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  Home > SCOP hierarchy > Cystine-knot cytokines superfamily


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 limbs0.1795Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.9045Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.04361Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.2068Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.2705Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.2847Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal physiology0.2907Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.5413Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.8885Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal lower limb bone morphology0.1253InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.2353InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.3274InformativeInherited
Phenotypic Abnormality (PA)Abnormal finger phalanx morphology0.9059InformativeInherited
Phenotypic Abnormality (PA)Abnormal sputum0.000975Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal 5th finger phalanx morphology0.00144Highly InformativeInherited
Phenotypic Abnormality (PA)Synostosis of joints0.03678Highly 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 phenotype0.003153Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.03976Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1308Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.1682Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.23Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3296Least InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.0001027Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.0001409Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.005322Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.01424Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.0504Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.0556Moderately 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 phenotype0.135Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.1795Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.1909Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.2296Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.2831Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.2908Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.6718Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7431Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.00001563InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.001318InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002517InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.005629InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.01106InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.05458InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.07223InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.07422InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.1169InformativeInherited
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 morphology0.8402InformativeInherited
Mammalian Phenotype (MP)abnormal follicle stimulating hormone level0.0000007464Highly InformativeDirect
Mammalian Phenotype (MP)cleft palate0.000001942Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.0000159Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.00003715Highly InformativeDirect
Mammalian Phenotype (MP)abnormal digit morphology0.0001509Highly InformativeDirect
Mammalian Phenotype (MP)abnormal oocyte number0.0002906Highly InformativeDirect
Mammalian Phenotype (MP)small nasal bone0.0006105Highly InformativeDirect
Mammalian Phenotype (MP)absent allantois0.0006589Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.00074Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.0007404Highly InformativeDirect
Mammalian Phenotype (MP)decreased nephron number0.0008609Highly InformativeDirect
Mammalian Phenotype (MP)abnormal atrioventricular valve morphology0.0009549Highly InformativeDirect
Mammalian Phenotype (MP)abnormal incisor morphology0.0009549Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cornea morphology0.0067Highly InformativeInherited
Mammalian Phenotype (MP)abnormal embryonic-extraembryonic boundary morphology0.01077Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart right ventricle morphology0.01572Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart atrium morphology0.0174Highly 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 size0.07931Highly InformativeInherited
Mammalian Phenotype (MP)abnormal dorsal root ganglion morphology0.08266Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ovary size0.09972Highly 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)organ system morphology variant0.3971Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.4137Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.6107Least InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.01161Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.09493Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.1789Moderately InformativeInherited
Worm Phenotype (WP)anchor cell invasion variant0.0000946InformativeDirect
Worm Phenotype (WP)nicotine response variant0.0002034InformativeDirect
Worm Phenotype (WP)synapse morphology variant0.00005628Highly 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 defective0.0000000002785InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.05857Least InformativeInherited
Fly Anatomy (FA)larva0.1118Least InformativeInherited
Fly Anatomy (FA)organism subdivision0.4223Least InformativeInherited
Fly Anatomy (FA)epithelium0.1469Moderately InformativeInherited
Fly Anatomy (FA)embryo0.2123Moderately InformativeInherited
Fly Anatomy (FA)region of integument0.7071Moderately InformativeInherited
Fly Anatomy (FA)integumentary specialisation0.0137InformativeInherited
Fly Anatomy (FA)abdominal segment0.01555InformativeInherited
Fly Anatomy (FA)tracheal system0.04049InformativeInherited
Fly Anatomy (FA)stage 7 embryo0.0004041Highly InformativeDirect
Fly Anatomy (FA)epithelial furrow0.00147Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0.1964Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.3315Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.5422Moderately InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.08813InformativeInherited
Zebrafish Anatomy (ZA)male organism0.0003046Highly InformativeDirect
Zebrafish Anatomy (ZA)female organism0.0006749Highly InformativeDirect
Zebrafish Anatomy (ZA)reproductive system0.002021Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.1355Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.4371Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous 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)embryonic structure0.0001161Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0001745Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.7688Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.9129Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.000000003209InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.0000009237InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.000001128InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.00000115InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.00001113InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.00009435InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0004838InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0006124InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.002314InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.003194InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.02754InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.9727InformativeInherited
Xenopus ANatomical entity (XAN)limb1InformativeInherited
Xenopus ANatomical entity (XAN)head mesenchyme0.00000001734Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.0000009796Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.000001236Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.000001244Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.000001939Highly InformativeDirect
Xenopus ANatomical entity (XAN)pelvic appendage0.000002638Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.00001143Highly InformativeDirect
Xenopus ANatomical entity (XAN)neurogenic placode0.00004408Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00007985Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0002054Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.0004922Highly InformativeDirect
Xenopus ANatomical entity (XAN)vegetal hemisphere0.0006122Highly InformativeDirect
Xenopus ANatomical entity (XAN)branchial arch0.1601Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.894Highly 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 ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.