SUPERFAMILY 1.75 HMM library and genome assignments server

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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 0 207
Proteins 189,461 0 197


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 disease0.6972Moderately 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 inheritance0.000002994Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the head0.008945Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.02808Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.02889Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.3019Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.6573Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.9016Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ear0.01019Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.1373Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the orbital region0.2057Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.215Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.4704Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.5392Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.639Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal fundus morphology0.6483Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the oral cavity0.7639Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal anterior segment morphology0.8344Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.9056Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the palate0.01125InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.02432InformativeInherited
Phenotypic Abnormality (PA)Short stature0.04854InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hypothalamus-pituitary axis0.07567InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.1278InformativeInherited
Phenotypic Abnormality (PA)Abnormality of upper lip0.1353InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the calvaria0.215InformativeInherited
Phenotypic Abnormality (PA)Abdominal symptom0.3796InformativeInherited
Phenotypic Abnormality (PA)Abnormality of circulating hormone level0.3997InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the optic nerve0.4118InformativeInherited
Phenotypic Abnormality (PA)Abnormal cornea morphology0.736InformativeInherited
Phenotypic Abnormality (PA)Abnormal ear morphology0.867InformativeInherited
Phenotypic Abnormality (PA)Abdominal distention0.00004443Highly InformativeDirect
Phenotypic Abnormality (PA)Cleft upper lip0.0002681Highly InformativeDirect
Phenotypic Abnormality (PA)Anterior segment dysgenesis0.0006746Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of circulating adrenocorticotropin level0.0008843Highly InformativeDirect
Phenotypic Abnormality (PA)Hypothyroidism0.001997Highly InformativeInherited
Phenotypic Abnormality (PA)Cleft palate0.3436Highly InformativeInherited
Phenotypic Abnormality (PA)Reduced bone mineral density0.7877Highly 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 phenotype0.0000000000005256Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00000004224Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.0000000809Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.004874Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.3519Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.7204Least 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 weaning0.0000000000008944Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.000000000004164Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000000003006Moderately InformativeDirect
Mammalian Phenotype (MP)limbs/digits/tail phenotype0.000000001288Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.0000002669Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.000003662Moderately InformativeDirect
Mammalian Phenotype (MP)respiratory system phenotype0.0000111Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal digestive system morphology0.0007244Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal muscle morphology0.006622Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.01343Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.01755Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.04339Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.04814Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.05214Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1888Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.2999Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.3408Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.4438Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.7018Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.8068Moderately 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 lethality0.000000000328InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.0000003857InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.000006619InformativeDirect
Mammalian Phenotype (MP)abnormal cell differentiation0.0000603InformativeDirect
Mammalian Phenotype (MP)abnormal gas homeostasis0.00006046InformativeDirect
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.0001057InformativeDirect
Mammalian Phenotype (MP)abnormal spinal cord morphology0.000302InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.001051InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.001103InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.002029InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.002405InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.00289InformativeInherited
