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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)
Phenotypic Abnormality (PA)Abnormality of limbs0.1684Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.9003Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.03948Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.2723Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.2846Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal physiology0.2888Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.5343Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.8984Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal lower limb bone morphology0.1288InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.2308InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.3357InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.4086InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.4967InformativeInherited
Phenotypic Abnormality (PA)Abnormal finger phalanx morphology0.9136InformativeInherited
Phenotypic Abnormality (PA)Synostosis of joints0.03621Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of toe0.03762Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the phalanges of the hand0.05273Highly InformativeInherited
Phenotypic Abnormality (PA)Short digit0.2709Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal 5th finger morphology0.2729Highly 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 phenotype0.003161Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.03962Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1306Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.1683Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2301Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3292Least InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.0001029Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.0001389Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.005328Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.01424Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.05045Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.0556Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.07692Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.08802Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.135Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.1797Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.1905Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.2296Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.283Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.2907Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.6719Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7428Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.00001568InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.001317InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002516InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.005634InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.01106InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.05473InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.07218InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.07419InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.1175InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.1672InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.1957InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.454InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.8401InformativeInherited
Mammalian Phenotype (MP)abnormal follicle stimulating hormone level0.0000007486Highly InformativeDirect
Mammalian Phenotype (MP)cleft palate0.00000195Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.00001592Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.00003721Highly InformativeDirect
Mammalian Phenotype (MP)abnormal digit morphology0.0001511Highly InformativeDirect
Mammalian Phenotype (MP)abnormal oocyte number0.0002905Highly InformativeDirect
Mammalian Phenotype (MP)small nasal bone0.0006109Highly InformativeDirect
Mammalian Phenotype (MP)absent allantois0.0006594Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.00074Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.0007405Highly InformativeDirect
Mammalian Phenotype (MP)decreased nephron number0.0008611Highly InformativeDirect
Mammalian Phenotype (MP)abnormal atrioventricular valve morphology0.0009556Highly InformativeDirect
Mammalian Phenotype (MP)abnormal incisor morphology0.0009556Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cornea morphology0.006698Highly InformativeInherited
Mammalian Phenotype (MP)abnormal embryonic-extraembryonic boundary morphology0.01076Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart right ventricle morphology0.01571Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart atrium morphology0.01745Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.01776Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digit development0.01957Highly InformativeInherited
Mammalian Phenotype (MP)abnormal muscle weight0.04686Highly InformativeInherited
Mammalian Phenotype (MP)increased heart ventricle size0.07929Highly InformativeInherited
Mammalian Phenotype (MP)abnormal dorsal root ganglion morphology0.08267Highly 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 variant0.4619Least InformativeInherited
Worm Phenotype (WP)drug response variant0.07309Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.07743Moderately InformativeInherited
Worm Phenotype (WP)anchor cell invasion variant0.0000945InformativeDirect
Worm Phenotype (WP)nicotine response variant0.00018InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.07145Least InformativeInherited
Fly Anatomy (FA)larva0.09517Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)embryo0.155Moderately InformativeInherited
Fly Anatomy (FA)epithelium0.1565Moderately InformativeInherited
Fly Anatomy (FA)region of integument0.7342Moderately InformativeInherited
Fly Anatomy (FA)abdominal segment0.01357InformativeInherited
Fly Anatomy (FA)integumentary specialisation0.01374InformativeInherited
Fly Anatomy (FA)tracheal system0.04698InformativeInherited
Fly Anatomy (FA)stage 7 embryo0.0003981Highly InformativeDirect
Fly Anatomy (FA)epithelial furrow0.00224Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0.2628Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.2871Least InformativeInherited
Zebrafish Anatomy (ZA)cavitated compound organ0.7661Least InformativeInherited
Zebrafish Anatomy (ZA)cardiovascular system0.04136Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.3774Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.4662Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.4857Moderately InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.08365InformativeInherited
Zebrafish Anatomy (ZA)blood vessel0.3946InformativeInherited
Zebrafish Anatomy (ZA)male organism0.000185Highly InformativeDirect
Zebrafish Anatomy (ZA)female organism0.0005407Highly InformativeDirect
Zebrafish Anatomy (ZA)reproductive system0.001552Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial vasculature0.007276Highly InformativeInherited
Zebrafish Anatomy (ZA)endocrine system0.009269Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.1615Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.4777Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system0.9877Least 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 structure0.00002849Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0002243Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.7396Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.9378Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.00000001652InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0000008759InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.000002343InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.000004594InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.00006899InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0003806InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0005498InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.001791InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.002566InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.02188InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.9594InformativeInherited
Xenopus ANatomical entity (XAN)limb1InformativeInherited
Xenopus ANatomical entity (XAN)head mesenchyme0.00000001458Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.0000007991Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.000001724Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.000002128Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.000007691Highly InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.000007873Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.000009467Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.00001193Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00006802Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0001509Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.0004282Highly InformativeDirect
Xenopus ANatomical entity (XAN)branchial arch0.1587Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.9417Highly 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 ]