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Cystine-knot cytokines superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Cystine-knot cytokines [ 57500]
Superfamily:   Cystine-knot cytokines [ 57501] (7)
Families:   Platelet-derived growth factor-like [ 57502] (3)
  Transforming growth factor (TGF)-beta [ 57507] (7)
  Noggin [ 82904]
  Neurotrophin [ 57520] (4)
  Gonadodropin/Follitropin [ 57528] (3)
  Interleukin 17F, IL-17F [ 69955]
  Coagulogen [ 57531]


Superfamily statistics
Genomes (146) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 6,332 28,686 40
Proteins 6,300 28,546 40


Functional annotation
General category Processes_IC
Detailed category Cell cycle, Apoptosis

Document:
Function annotation of SCOP domain superfamilies

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)cardiovascular system disease0.009116Least InformativeInherited
Disease Ontology (DO)organ system cancer0.1128Least InformativeInherited
Disease Ontology (DO)nervous system disease0.5989Least InformativeInherited
Disease Ontology (DO)benign neoplasm0.00000001237Moderately InformativeDirect
Disease Ontology (DO)lower respiratory tract disease0.00005718Moderately InformativeDirect
Disease Ontology (DO)sensory system disease0.01252Moderately InformativeInherited
Disease Ontology (DO)skin disease0.06027Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.1957Moderately InformativeInherited
Disease Ontology (DO)connective tissue disease0.3463Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.3812Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.7713Moderately InformativeInherited
Disease Ontology (DO)asthma0.00003507InformativeDirect
Disease Ontology (DO)prostate cancer0.0001372InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.002934InformativeInherited
Disease Ontology (DO)arthropathy0.00862InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.07643InformativeInherited
Disease Ontology (DO)aggressive systemic mastocytosis0.00008005Highly InformativeDirect
Disease Ontology (DO)rhabdomyosarcoma0.0004526Highly InformativeDirect
Disease Ontology (DO)cholesteatoma0.0008907Highly InformativeDirect
Disease Ontology (DO)atopic dermatitis0.0009311Highly InformativeDirect
Disease Ontology (DO)inner ear disease0.009149Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Multifactorial inheritance0.0002108InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.09926Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.2936Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.4802Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.5431Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.05126Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.1125Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.4961Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.5012Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.6127Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.6708Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.7743Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.7967Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal cardiovascular system physiology0.9163Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb bone0.06037InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral vasculature0.06104InformativeInherited
Phenotypic Abnormality (PA)Abnormality of joint mobility0.2256InformativeInherited
Phenotypic Abnormality (PA)Internal hemorrhage0.2352InformativeInherited
Phenotypic Abnormality (PA)Abnormality of finger0.2354InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.3013InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.3102InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.3111InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.3334InformativeInherited
Phenotypic Abnormality (PA)Subarachnoid hemorrhage0.0002733Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal sputum0.0004406Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal 5th finger phalanx morphology0.0007606Highly InformativeDirect
Phenotypic Abnormality (PA)Absent toe0.006235Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the phalanges of the hand0.03003Highly InformativeInherited
Phenotypic Abnormality (PA)Synostosis of joints0.04482Highly InformativeInherited
Phenotypic Abnormality (PA)Short toe0.04784Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body region phenotype0.003173Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.04009Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1308Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.1683Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2317Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3294Least InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.0000001749Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal craniofacial morphology0.0001009Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.0001399Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.005332Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.01414Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.05063Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.05579Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.07595Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.08799Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.1344Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.1793Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.1908Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.231Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.2911Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.6715Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7426Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.00001617InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.00133InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002613InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.005664InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.01115InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.05489InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.07249InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.07681InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.1167InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.1662InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.194InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.454InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.8402InformativeInherited