Mammalian Phenotype (MP)abnormal consumption behavior0.002978InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.02463InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.03188InformativeInherited
Mammalian Phenotype (MP)abnormal hypaxial muscle morphology0.06347InformativeInherited
Mammalian Phenotype (MP)abnormal hearing physiology0.06402InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.09497InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.1155InformativeInherited
Mammalian Phenotype (MP)abnormal uvea morphology0.131InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.1628InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.2041InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.2345InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.2774InformativeInherited
Mammalian Phenotype (MP)abnormal pancreas morphology0.3482InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5328InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.5336InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.6512InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.6804InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.7613InformativeInherited
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 morphology0.9616InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.9765InformativeInherited
Mammalian Phenotype (MP)cyanosis0.000000002741Highly InformativeDirect
Mammalian Phenotype (MP)abnormal middle ear morphology0.000000004075Highly InformativeDirect
Mammalian Phenotype (MP)abnormal joint morphology0.0000002198Highly InformativeDirect
Mammalian Phenotype (MP)taste/olfaction phenotype0.0000006432Highly InformativeDirect
Mammalian Phenotype (MP)abnormal brain ventricle morphology0.000001297Highly InformativeDirect
Mammalian Phenotype (MP)distended abdomen0.000001446Highly InformativeDirect
Mammalian Phenotype (MP)abnormal forelimb morphology0.000005167Highly InformativeDirect
Mammalian Phenotype (MP)abnormal secondary palate development0.00000542Highly InformativeDirect
Mammalian Phenotype (MP)postnatal lethality0.00002368Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neurocranium morphology0.0000374Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vas deferens morphology0.00003895Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circumventricular organ morphology0.00005699Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.0001831Highly InformativeDirect
Mammalian Phenotype (MP)abnormal nose morphology0.0003168Highly InformativeDirect
Mammalian Phenotype (MP)abnormal telencephalon development0.0003448Highly InformativeDirect
Mammalian Phenotype (MP)abnormal kidney development0.0004257Highly InformativeDirect
Mammalian Phenotype (MP)abnormal right subclavian artery morphology0.0006038Highly InformativeDirect
Mammalian Phenotype (MP)impaired branching involved in ureteric bud morphogenesis0.0006352Highly InformativeDirect
Mammalian Phenotype (MP)abnormal tongue morphology0.001204Highly InformativeInherited
Mammalian Phenotype (MP)abnormal aortic arch morphology0.00152Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary gland morphology0.007704Highly InformativeInherited
Mammalian Phenotype (MP)abnormal sternum morphology0.01072Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.01156Highly InformativeInherited
Mammalian Phenotype (MP)abnormal optic nerve morphology0.01396Highly InformativeInherited
Mammalian Phenotype (MP)abnormal limb long bone morphology0.02086Highly InformativeInherited
Mammalian Phenotype (MP)impaired hearing0.02658Highly InformativeInherited
Mammalian Phenotype (MP)abnormal rib morphology0.03426Highly InformativeInherited
Mammalian Phenotype (MP)abnormal alveolar process morphology0.2652Highly InformativeInherited
Mammalian Phenotype (MP)abnormal olfactory bulb layer morphology0.2678Highly InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular meshwork morphology0.2766Highly InformativeInherited
Mammalian Phenotype (MP)abnormal mesonephros morphology0.2921Highly InformativeInherited
Mammalian Phenotype (MP)abnormal food intake0.4944Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.614Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pancreatic islet morphology0.9792Highly 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 variant0.00000002009Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000001709Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000000212Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.05959Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.1269Least InformativeInherited
Worm Phenotype (WP)larval lethal0.3519Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.7692Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.0000000009919Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.000000007551Moderately InformativeDirect
Worm Phenotype (WP)nervous system morphology variant0.00000527Moderately InformativeDirect
Worm Phenotype (WP)metabolic pathway variant0.6005Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.7774Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.8026Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.8058Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.8141Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.9278Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant1Moderately InformativeInherited
