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  Home > SCOP hierarchy > Homeodomain-like superfamily


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 disease0.6967Moderately 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 inheritance0.00001132Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the eye0.03134Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.12Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1674Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.5002Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.7168Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.9543Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.123Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.1805Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.2545Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.3727Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.3942Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.5637Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal anterior eye segment morphology0.6217Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.8203Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.9066Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.9801Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal posterior eye segment morphology0.9933Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal lip morphology0.007001InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.01665InformativeInherited
Phenotypic Abnormality (PA)Abnormal palate morphology0.03395InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral white matter0.03984InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the calvaria0.1289InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1541InformativeInherited
Phenotypic Abnormality (PA)Short stature0.2108InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.2145InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.642InformativeInherited
Phenotypic Abnormality (PA)Abnormal cornea morphology0.7366InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.7812InformativeInherited
Phenotypic Abnormality (PA)Cleft upper lip0.00008398Highly InformativeDirect
Phenotypic Abnormality (PA)Abdominal distention0.000626Highly InformativeDirect
Phenotypic Abnormality (PA)Agenesis of corpus callosum0.0006893Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of circulating adrenocorticotropin level0.00738Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal pancreas morphology0.01082Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal nasal morphology0.03016Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal ureter physiology0.07139Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cervical spine0.2122Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cheek0.3378Highly InformativeInherited
Phenotypic Abnormality (PA)Cleft palate0.6585Highly InformativeInherited
Phenotypic Abnormality (PA)Reduced bone mineral density0.8739Highly InformativeInherited
Phenotypic Abnormality (PA)Anterior hypopituitarism0.8824Highly 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 phenotype0.0000000000008705Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00000002868Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.00000006114Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.005474Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.3627Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.7348Least 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 weaning0.0000000000005699Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.000000000005782Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000000003686Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.0000003113Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.000003855Moderately InformativeDirect
Mammalian Phenotype (MP)respiratory system phenotype0.00001261Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal digestive system morphology0.0007253Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal muscle morphology0.006681Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.013Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.01744Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.04669Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.04835Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1889Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.3078Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.3351Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.4514Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.6954Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.8137Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.9536Moderately 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 lethality0.0000000004823InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.0000005377InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.000007663InformativeDirect
Mammalian Phenotype (MP)abnormal cell differentiation0.00006099InformativeDirect
Mammalian Phenotype (MP)abnormal gas homeostasis0.00006725InformativeDirect
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.0001005InformativeDirect
Mammalian Phenotype (MP)abnormal spinal cord morphology0.0002948InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.001035InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.001275InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.002026InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.002411InformativeInherited
Mammalian Phenotype (MP)abnormal consumption behavior0.002938InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.002951InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.01899InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.03243InformativeInherited
Mammalian Phenotype (MP)abnormal hypaxial muscle morphology0.06244InformativeInherited
Mammalian Phenotype (MP)abnormal hearing physiology0.06662InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.09472InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.1203InformativeInherited
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 morphology0.2362InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.2758InformativeInherited