Mammalian Phenotype (MP)abnormal follicle stimulating hormone level0.0000008279Highly InformativeDirect
Mammalian Phenotype (MP)cleft palate0.000001958Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.00001739Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.00003731Highly InformativeDirect
Mammalian Phenotype (MP)abnormal digit morphology0.0001517Highly InformativeDirect
Mammalian Phenotype (MP)abnormal oocyte number0.0002913Highly InformativeDirect
Mammalian Phenotype (MP)small nasal bone0.0006119Highly InformativeDirect
Mammalian Phenotype (MP)absent allantois0.0006613Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.0007004Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.0007444Highly InformativeDirect
Mammalian Phenotype (MP)decreased nephron number0.000866Highly InformativeDirect
Mammalian Phenotype (MP)abnormal atrioventricular valve morphology0.0009614Highly InformativeDirect
Mammalian Phenotype (MP)abnormal incisor morphology0.0009614Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cornea morphology0.006705Highly InformativeInherited
Mammalian Phenotype (MP)abnormal embryonic-extraembryonic boundary morphology0.01078Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart right ventricle morphology0.01569Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart atrium morphology0.01738Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.01792Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digit development0.01956Highly InformativeInherited
Mammalian Phenotype (MP)abnormal muscle weight0.04695Highly InformativeInherited
Mammalian Phenotype (MP)increased heart ventricle size0.07923Highly InformativeInherited
Mammalian Phenotype (MP)abnormal dorsal root ganglion morphology0.08447Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ovary size0.09965Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.264Highly InformativeInherited
Mammalian Phenotype (MP)abnormal maxilla morphology0.3609Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.452Least InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.07725Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.1768Moderately InformativeInherited
Worm Phenotype (WP)nicotine response variant0.0001899InformativeDirect
Worm Phenotype (WP)anchor cell invasion variant0.00007589Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)circadian rhythm defective0.0000000001595InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.08856Least InformativeInherited
Fly Anatomy (FA)larva0.2417Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)late embryo0.01955Moderately InformativeInherited
Fly Anatomy (FA)portion of tissue0.1913Moderately InformativeInherited
Fly Anatomy (FA)abdominal segment0.00909InformativeInherited
Fly Anatomy (FA)integumentary specialisation0.009948InformativeInherited
Fly Anatomy (FA)gastrula embryo0.03227InformativeInherited
Fly Anatomy (FA)tracheal system0.03863InformativeInherited
Fly Anatomy (FA)epithelial furrow0.002284Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0.1877Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.2513Least InformativeInherited
Zebrafish Anatomy (ZA)organism subdivision0.2908Least InformativeInherited
Zebrafish Anatomy (ZA)cardiovascular system0.04259Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.397Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.404Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.44Moderately InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.07817InformativeInherited
Zebrafish Anatomy (ZA)blood vessel0.3961InformativeInherited
Zebrafish Anatomy (ZA)cranial vasculature0.00681Highly InformativeInherited
Zebrafish Anatomy (ZA)endocrine system0.007653Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.196Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.4279Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system1Least InformativeInherited
Xenopus ANatomical entity (XAN)cell1Least InformativeInherited
Xenopus ANatomical entity (XAN)head1Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk1Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ1Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.00001747Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0002279Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.8425Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.00000001279InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.0000005023InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.000002087InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.000002755InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.00006416InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0001592InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.0002124InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.0002749InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0003476InformativeDirect
Xenopus ANatomical entity (XAN)peripheral nervous system0.0007263InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.0009857InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.001544InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.013InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.953InformativeInherited
Xenopus ANatomical entity (XAN)limb1InformativeInherited
Xenopus ANatomical entity (XAN)head mesenchyme0.0000000002985Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.0000005084Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.000007545Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.00001257Highly InformativeDirect
Xenopus ANatomical entity (XAN)neurogenic placode0.00001906Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.00002051Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00003266Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.0000398Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.0003867Highly InformativeDirect
Xenopus ANatomical entity (XAN)branchial arch0.1417Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.9732Highly InformativeInherited

Document: XA annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) ]

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 43 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 Cystine-knot cytokines 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 43 hidden Markov models representing the Cystine-knot cytokines superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Internal database links ]