (WP)foraging behavior variant0.1516InformativeInherited
Worm Phenotype (WP)body posture variant0.2075InformativeInherited
Worm Phenotype (WP)vulva development variant0.2148InformativeInherited
Worm Phenotype (WP)egg laying variant0.3179InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.4305InformativeInherited
Worm Phenotype (WP)locomotion reduced0.6029InformativeInherited
Worm Phenotype (WP)drug resistant0.6602InformativeInherited
Worm Phenotype (WP)VPC competence variant1InformativeInherited
Worm Phenotype (WP)cell number increased1InformativeInherited
Worm Phenotype (WP)lineage variant0.00000006271Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.00000007054Highly InformativeDirect
Worm Phenotype (WP)body axis morphology variant0.0000007182Highly InformativeDirect
Worm Phenotype (WP)forward locomotion decreased0.00001414Highly InformativeDirect
Worm Phenotype (WP)cell number decreased0.00004554Highly InformativeDirect
Worm Phenotype (WP)carbon dioxide avoidance variant0.00005488Highly InformativeDirect
Worm Phenotype (WP)growth rate variant0.000119Highly InformativeDirect
Worm Phenotype (WP)neuronal cell fate specification variant0.0002346Highly InformativeDirect
Worm Phenotype (WP)male tail development variant0.0002714Highly InformativeDirect
Worm Phenotype (WP)vulvaless0.0002993Highly InformativeDirect
Worm Phenotype (WP)coiling frequency0.0003724Highly InformativeDirect
Worm Phenotype (WP)multiple anchor cells0.0004395Highly InformativeDirect
Worm Phenotype (WP)male nervous system development variant0.0006364Highly InformativeDirect
Worm Phenotype (WP)early larval lethal0.0009102Highly InformativeDirect
Worm Phenotype (WP)body posture amplitude variant0.000958Highly InformativeDirect
Worm Phenotype (WP)cell fusion variant0.0009601Highly InformativeDirect
Worm Phenotype (WP)roaming variant0.02022Highly InformativeInherited
Worm Phenotype (WP)egg retention0.4205Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.0971Least InformativeInherited
Fly Phenotype (FP)visible0Moderately InformativeDirect
Fly Phenotype (FP)lethal0.25Moderately InformativeInherited
Fly Phenotype (FP)lethal - all die before end of first instar larval stage0.0000000003451InformativeDirect
Fly Phenotype (FP)wild-type0.0005364InformativeDirect
Fly Phenotype (FP)lethal - all die before end of embryonic stage0.00000000001433Highly InformativeDirect
Fly Phenotype (FP)homeotic0.00000006317Highly InformativeDirect
Fly Phenotype (FP)some die during embryonic stage0.000008296Highly InformativeDirect
Fly Phenotype (FP)some die during P-stage0.3411Highly 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 subdivision0.0000000001759Least InformativeDirect
Fly Anatomy (FA)adult0.000000005877Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0.0004897Least InformativeDirect
Fly Anatomy (FA)larva0.02021Least InformativeInherited
Fly Anatomy (FA)nervous system0.3183Least InformativeInherited
Fly Anatomy (FA)somatic cell0.3618Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)region of integument0.00000002615Moderately InformativeDirect
Fly Anatomy (FA)adult integumentary system0.0000001113Moderately InformativeDirect
Fly Anatomy (FA)appendage0.000009399Moderately InformativeDirect
Fly Anatomy (FA)multi-cell-component structure0.00002366Moderately InformativeDirect
Fly Anatomy (FA)acellular anatomical structure0.0001394Moderately InformativeDirect
Fly Anatomy (FA)thorax0.001064Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.00193Moderately InformativeInherited
Fly Anatomy (FA)ganglion0.002698Moderately InformativeInherited
Fly Anatomy (FA)neuron0.05906Moderately InformativeInherited
Fly Anatomy (FA)late embryo0.129Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.1703Moderately InformativeInherited
Fly Anatomy (FA)stem cell0.3314Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.4172Moderately InformativeInherited
Fly Anatomy (FA)somatic precursor cell0.4315Moderately InformativeInherited
Fly Anatomy (FA)sensory system0.5863Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.8216Moderately InformativeInherited
Fly Anatomy (FA)head0.9093Moderately InformativeInherited
Fly Anatomy (FA)larval abdomen0.00000000002918InformativeDirect
Fly Anatomy (FA)larval segment0.0000000003382InformativeDirect
Fly Anatomy (FA)antennal segment0.000002933InformativeDirect
Fly Anatomy (FA)interneuron0.000008785InformativeDirect
Fly Anatomy (FA)adult external head0.00001057InformativeDirect
Fly Anatomy (FA)syncytium0.0001934InformativeDirect
Fly Anatomy (FA)abdominal segment0.000232InformativeDirect