Mammalian Phenotype (MP)abnormal pancreas morphology0.3493InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5317InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.6039InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.6484InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.6802InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.7616InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.8222InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.8395InformativeInherited
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.8532InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.9635InformativeInherited
Mammalian Phenotype (MP)abnormal cerebellum morphology1InformativeInherited
Mammalian Phenotype (MP)cyanosis0.000000002978Highly InformativeDirect
Mammalian Phenotype (MP)abnormal middle ear morphology0.000000003814Highly InformativeDirect
Mammalian Phenotype (MP)abnormal joint morphology0.00000009722Highly InformativeDirect
Mammalian Phenotype (MP)taste/olfaction phenotype0.0000006803Highly InformativeDirect
Mammalian Phenotype (MP)abnormal brain ventricle morphology0.000001385Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.000001583Highly InformativeDirect
Mammalian Phenotype (MP)abnormal forelimb morphology0.000005177Highly InformativeDirect
Mammalian Phenotype (MP)abnormal secondary palate development0.00000561Highly InformativeDirect
Mammalian Phenotype (MP)postnatal lethality0.00001521Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neurocranium morphology0.00002115Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vas deferens morphology0.00003932Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circumventricular organ morphology0.00005696Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.0001869Highly InformativeDirect
Mammalian Phenotype (MP)abnormal nose morphology0.0003135Highly InformativeDirect
Mammalian Phenotype (MP)abnormal telencephalon development0.0003456Highly InformativeDirect
Mammalian Phenotype (MP)abnormal kidney development0.0004389Highly InformativeDirect
Mammalian Phenotype (MP)abnormal right subclavian artery morphology0.0006161Highly InformativeDirect
Mammalian Phenotype (MP)impaired branching involved in ureteric bud morphogenesis0.000646Highly InformativeDirect
Mammalian Phenotype (MP)abnormal basicranium morphology0.0007977Highly InformativeDirect
Mammalian Phenotype (MP)abnormal tongue morphology0.001189Highly InformativeInherited
Mammalian Phenotype (MP)abnormal aortic arch morphology0.001554Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary gland morphology0.007712Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.01157Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.01398Highly InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.01501Highly 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 morphology0.2642Highly 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 morphology0.2908Highly InformativeInherited
Mammalian Phenotype (MP)abnormal food intake0.4946Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.6153Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pancreatic islet morphology0.9795Highly 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 variant0.00000002991Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000002593Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0000002635Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.02377Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.2385Least InformativeInherited
Worm Phenotype (WP)larval lethal0.2538Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.7693Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.0000000001677Moderately InformativeDirect
Worm Phenotype (WP)body region morphology variant0.0000000001887Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.0000001661Moderately InformativeDirect
Worm Phenotype (WP)nervous system morphology variant0.000004174Moderately InformativeDirect
Worm Phenotype (WP)neuron development variant0.0001394Moderately InformativeDirect
Worm Phenotype (WP)drug response variant0.2273Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.6602Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.7992Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.9915Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant1Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant1Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant1Moderately InformativeInherited
Worm Phenotype (WP)male morphology variant0.0000000000885InformativeDirect
Worm Phenotype (WP)cell fate specification variant0.0000001982InformativeDirect
Worm Phenotype (WP)tail morphology variant0.0000371InformativeDirect
Worm Phenotype (WP)anesthetic response variant0.00161InformativeInherited
Worm Phenotype (WP)directionality variant0.05888InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.06947InformativeInherited
Worm Phenotype (WP)vulva development variant0.0915InformativeInherited
Worm Phenotype (WP)foraging behavior variant0.1373InformativeInherited
Worm Phenotype (WP)body posture variant0.1898InformativeInherited
Worm Phenotype (WP)egg laying variant0.1948InformativeInherited
Worm Phenotype (WP)locomotion reduced0.5313InformativeInherited
Worm Phenotype (WP)chemical resistant0.9922InformativeInherited
Worm Phenotype (WP)drug resistant1InformativeInherited
Worm Phenotype (WP)cell number increased1InformativeInherited
Worm Phenotype (WP)ectopic expression transgene0.00000002203Highly InformativeDirect
Worm Phenotype (WP)forward locomotion decreased0.000016Highly InformativeDirect
Worm Phenotype (WP)cell number decreased0.00002268Highly InformativeDirect
Worm Phenotype (WP)carbon dioxide avoidance variant0.00006695Highly InformativeDirect
Worm Phenotype (WP)growth rate variant0.0001701Highly InformativeDirect
Worm Phenotype (WP)male nervous system development variant0.0001979Highly InformativeDirect
Worm Phenotype (WP)cell fusion variant0.0002464Highly InformativeDirect
Worm Phenotype (WP)early larval lethal0.0002595Highly InformativeDirect
Worm Phenotype (WP)male tail development variant0.0003335Highly InformativeDirect
