SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 phenotype0.003162Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.03962Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.131Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.1679Least 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 morphology0.000139Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.005329Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.01423Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.05044Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.0556Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.07645Moderately 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 morphology0.6718Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7427Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.00001568InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.001317InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002515InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.005634InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.01105InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.05473InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.07219InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.0742InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.1175InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.1671InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.1957InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.4541InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.84InformativeInherited
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 number0.0002904Highly InformativeDirect
Mammalian Phenotype (MP)small nasal bone0.0006109Highly InformativeDirect
Mammalian Phenotype (MP)absent allantois0.0006594Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.0006975Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.0007394Highly InformativeDirect
Mammalian Phenotype (MP)decreased nephron number0.0008607Highly InformativeDirect
Mammalian Phenotype (MP)abnormal atrioventricular valve morphology0.0009558Highly InformativeDirect
Mammalian Phenotype (MP)abnormal incisor morphology0.0009558Highly 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 morphology0.01746Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.01776Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digit development0.01957Highly InformativeInherited
Mammalian Phenotype (MP)abnormal muscle weight0.04685Highly InformativeInherited
Mammalian Phenotype (MP)increased heart ventricle size0.07929Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ovary size0.09966Highly 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 variant0.461Least InformativeInherited
Worm Phenotype (WP)drug response variant0.0727Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.077Moderately InformativeInherited
Worm Phenotype (WP)anchor cell invasion variant0.00009375InformativeDirect
Worm Phenotype (WP)nicotine response variant0.0001786InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)circadian rhythm defective0.0000000001535InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.07259Least InformativeInherited
Fly Anatomy (FA)larva0.202Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)late embryo0.01246Moderately InformativeInherited
Fly Anatomy (FA)portion of tissue0.4363Moderately InformativeInherited
Fly Anatomy (FA)region of integument0.7574Moderately InformativeInherited
Fly Anatomy (FA)abdominal segment0.0122InformativeInherited
Fly Anatomy (FA)integumentary specialisation0.01294InformativeInherited
Fly Anatomy (FA)tracheal system0.04666InformativeInherited
Fly Anatomy (FA)stage 7 embryo0.0004117Highly InformativeDirect
Fly Anatomy (FA)epithelial furrow0.0007291Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0.223Least InformativeInherited
Zebrafish Anatomy (ZA)organism subdivision0.2654Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.2876Least InformativeInherited
Zebrafish Anatomy (ZA)cardiovascular system0.04147Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.3797Moderately InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.463Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.482Moderately InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.07972InformativeInherited
Zebrafish Anatomy (ZA)blood vessel0.3941InformativeInherited
Zebrafish Anatomy (ZA)male organism0.0001478Highly InformativeDirect
Zebrafish Anatomy (ZA)female organism0.0004541Highly InformativeDirect
Zebrafish Anatomy (ZA)reproductive system0.001356Highly InformativeInherited
Zebrafish Anatomy (ZA)cranial vasculature0.006754Highly InformativeInherited
Zebrafish Anatomy (ZA)endocrine system0.008846Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.1623Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.4785Least 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 structure0.00002493Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0002246Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.7375Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.9369Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.00000001702InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0000008631InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.000002035InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.000004002InformativeDirect
Xenopus ANatomical entity (XAN)anatomical space0.0000645InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.000344InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0005502InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.00186InformativeInherited
Xenopus ANatomical entity (XAN)pharyngeal region0.002327InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.02097InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.9575InformativeInherited
Xenopus ANatomical entity (XAN)limb1InformativeInherited
Xenopus ANatomical entity (XAN)head mesenchyme0.00000000851Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.0000007809Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.000001802Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.000001976Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.000007248Highly InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.000008477Highly InformativeDirect
Xenopus ANatomical entity (XAN)periocular region0.000009842Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.00001242Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00006369Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0001375Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural groove0.0004424Highly InformativeDirect
Xenopus ANatomical entity (XAN)branchial arch0.1678Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.9443Highly 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 ]