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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)organ system cancer0.1633Least InformativeInherited
Disease Ontology (DO)nervous system disease0.6498Least InformativeInherited
Disease Ontology (DO)benign neoplasm0.00000002116Moderately InformativeDirect
Disease Ontology (DO)lower respiratory tract disease0.00007406Moderately InformativeDirect
Disease Ontology (DO)sensory system disease0.0126Moderately InformativeInherited
Disease Ontology (DO)skin disease0.06586Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.2149Moderately InformativeInherited
Disease Ontology (DO)connective tissue disease0.3505Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.4025Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.8014Moderately InformativeInherited
Disease Ontology (DO)asthma0.00004335InformativeDirect
Disease Ontology (DO)prostate cancer0.0001575InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.003336InformativeInherited
Disease Ontology (DO)arthropathy0.008618InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.07643InformativeInherited
Disease Ontology (DO)aggressive systemic mastocytosis0.00008742Highly InformativeDirect
Disease Ontology (DO)rhabdomyosarcoma0.0005001Highly InformativeDirect
Disease Ontology (DO)cholesteatoma0.0009469Highly InformativeDirect
Disease Ontology (DO)inner ear disease0.009663Highly 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 inheritance0.0001853Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limbs0.2437Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.9019Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.104Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.1421Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.5009Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.5398Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.6854Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.832Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal lower limb bone morphology0.07873InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.2306InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.289InformativeInherited
Phenotypic Abnormality (PA)Abnormality of joint mobility0.3304InformativeInherited
Phenotypic Abnormality (PA)Abnormal finger phalanx morphology0.9253InformativeInherited
Phenotypic Abnormality (PA)Abnormal sputum0.000714Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the phalanges of the hand0.03365Highly InformativeInherited
Phenotypic Abnormality (PA)Synostosis of joints0.0359Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal 5th finger morphology0.3381Highly 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 phenotype0.003163Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.03975Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1309Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.1678Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2305Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3292Least InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.0000001737Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal craniofacial morphology0.0001032Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.0001395Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.005305Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.01423Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.05054Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.05561Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.07673Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.08803Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.1351Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.1797Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.1905Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.2299Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.2907Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.6717Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7428Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.00001573InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.001324InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002518InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.005648InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.01105InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.05474InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.07252InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.07423InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.1175InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.1672InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.1958InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.454InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.84InformativeInherited
Mammalian Phenotype (MP)abnormal follicle stimulating hormone level0.0000007501Highly InformativeDirect
Mammalian Phenotype (MP)cleft palate0.000001956Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.00001593Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.0000373Highly InformativeDirect
Mammalian Phenotype (MP)abnormal digit morphology0.0001515Highly InformativeDirect
Mammalian Phenotype (MP)abnormal oocyte number0.0002906Highly InformativeDirect
Mammalian Phenotype (MP)small nasal bone0.0006119Highly InformativeDirect
Mammalian Phenotype (MP)absent allantois0.0006608Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.0006995Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.0007398Highly InformativeDirect
Mammalian Phenotype (MP)decreased nephron number0.0008627Highly InformativeDirect
Mammalian Phenotype (MP)abnormal atrioventricular valve morphology0.0009577Highly InformativeDirect
Mammalian Phenotype (MP)abnormal incisor morphology0.0009577Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cornea morphology0.006699Highly InformativeInherited
Mammalian Phenotype (MP)abnormal embryonic-extraembryonic boundary morphology0.01078Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart right ventricle morphology0.0157Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart atrium morphology0.01746Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.01776Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digit development0.01957Highly InformativeInherited
Mammalian Phenotype (MP)abnormal muscle weight0.04687Highly InformativeInherited
Mammalian Phenotype (MP)increased heart ventricle size0.07931Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ovary size0.09968Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.2649Highly 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 variant0.4523Least InformativeInherited
Worm Phenotype (WP)drug response variant0.07156Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.07544Moderately InformativeInherited
Worm Phenotype (WP)anchor cell invasion variant0.00009147InformativeDirect
Worm Phenotype (WP)nicotine response variant0.0001743InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)circadian rhythm defective0.0000000001651InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.07051Least InformativeInherited
Fly Anatomy (FA)larva0.1969Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)late embryo0.01171Moderately InformativeInherited
Fly Anatomy (FA)epithelium0.1568Moderately InformativeInherited
Fly Anatomy (FA)region of integument0.7688Moderately InformativeInherited
Fly Anatomy (FA)abdominal segment0.01229InformativeInherited
Fly Anatomy (FA)integumentary specialisation0.01279InformativeInherited
Fly Anatomy (FA)tracheal system0.04593InformativeInherited
Fly Anatomy (FA)stage 7 embryo0.0004072Highly InformativeDirect
Fly Anatomy (FA)epithelial furrow0.0023Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0.2259Least InformativeInherited
Zebrafish Anatomy (ZA)organism subdivision0.2724Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.2905Least InformativeInherited
Zebrafish Anatomy (ZA)cardiovascular system0.04193Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.463Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.4844Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.4992Moderately InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.07916InformativeInherited
Zebrafish Anatomy (ZA)blood vasculature0.4092InformativeInherited
Zebrafish Anatomy (ZA)male organism0.0000569Highly InformativeDirect
Zebrafish Anatomy (ZA)female organism0.0002211Highly InformativeDirect
Zebrafish Anatomy (ZA)reproductive system0.001282Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial vasculature0.006951Highly InformativeInherited
Zebrafish Anatomy (ZA)endocrine system0.008643Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.2398Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.4712Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least 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 structure0.00007576Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0006241Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.7324Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.8346Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.00000001729InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.000004463InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.000004741InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.00001414InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.000242InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0002943InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0005469InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.001325InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.005599InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.01997InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.9554InformativeInherited
Xenopus ANatomical entity (XAN)limb1InformativeInherited
Xenopus ANatomical entity (XAN)head mesenchyme0.000000004493Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.000000777Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.000001971Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.000005224Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.000008973Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.00001311Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.00002915Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00005484Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0001173Highly InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.0003468Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.000445Highly InformativeDirect
Xenopus ANatomical entity (XAN)branchial arch0.1004Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.9063Highly 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 ]