Worm Phenotype (WP)male morphology variant0.00000000006222InformativeDirect
Worm Phenotype (WP)cell fate specification variant0.0000002933InformativeDirect
Worm Phenotype (WP)tail morphology variant0.0000433InformativeDirect
Worm Phenotype (WP)growth rate variant0.0001141InformativeDirect
Worm Phenotype (WP)protein degradation variant0.0006331InformativeDirect
Worm Phenotype (WP)forward locomotion variant0.05143InformativeInherited
Worm Phenotype (WP)locomotor coordination variant0.05321InformativeInherited
Worm Phenotype (WP)foraging behavior variant0.157InformativeInherited
Worm Phenotype (WP)body posture variant0.2107InformativeInherited
Worm Phenotype (WP)vulva development variant0.2279InformativeInherited
Worm Phenotype (WP)egg laying variant0.2945InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.487InformativeInherited
Worm Phenotype (WP)locomotion reduced0.6182InformativeInherited
Worm Phenotype (WP)drug resistant0.6827InformativeInherited
Worm Phenotype (WP)cell number increased1InformativeInherited
Worm Phenotype (WP)ectopic expression transgene0.00000006462Highly InformativeDirect
Worm Phenotype (WP)lineage variant0.00000006933Highly InformativeDirect
Worm Phenotype (WP)body axis morphology variant0.0000007232Highly InformativeDirect
Worm Phenotype (WP)forward locomotion decreased0.00001427Highly InformativeDirect
Worm Phenotype (WP)carbon dioxide avoidance variant0.00005542Highly InformativeDirect
Worm Phenotype (WP)cell number decreased0.00006363Highly InformativeDirect
Worm Phenotype (WP)neuronal cell fate specification variant0.0001676Highly InformativeDirect
Worm Phenotype (WP)male tail development variant0.0003101Highly InformativeDirect
Worm Phenotype (WP)vulvaless0.0003302Highly InformativeDirect
Worm Phenotype (WP)coiling frequency0.0003757Highly InformativeDirect
Worm Phenotype (WP)multiple anchor cells0.0004879Highly InformativeDirect
Worm Phenotype (WP)male nervous system development variant0.0006343Highly InformativeDirect
Worm Phenotype (WP)early larval lethal0.0008208Highly InformativeDirect
Worm Phenotype (WP)body posture amplitude variant0.0009677Highly InformativeDirect
Worm Phenotype (WP)roaming variant0.01989Highly InformativeInherited
Worm Phenotype (WP)egg retention0.416Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.09968Least InformativeInherited
Fly Phenotype (FP)lethal - all die before end of P-stage0.02815Moderately InformativeInherited
Fly Phenotype (FP)visible0InformativeDirect
Fly Phenotype (FP)lethal - all die before end of first instar larval stage0.0000000002491InformativeDirect
Fly Phenotype (FP)wild-type0.0005549InformativeDirect
Fly Phenotype (FP)lethal - all die before end of embryonic stage0.00000000001503Highly InformativeDirect
Fly Phenotype (FP)homeotic0.00000007662Highly InformativeDirect
Fly Phenotype (FP)some die during embryonic stage0.000008906Highly InformativeDirect
Fly Phenotype (FP)some die during P-stage0.3336Highly 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 subdivision0.000000000002788Least InformativeDirect
Fly Anatomy (FA)integumentary system0.000000000009377Least InformativeDirect
Fly Anatomy (FA)adult0.0000000009589Least InformativeDirect
Fly Anatomy (FA)anatomical group0.0006986Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0.0008164Least InformativeDirect
Fly Anatomy (FA)embryo0.006083Least InformativeInherited
Fly Anatomy (FA)larva0.02195Least InformativeInherited
Fly Anatomy (FA)nervous system0.3119Least InformativeInherited
Fly Anatomy (FA)somatic cell0.3785Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)adult integumentary system0.0000004982Moderately InformativeDirect
Fly Anatomy (FA)developing embryonic structure0.000001017Moderately InformativeDirect
Fly Anatomy (FA)multi-cell-component structure0.00001712Moderately InformativeDirect
Fly Anatomy (FA)appendage0.00002033Moderately InformativeDirect
Fly Anatomy (FA)acellular anatomical structure0.0001297Moderately InformativeDirect
Fly Anatomy (FA)adult thorax0.0001507Moderately InformativeDirect
Fly Anatomy (FA)cell cluster organ0.0002582Moderately InformativeDirect
Fly Anatomy (FA)sense organ0.001292Moderately InformativeInherited
Fly Anatomy (FA)ganglion0.001484Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.002215Moderately InformativeInherited
Fly Anatomy (FA)non-connected developing system0.002407Moderately InformativeInherited
Fly Anatomy (FA)tagmatic subdivision of integument0.07945Moderately InformativeInherited
Fly Anatomy (FA)sensory neuron0.106Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.2107Moderately InformativeInherited
Fly Anatomy (FA)late embryo0.2586Moderately InformativeInherited
Fly Anatomy (FA)stem cell0.3007Moderately InformativeInherited
Fly Anatomy (FA)thoracic segment0.3363Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.3502Moderately InformativeInherited
Fly Anatomy (FA)somatic precursor cell0.4934Moderately InformativeInherited
Fly Anatomy (FA)adult head0.6416Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.8502Moderately InformativeInherited
Fly Anatomy (FA)larval abdomen0.000000000278InformativeDirect
Fly Anatomy (FA)adult external head0.00001091InformativeDirect
Fly Anatomy (FA)interneuron0.00001498InformativeDirect
Fly Anatomy (FA)gland0.0001824InformativeDirect
Fly Anatomy (FA)syncytium0.0001934InformativeDirect
Fly Anatomy (FA)abdominal segment0.0003924InformativeDirect