Worm Phenotype (WP)vulvaless0.0003589Highly InformativeDirect
Worm Phenotype (WP)multiple anchor cells0.0003752Highly InformativeDirect
Worm Phenotype (WP)coiling frequency variant0.0004628Highly InformativeDirect
Worm Phenotype (WP)body axis morphology variant0.0004825Highly InformativeDirect
Worm Phenotype (WP)neuronal cell fate specification variant0.0006657Highly InformativeDirect
Worm Phenotype (WP)imipramine resistant0.0007416Highly InformativeDirect
Worm Phenotype (WP)protein degradation variant0.0009331Highly InformativeDirect
Worm Phenotype (WP)roaming variant0.01775Highly InformativeInherited
Worm Phenotype (WP)postembryonic cell lineage variant0.09952Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.06469Least InformativeInherited
Fly Phenotype (FP)lethal0.2463Moderately InformativeInherited
Fly Phenotype (FP)visible0InformativeDirect
Fly Phenotype (FP)lethal - all die before end of larval stage0.0000008091InformativeDirect
Fly Phenotype (FP)wild-type0.0005787InformativeDirect
Fly Phenotype (FP)lethal - all die before end of embryonic stage0.00000000002346Highly InformativeDirect
Fly Phenotype (FP)homeotic0.00000006234Highly InformativeDirect
Fly Phenotype (FP)some die during embryonic stage0.00001527Highly InformativeDirect
Fly Phenotype (FP)some die during P-stage0.396Highly InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organism subdivision0.000000000000003801Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0.00000000002783Least InformativeDirect
Fly Anatomy (FA)adult0.0000000004212Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0.00002939Least InformativeDirect
Fly Anatomy (FA)cell0.06019Least InformativeInherited
Fly Anatomy (FA)nervous system0.1066Least InformativeInherited
Fly Anatomy (FA)larva0.1363Least InformativeInherited
Fly Anatomy (FA)adult integumentary system0.000000003477Moderately InformativeDirect
Fly Anatomy (FA)region of integument0.000000004585Moderately InformativeDirect
Fly Anatomy (FA)appendage0.0000000603Moderately InformativeDirect
Fly Anatomy (FA)multi-cell-component structure0.000005987Moderately InformativeDirect
Fly Anatomy (FA)adult segment0.00001385Moderately InformativeDirect
Fly Anatomy (FA)acellular anatomical structure0.00008097Moderately InformativeDirect
Fly Anatomy (FA)thorax0.0002822Moderately InformativeDirect
Fly Anatomy (FA)ganglion0.0006594Moderately InformativeDirect
Fly Anatomy (FA)adult tagma0.006682Moderately InformativeInherited
Fly Anatomy (FA)embryo0.01733Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.07733Moderately InformativeInherited
Fly Anatomy (FA)neuron0.08828Moderately InformativeInherited
Fly Anatomy (FA)somatic precursor cell0.3658Moderately InformativeInherited
Fly Anatomy (FA)stem cell0.3735Moderately InformativeInherited
Fly Anatomy (FA)female-specific anatomical entity0.6477Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.8763Moderately InformativeInherited
Fly Anatomy (FA)sensory system0.8915Moderately InformativeInherited
Fly Anatomy (FA)head0.9325Moderately InformativeInherited
Fly Anatomy (FA)larval segment0.0000000000002963InformativeDirect
Fly Anatomy (FA)interneuron0.000002627InformativeDirect
Fly Anatomy (FA)larval abdomen0.00003243InformativeDirect
Fly Anatomy (FA)central brain0.00006316InformativeDirect
Fly Anatomy (FA)abdominal segment0.0001585InformativeDirect
Fly Anatomy (FA)extended germ band embryo0.0004444InformativeDirect
Fly Anatomy (FA)mechanosensory system0.0004973InformativeDirect
Fly Anatomy (FA)head capsule0.0009336InformativeDirect
Fly Anatomy (FA)primordium0.001184InformativeInherited
Fly Anatomy (FA)syncytium0.001225InformativeInherited
Fly Anatomy (FA)muscle system0.004173InformativeInherited
Fly Anatomy (FA)embryonic/larval integumentary system0.008588InformativeInherited
Fly Anatomy (FA)dorsal closure embryo0.0092InformativeInherited
Fly Anatomy (FA)nerve0.01745InformativeInherited
Fly Anatomy (FA)neuromere0.0235InformativeInherited
Fly Anatomy (FA)ventral nerve cord0.02436InformativeInherited
Fly Anatomy (FA)cuticular specialization0.03919InformativeInherited
Fly Anatomy (FA)leg0.0561InformativeInherited
Fly Anatomy (FA)embryonic/larval circulatory system0.06793InformativeInherited
Fly Anatomy (FA)tract0.09894InformativeInherited
Fly Anatomy (FA)adult head sensillum0.1527InformativeInherited
Fly Anatomy (FA)supraesophageal ganglion0.2098InformativeInherited
Fly Anatomy (FA)sensory organ cell0.3389InformativeInherited
Fly Anatomy (FA)rhabdomeric photoreceptor cell0.3417InformativeInherited
Fly Anatomy (FA)wing0.3654InformativeInherited
Fly Anatomy (FA)adult brain0.3729InformativeInherited
Fly Anatomy (FA)adult optic lobe neuron0.4121InformativeInherited
Fly Anatomy (FA)retina0.5311InformativeInherited
Fly Anatomy (FA)histaminergic neuron0.5487InformativeInherited
Fly Anatomy (FA)embryonic/larval peripheral nervous system0.7457InformativeInherited
Fly Anatomy (FA)chaeta0.7509InformativeInherited
Fly Anatomy (FA)adult procephalic segment0.7651InformativeInherited
Fly Anatomy (FA)neuroblast0.7778InformativeInherited
Fly Anatomy (FA)presumptive embryonic/larval system0.7898InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.9326InformativeInherited
Fly Anatomy (FA)labral segment1InformativeInherited
Fly Anatomy (FA)ventral nerve cord primordium0.000000003495Highly InformativeDirect
Fly Anatomy (FA)larval neuromere0.00001234Highly InformativeDirect
Fly Anatomy (FA)denticle belt0.00001487Highly InformativeDirect
Fly Anatomy (FA)embryonic neuroblast0.00001498Highly InformativeDirect
Fly Anatomy (FA)commissure0.00001533Highly InformativeDirect
Fly Anatomy (FA)mesothoracic tergum0.00004708Highly InformativeDirect
Fly Anatomy (FA)antennal lobe glomerulus VA1v0.00005918Highly InformativeDirect
Fly Anatomy (FA)ventral nervous system0.0002122Highly InformativeDirect
Fly Anatomy (FA)head bristle0.0002929Highly InformativeDirect
Fly Anatomy (FA)antenna0.0002942Highly InformativeDirect
Fly Anatomy (FA)adult metathoracic segment0.000363Highly InformativeDirect
Fly Anatomy (FA)embryonic head0.0004591Highly InformativeDirect
Fly Anatomy (FA)EL neuron0.0006625Highly InformativeDirect
Fly Anatomy (FA)embryonic/larval dorsal vessel0.0007629Highly InformativeDirect