Fly Anatomy (FA)mechanosensory system0.0003985InformativeDirect
Fly Anatomy (FA)extended germ band embryo0.0004605InformativeDirect
Fly Anatomy (FA)adult procephalic segment0.0008494InformativeDirect
Fly Anatomy (FA)primordium0.0009157InformativeDirect
Fly Anatomy (FA)eo-type sensillum0.001354InformativeInherited
Fly Anatomy (FA)muscle system0.002739InformativeInherited
Fly Anatomy (FA)presumptive embryonic/larval system0.004383InformativeInherited
Fly Anatomy (FA)dorsal closure embryo0.008805InformativeInherited
Fly Anatomy (FA)nerve0.01391InformativeInherited
Fly Anatomy (FA)chemosensory system0.01736InformativeInherited
Fly Anatomy (FA)embryonic/larval integumentary system0.03194InformativeInherited
Fly Anatomy (FA)neuromere0.03448InformativeInherited
Fly Anatomy (FA)cuticular specialization0.04266InformativeInherited
Fly Anatomy (FA)embryonic/larval circulatory system0.1151InformativeInherited
Fly Anatomy (FA)tract0.1897InformativeInherited
Fly Anatomy (FA)eye photoreceptor cell0.3751InformativeInherited
Fly Anatomy (FA)adult central nervous system0.3904InformativeInherited
Fly Anatomy (FA)brain0.438InformativeInherited
Fly Anatomy (FA)embryonic/larval peripheral nervous system0.6724InformativeInherited
Fly Anatomy (FA)neuroblast0.8194InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.9423InformativeInherited
Fly Anatomy (FA)labral segment1InformativeInherited
Fly Anatomy (FA)ventral nerve cord primordium0.000000009093Highly InformativeDirect
Fly Anatomy (FA)embryonic neuroblast0.000001789Highly InformativeDirect
Fly Anatomy (FA)commissure0.00001268Highly InformativeDirect
Fly Anatomy (FA)embryonic head0.00003124Highly InformativeDirect
Fly Anatomy (FA)mesothoracic tergum0.00004506Highly InformativeDirect
Fly Anatomy (FA)antennal lobe glomerulus VA1v0.00006463Highly InformativeDirect
Fly Anatomy (FA)presumptive embryonic/larval central nervous system0.0001309Highly InformativeDirect
Fly Anatomy (FA)segment of leg0.0001415Highly InformativeDirect
Fly Anatomy (FA)ventral nervous system0.000215Highly InformativeDirect
Fly Anatomy (FA)head bristle0.000292Highly InformativeDirect
Fly Anatomy (FA)adult metathoracic segment0.000312Highly InformativeDirect
Fly Anatomy (FA)larval abdominal segment 20.0006268Highly InformativeDirect
Fly Anatomy (FA)embryonic/larval dorsal vessel0.0009012Highly InformativeDirect
Fly Anatomy (FA)maxillary palp sense organ0.0009561Highly InformativeDirect
Fly Anatomy (FA)subesophageal ganglion0.00131Highly InformativeInherited
Fly Anatomy (FA)denticle belt0.001703Highly InformativeInherited
Fly Anatomy (FA)neuroblast lineage clone0.002331Highly InformativeInherited
Fly Anatomy (FA)germ layer derivative0.02563Highly InformativeInherited
Fly Anatomy (FA)sensillum basiconicum0.03989Highly InformativeInherited
Fly Anatomy (FA)third segment of antenna0.04331Highly InformativeInherited
Fly Anatomy (FA)antennal lobe projection neuron iPN0.2257Highly InformativeInherited
Fly Anatomy (FA)antennal lobe projection neuron adPN0.3285Highly InformativeInherited
Fly Anatomy (FA)olfactory sensory organ0.34Highly InformativeInherited
Fly Anatomy (FA)unilateral ACT relay interneuron0.3682Highly InformativeInherited
Fly Anatomy (FA)larval mesothoracic segment0.475Highly InformativeInherited
Fly Anatomy (FA)adult antennal sense organ0.4839Highly InformativeInherited
Fly Anatomy (FA)late extended germ band embryo0.4894Highly 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 structure0.008266Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.1145Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.1574Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.1727Least InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.2989Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.801Moderately InformativeInherited
Zebrafish Anatomy (ZA)forebrain0.0002974InformativeDirect
Zebrafish Anatomy (ZA)embryonic structure0.1795InformativeInherited
Zebrafish Anatomy (ZA)digestive system0.262InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.9636InformativeInherited
Zebrafish Anatomy (ZA)endocrine system0.006548Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.0000000000005116Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.000008553Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.3168Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least 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)musculoskeletal system0.001537Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.001832Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.07131Moderately InformativeInherited