Fly Anatomy (FA)primordium0.0006334InformativeDirect
Fly Anatomy (FA)mechanosensory system0.0006375InformativeDirect
Fly Anatomy (FA)adult procephalic segment0.00104InformativeInherited
Fly Anatomy (FA)extended germ band embryo0.001765InformativeInherited
Fly Anatomy (FA)muscle system0.003273InformativeInherited
Fly Anatomy (FA)synaptic neuropil0.009195InformativeInherited
Fly Anatomy (FA)nerve0.01262InformativeInherited
Fly Anatomy (FA)chemosensory system0.01558InformativeInherited
Fly Anatomy (FA)dorsal closure embryo0.01984InformativeInherited
Fly Anatomy (FA)neuromere0.02607InformativeInherited
Fly Anatomy (FA)embryonic/larval integumentary system0.05948InformativeInherited
Fly Anatomy (FA)leg0.0616InformativeInherited
Fly Anatomy (FA)midline crossing tract0.06699InformativeInherited
Fly Anatomy (FA)adult central nervous system0.2626InformativeInherited
Fly Anatomy (FA)brain0.3288InformativeInherited
Fly Anatomy (FA)eye photoreceptor cell0.3809InformativeInherited
Fly Anatomy (FA)larval thoracic segment0.454InformativeInherited
Fly Anatomy (FA)chaeta0.6819InformativeInherited
Fly Anatomy (FA)neuroblast0.7824InformativeInherited
Fly Anatomy (FA)neuroblast of ventral nerve cord primordium0.000000001456Highly InformativeDirect
Fly Anatomy (FA)trunk mesoderm derivative0.000007005Highly InformativeDirect
Fly Anatomy (FA)maxillary palpus0.00001061Highly InformativeDirect
Fly Anatomy (FA)commissure0.00001561Highly InformativeDirect
Fly Anatomy (FA)antennal lobe glomerulus VA1v0.00002897Highly InformativeDirect
Fly Anatomy (FA)presumptive embryonic/larval central nervous system0.00006735Highly InformativeDirect
Fly Anatomy (FA)segment of leg0.00008481Highly InformativeDirect
Fly Anatomy (FA)head bristle0.0003208Highly InformativeDirect
Fly Anatomy (FA)ventral nervous system0.0003343Highly InformativeDirect
Fly Anatomy (FA)adult metathoracic segment0.0003517Highly InformativeDirect
Fly Anatomy (FA)larval abdominal segment 20.0005113Highly InformativeDirect
Fly Anatomy (FA)denticle belt0.001074Highly InformativeInherited
Fly Anatomy (FA)sensillum basiconicum0.03682Highly InformativeInherited
Fly Anatomy (FA)third segment of antenna0.03896Highly InformativeInherited
Fly Anatomy (FA)olfactory sensory organ0.2638Highly InformativeInherited
Fly Anatomy (FA)antennal lobe projection neuron iPN0.3556Highly InformativeInherited
Fly Anatomy (FA)adult antennal sense organ0.429Highly InformativeInherited
Fly Anatomy (FA)antennal lobe projection neuron adPN0.4909Highly InformativeInherited
Fly Anatomy (FA)unilateral ACT relay interneuron0.7487Highly 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 structure0.00613Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.05042Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.08389Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.1979Least InformativeInherited
Zebrafish Anatomy (ZA)organism subdivision1Least InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.3289Moderately InformativeInherited
Zebrafish Anatomy (ZA)trunk1Moderately InformativeInherited
Zebrafish Anatomy (ZA)brain0.005765InformativeInherited
Zebrafish Anatomy (ZA)digestive system0.3584InformativeInherited
Zebrafish Anatomy (ZA)musculature system0.7584InformativeInherited
Zebrafish Anatomy (ZA)coelom1InformativeInherited
Zebrafish Anatomy (ZA)embryonic structure0.2612Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.000000000000176Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.00001239Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.03038Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.3144Least 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)ectoderm0.002521Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.2429Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.3178Moderately 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)mesoderm0.000000000000001455InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0000000000001984InformativeDirect
Xenopus ANatomical entity (XAN)eye0.0000000000005888InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.0000000000009839InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.00000000002429InformativeDirect
Xenopus ANatomical entity (XAN)peripheral nervous system0.00000000003626InformativeDirect
Xenopus ANatomical entity (XAN)epithelium0.0000001036InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.00003646InformativeDirect
Xenopus ANatomical entity (XAN)vestibuloauditory system0.001531InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.02919InformativeInherited
Xenopus ANatomical entity (XAN)tail0.8146InformativeInherited
Xenopus ANatomical entity (XAN)intestine1InformativeInherited
Xenopus ANatomical entity (XAN)endocrine system1InformativeInherited
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)anterior neural fold0.00000000000001816Highly InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.00000000000003629Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.0000000000004864Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.0000000000006349Highly InformativeDirect
Xenopus ANatomical entity (XAN)pronephric tubule0.000000000001161Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural plate border0.000000000002337Highly InformativeDirect
Xenopus ANatomical entity (XAN)neuron0.000000000007218Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.00000000007628Highly InformativeDirect