Fly Anatomy (FA)embryonic thorax0.001085Highly InformativeInherited
Fly Anatomy (FA)subesophageal ganglion0.001667Highly InformativeInherited
Fly Anatomy (FA)germ layer derivative0.0209Highly InformativeInherited
Fly Anatomy (FA)A1-7 acute muscle0.4988Highly InformativeInherited
Fly Anatomy (FA)late extended germ band embryo0.5137Highly InformativeInherited
Fly Anatomy (FA)larval mesothoracic segment0.5666Highly 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 structure0.006682Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.04773Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.08204Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.1646Least InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.2088Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.6263Moderately InformativeInherited
Zebrafish Anatomy (ZA)forebrain0.0005307InformativeDirect
Zebrafish Anatomy (ZA)digestive system0.2572InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.9542InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.000000000001064Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00001111Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.0005416Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.2584Least InformativeInherited
Xenopus ANatomical entity (XAN)urogenital 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 system0.001471Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.003506Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.09021Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)forebrain0InformativeDirect
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)eye0.00000000000003319InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.00000000000007097InformativeDirect
Xenopus ANatomical entity (XAN)neural crest0.000000000001361InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.000000000002166InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.00000000004059InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0000000001377InformativeDirect
Xenopus ANatomical entity (XAN)peripheral nervous system0.0000000006209InformativeDirect
Xenopus ANatomical entity (XAN)epithelium0.0000002915InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.0000179InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.00003176InformativeDirect
Xenopus ANatomical entity (XAN)vestibuloauditory system0.02229InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.03841InformativeInherited
Xenopus ANatomical entity (XAN)tail0.7514InformativeInherited
Xenopus ANatomical entity (XAN)urinary system0.773InformativeInherited
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)hindbrain0Highly 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)anterior neural fold0.000000000000003092Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0000000000001625Highly InformativeDirect
Xenopus ANatomical entity (XAN)preplacodal ectoderm0.000000000002249Highly InformativeDirect
Xenopus ANatomical entity (XAN)neuron0.000000000002705Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesenchyme0.000000000005555Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural plate border0.000000000006674Highly InformativeDirect
Xenopus ANatomical entity (XAN)pronephric tubule0.00000000003428Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.0000000002501Highly InformativeDirect
Xenopus ANatomical entity (XAN)anterior neural ridge0.0000000002779Highly InformativeDirect
Xenopus ANatomical entity (XAN)anatomical line0.0000000006954Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.000000002238Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000000005023Highly InformativeDirect
Xenopus ANatomical entity (XAN)limb bud0.00000001326Highly InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.00000009836Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindgut0.0000001295Highly InformativeDirect
Xenopus ANatomical entity (XAN)intermediate mesoderm0.0000002639Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural nucleus0.0000003199Highly InformativeDirect
Xenopus ANatomical entity (XAN)ventricular zone0.0000003497Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.0000008653Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.000003708Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail bud0.00002591Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.00003063Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00005651Highly InformativeDirect
Xenopus ANatomical entity (XAN)presomitic mesoderm0.0001263Highly InformativeDirect
Xenopus ANatomical entity (XAN)ganglion0.000142Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic vesicle0.0006981Highly InformativeDirect
Xenopus ANatomical entity (XAN)archenteron0.02605Highly InformativeInherited
Xenopus ANatomical entity (XAN)olfactory system0.04846Highly InformativeInherited
Xenopus ANatomical entity (XAN)retinal neural layer0.407Highly InformativeInherited
Xenopus ANatomical entity (XAN)neurogenic placode0.5338Highly InformativeInherited
Xenopus ANatomical entity (XAN)pelvic appendage0.7676Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone1Highly InformativeInherited
Xenopus DEvelopment stage (XDE)post-embryonic stage1Least InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.00000000002283Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage1Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.1055InformativeInherited
Xenopus DEvelopment stage (XDE)adult frog stage0.000003065Highly InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage 100.000005366Highly InformativeDirect
Xenopus DEvelopment stage (XDE)premetamorphosis stage0.0002587Highly 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 groups0.7071Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.00001413Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.01917Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.5774Moderately InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationDNA-binding0Moderately InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 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) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.