Xenopus ANatomical entity (XAN)tail region0.2886Moderately 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)neural tube0InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0InformativeDirect
Xenopus ANatomical entity (XAN)eye0.000000000000009266InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.00000000000002466InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.00000000000003389InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.000000000008895InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.00000000001404InformativeDirect
Xenopus ANatomical entity (XAN)peripheral nervous system0.0000000001588InformativeDirect
Xenopus ANatomical entity (XAN)epithelium0.00000002441InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.00002251InformativeDirect
Xenopus ANatomical entity (XAN)vestibuloauditory system0.01015InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.0332InformativeInherited
Xenopus ANatomical entity (XAN)tail0.6523InformativeInherited
Xenopus ANatomical entity (XAN)urinary system0.7027InformativeInherited
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)presumptive midbrain-hindbrain boundary0Highly InformativeDirect
Xenopus ANatomical entity (XAN)neuromere0Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural fold0.00000000000000232Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesenchyme0.00000000000002159Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0000000000001323Highly InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.0000000000001462Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.000000000001266Highly InformativeDirect
Xenopus ANatomical entity (XAN)neuron0.000000000002489Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural plate border0.000000000004938Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior placodal area0.000000000006579Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural ridge0.0000000002557Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000000004574Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain-hindbrain boundary0.000000007281Highly InformativeDirect
Xenopus ANatomical entity (XAN)proliferative region0.000000008791Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindgut0.00000002518Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.00000008781Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordoneural hinge0.0000001531Highly InformativeDirect
Xenopus ANatomical entity (XAN)ventricular zone0.000000253Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.0000002999Highly InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.0000004226Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.000001039Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial nerve0.000001683Highly InformativeDirect
Xenopus ANatomical entity (XAN)proximal tubule0.000002064Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.000002477Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural nucleus0.000002864Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00001756Highly InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.00001812Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.00002973Highly InformativeDirect
Xenopus ANatomical entity (XAN)ganglion0.00006311Highly InformativeDirect
Xenopus ANatomical entity (XAN)presomitic mesoderm0.0002764Highly InformativeDirect
Xenopus ANatomical entity (XAN)somite0.0003779Highly InformativeDirect
Xenopus ANatomical entity (XAN)intersomitic region0.0004249Highly InformativeDirect
Xenopus ANatomical entity (XAN)archenteron0.01787Highly InformativeInherited
Xenopus ANatomical entity (XAN)olfactory system0.03527Highly InformativeInherited
Xenopus ANatomical entity (XAN)retinal neural layer0.4239Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone1Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage1Least InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.00000000002338Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage1Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.1006InformativeInherited
Xenopus DEvelopment stage (XDE)adult frog stage0.000001355Highly InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage 100.000004501Highly InformativeDirect
Xenopus DEvelopment stage (XDE)premetamorphosis stage0.0002698Highly InformativeDirect

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 groups0.3358Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.00000006886Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.1762Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.2532Moderately 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 ]