Xenopus ANatomical entity (XAN)midbrain-hindbrain boundary0.0000000003149Highly InformativeDirect
Xenopus ANatomical entity (XAN)retinal inner nuclear layer0.0000000006041Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesenchyme0.000000001235Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.000000002528Highly InformativeDirect
Xenopus ANatomical entity (XAN)proliferative region0.00000001641Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindgut0.00000005447Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.000000234Highly InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.0000007997Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.0000008262Highly InformativeDirect
Xenopus ANatomical entity (XAN)dorsal marginal zone0.000001039Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.000005224Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted ventral mesoderm0.000005404Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail bud0.000007981Highly InformativeDirect
Xenopus ANatomical entity (XAN)retinal ganglion cell layer0.000008856Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial nerve0.000009284Highly InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.00001348Highly InformativeDirect
Xenopus ANatomical entity (XAN)ganglion0.00001625Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.00002627Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00005339Highly InformativeDirect
Xenopus ANatomical entity (XAN)intersomitic region0.00008111Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic vesicle0.0009518Highly InformativeDirect
Xenopus DEvelopment stage (XDE)post-embryonic stage1Least InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.00000000018Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage1Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.08254InformativeInherited
Xenopus DEvelopment stage (XDE)premetamorphosis stage0.0608Highly InformativeInherited
Xenopus DEvelopment stage (XDE)gastrula stage0.1124Highly 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)flower0.6372Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.8214Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.8881Least 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 tip0.000000003819InformativeDirect
Plant ANatomical entity (PAN)portion of vascular tissue0.000000004845InformativeDirect
Plant ANatomical entity (PAN)primordium0.00000004156InformativeDirect
Plant ANatomical entity (PAN)portion of ground tissue0.00000009836InformativeDirect
Plant ANatomical entity (PAN)fruit0.0005241InformativeDirect
Plant ANatomical entity (PAN)root epidermis0.04584InformativeInherited
Plant ANatomical entity (PAN)shoot apical meristem0.00000000000009703Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex0.0000000001163Highly InformativeDirect
Plant ANatomical entity (PAN)primary root0.000000005808Highly InformativeDirect
Plant ANatomical entity (PAN)vegetative shoot apex0.000000008114Highly InformativeDirect
Plant ANatomical entity (PAN)plant ovule0.00000003728Highly InformativeDirect
Plant ANatomical entity (PAN)phyllome primordium0.00000009103Highly InformativeDirect
Plant ANatomical entity (PAN)trichome0.000001876Highly InformativeDirect
Plant ANatomical entity (PAN)plant axis elongation zone0.000008834Highly InformativeDirect
Plant ANatomical entity (PAN)anther0.00001191Highly InformativeDirect
Plant ANatomical entity (PAN)juvenile vascular leaf0.00002116Highly InformativeDirect
Plant ANatomical entity (PAN)phyllome vascular system0.00006858Highly InformativeDirect
Plant ANatomical entity (PAN)style0.0001107Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.0002803Highly InformativeDirect
Plant ANatomical entity (PAN)lateral root0.0003871Highly InformativeDirect
Plant ANatomical entity (PAN)root meristem0.006474Highly InformativeInherited
Plant structure DEvelopment stage (PDE)seedling development stage0.0005929InformativeDirect

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 groups0.3569Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.00000007113Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.01417Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0.2239Moderately InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processNitrogen fixation0.000000375InformativeDirect
Biological processBiological rhythms0.00003277InformativeDirect
Biological processWnt signaling pathway0.0001198InformativeDirect
Biological processSensory transduction0.001803InformativeInherited
Biological processFlowering0Highly InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Biological processVision0.0000000000001912Highly InformativeDirect
Biological processDNA integration0.00000000001509Highly InformativeDirect
Biological processOsteogenesis0.000000001962Highly InformativeDirect
Biological processMyogenesis0.0000001945Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0.000000002134InformativeDirect
Cellular componentSpliceosome0.00002152InformativeDirect
Cellular componentTelomere6.626e-16Highly InformativeDirect
DiseaseDisease mutation0.000002805Least InformativeDirect
DiseaseMicrophthalmia0.000001697Highly InformativeDirect
DiseaseDwarfism0.0008145Highly InformativeDirect
DomainLIM domain0Highly InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately 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 137 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 137 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 ]