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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 cancer0.1632Least InformativeInherited
Disease Ontology (DO)nervous system disease0.6498Least InformativeInherited
Disease Ontology (DO)benign neoplasm0.00000002121Moderately InformativeDirect
Disease Ontology (DO)lower respiratory tract disease0.00007422Moderately InformativeDirect
Disease Ontology (DO)sensory system disease0.01259Moderately InformativeInherited
Disease Ontology (DO)skin disease0.0659Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.215Moderately InformativeInherited
Disease Ontology (DO)connective tissue disease0.3506Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.4025Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.8013Moderately InformativeInherited
Disease Ontology (DO)asthma0.00004342InformativeDirect
Disease Ontology (DO)prostate cancer0.0001577InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.003338InformativeInherited
Disease Ontology (DO)arthropathy0.008622InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.07643InformativeInherited
Disease Ontology (DO)aggressive systemic mastocytosis0.00008757Highly InformativeDirect
Disease Ontology (DO)rhabdomyosarcoma0.0005004Highly InformativeDirect
Disease Ontology (DO)cholesteatoma0.0009474Highly InformativeDirect
Disease Ontology (DO)inner ear disease0.009668Highly 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 phenotype0.003175Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.03981Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1306Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.1684Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2308Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3297Least InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.0000001749Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal craniofacial morphology0.0001029Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.0001411Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.005303Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.01424Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.05046Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.05584Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.07694Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.08801Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.1351Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.1802Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.1908Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.2306Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.291Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.6717Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.743Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.00001602InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.001323InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002595InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.005641InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.01116InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.05456InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.07253InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.07419InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.1169InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.1663InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.1957InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.4541InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.8401InformativeInherited
Mammalian Phenotype (MP)abnormal follicle stimulating hormone level0.0000008248Highly InformativeDirect
Mammalian Phenotype (MP)cleft palate0.000001945Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.00001721Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.00003722Highly InformativeDirect
Mammalian Phenotype (MP)abnormal digit morphology0.0001512Highly InformativeDirect
Mammalian Phenotype (MP)abnormal oocyte number0.0002908Highly InformativeDirect
Mammalian Phenotype (MP)small nasal bone0.0006119Highly InformativeDirect
Mammalian Phenotype (MP)absent allantois0.0006612Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.0007421Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.0007429Highly InformativeDirect
Mammalian Phenotype (MP)decreased nephron number0.000865Highly InformativeDirect
Mammalian Phenotype (MP)abnormal atrioventricular valve morphology0.0009595Highly InformativeDirect
Mammalian Phenotype (MP)abnormal incisor morphology0.0009595Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cornea morphology0.006709Highly InformativeInherited
Mammalian Phenotype (MP)abnormal embryonic-extraembryonic boundary morphology0.01079Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart right ventricle morphology0.0157Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart atrium morphology0.01739Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.01776Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digit development0.01956Highly InformativeInherited
Mammalian Phenotype (MP)abnormal muscle weight0.04686Highly InformativeInherited
Mammalian Phenotype (MP)increased heart ventricle size0.0793Highly InformativeInherited
Mammalian Phenotype (MP)abnormal dorsal root ganglion morphology0.08264Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ovary size0.0997Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.2649Highly InformativeInherited
Mammalian Phenotype (MP)abnormal maxilla morphology0.361Highly 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 organ0.192Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.2612Least InformativeInherited
Zebrafish Anatomy (ZA)organism subdivision0.2741Least InformativeInherited
Zebrafish Anatomy (ZA)cardiovascular system0.04353Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.4173Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.4199Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.4577Moderately InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.08328InformativeInherited
Zebrafish Anatomy (ZA)blood vessel0.4025InformativeInherited
Zebrafish Anatomy (ZA)male organism0.0000429Highly InformativeDirect
Zebrafish Anatomy (ZA)female organism0.0001604Highly InformativeDirect
Zebrafish Anatomy (ZA)reproductive system0.001155Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial vasculature0.007413Highly InformativeInherited
Zebrafish Anatomy (ZA)endocrine system0.008697Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.2308Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.466Least 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 structure0.00006172Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0005027Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.7284Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.8344Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.00000001788InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.000002828InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.000003489InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.000009864InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.0001817InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0002092InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0005194InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.0007689InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.001193InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.004253InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.01841InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.9548InformativeInherited
Xenopus ANatomical entity (XAN)limb1InformativeInherited
Xenopus ANatomical entity (XAN)head mesenchyme0.0000000007287Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.0000007699Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.000001952Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.000005695Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.00001371Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.00002683Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00004504Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.00007984Highly InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.0002941Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.0004258Highly InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.002363Highly InformativeInherited
Xenopus ANatomical entity (XAN)branchial arch0.1164Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.9217Highly 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 ]