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 cancer0.1126Least InformativeInherited
Disease Ontology (DO)nervous system disease0.5998Least InformativeInherited
Disease Ontology (DO)benign neoplasm0.00000001213Moderately InformativeDirect
Disease Ontology (DO)lower respiratory tract disease0.00005668Moderately InformativeDirect
Disease Ontology (DO)sensory system disease0.01247Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.01918Moderately InformativeInherited
Disease Ontology (DO)skin disease0.06006Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.1957Moderately InformativeInherited
Disease Ontology (DO)connective tissue disease0.3461Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.3812Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.7724Moderately InformativeInherited
Disease Ontology (DO)asthma0.0000347InformativeDirect
Disease Ontology (DO)prostate cancer0.0001361InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.002923InformativeInherited
Disease Ontology (DO)arthropathy0.008084InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.07618InformativeInherited
Disease Ontology (DO)aggressive systemic mastocytosis0.00007924Highly InformativeDirect
Disease Ontology (DO)rhabdomyosarcoma0.000448Highly InformativeDirect
Disease Ontology (DO)cholesteatoma0.0008822Highly InformativeDirect
Disease Ontology (DO)atopic dermatitis0.0009226Highly InformativeDirect
Disease Ontology (DO)inner ear disease0.009107Highly 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 limbs0.2584Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.5005Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.5484Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology1Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.09422Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.1061Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.4763Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.4925Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.5526Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.7414Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.8156Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.9203Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system physiology0.927Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral vasculature0.05571InformativeInherited
Phenotypic Abnormality (PA)Abnormal vertebral morphology0.2005InformativeInherited
Phenotypic Abnormality (PA)Abnormality of joint mobility0.2101InformativeInherited
Phenotypic Abnormality (PA)Internal hemorrhage0.2422InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.313InformativeInherited
Phenotypic Abnormality (PA)Abnormal lung morphology0.3263InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.513InformativeInherited
Phenotypic Abnormality (PA)Abnormality of phalanx of finger0.8866InformativeInherited
Phenotypic Abnormality (PA)Subarachnoid hemorrhage0.000254Highly InformativeDirect
Phenotypic Abnormality (PA)Hemoptysis0.0004044Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the phalanges of the 5th finger0.0005203Highly InformativeDirect
Phenotypic Abnormality (PA)Absent toe0.005558Highly InformativeInherited
Phenotypic Abnormality (PA)Short toe0.01721Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the phalanges of the hand0.02859Highly InformativeInherited
Phenotypic Abnormality (PA)Synostosis of joints0.04593Highly 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 phenotype0.003172Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.04009Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1308Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.1683Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2317Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3294Least InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.0000001748Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal craniofacial morphology0.0001009Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.0001399Moderately InformativeDirect
Mammalian Phenotype (MP)embryo phenotype0.005331Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.01414Moderately InformativeInherited
Mammalian Phenotype (MP)limbs/digits/tail phenotype0.02929Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.05063Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.0558Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.07596Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.088Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.1344Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.1793Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.1908Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.2311Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.2911Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.6715Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7427Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.00001616InformativeDirect
Mammalian Phenotype (MP)abnormal head morphology0.00133InformativeInherited
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002612InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.005662InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.01115InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.0549InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.07251InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.07683InformativeInherited
Mammalian Phenotype (MP)abnormal heart ventricle morphology0.1167InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.1662InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.194InformativeInherited
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 level0.0000008273Highly InformativeDirect
Mammalian Phenotype (MP)cleft palate0.000001957Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.00001738Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mandibular coronoid process morphology0.00003728Highly InformativeDirect
Mammalian Phenotype (MP)abnormal digit morphology0.0001517Highly InformativeDirect
Mammalian Phenotype (MP)abnormal oocyte number0.0002912Highly InformativeDirect
Mammalian Phenotype (MP)small nasal bone0.0006116Highly InformativeDirect
Mammalian Phenotype (MP)absent allantois0.000661Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.0007Highly InformativeDirect
Mammalian Phenotype (MP)abnormal autonomic nervous system morphology0.000744Highly InformativeDirect
Mammalian Phenotype (MP)decreased nephron number0.0008658Highly InformativeDirect
Mammalian Phenotype (MP)abnormal atrioventricular valve morphology0.0009612Highly InformativeDirect
Mammalian Phenotype (MP)abnormal incisor morphology0.0009612Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cornea morphology0.006702Highly InformativeInherited
Mammalian Phenotype (MP)abnormal embryonic-extraembryonic boundary morphology0.01078Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart right ventricle morphology0.01569Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart atrium morphology0.01737Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.01791Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digit development0.01955Highly InformativeInherited
Mammalian Phenotype (MP)abnormal muscle weight0.04695Highly InformativeInherited
Mammalian Phenotype (MP)increased heart ventricle size0.07924Highly InformativeInherited
Mammalian Phenotype (MP)abnormal dorsal root ganglion morphology0.08448Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ovary size0.09966Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.264Highly 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 variant0.4364Least InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.07742Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.1684Moderately InformativeInherited
Worm Phenotype (WP)nicotine response variant0.0001912InformativeDirect
Worm Phenotype (WP)anchor cell invasion variant0.00007344Highly 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 defective0.0000000001414InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)embryo0.01531Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.0649Least InformativeInherited
Fly Anatomy (FA)larva0.2337Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)late embryo0.3051Moderately InformativeInherited
Fly Anatomy (FA)epithelium0.3641Moderately InformativeInherited
Fly Anatomy (FA)abdominal segment0.008814InformativeInherited
Fly Anatomy (FA)integumentary specialisation0.01007InformativeInherited
Fly Anatomy (FA)tracheal system0.03979InformativeInherited
Fly Anatomy (FA)gastrula embryo0.04779InformativeInherited
Fly Anatomy (FA)epithelial furrow0.0006252Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)multi-tissue structure0.2435Least InformativeInherited
Zebrafish Anatomy (ZA)organism subdivision0.2746Least InformativeInherited
Zebrafish Anatomy (ZA)cardiovascular system0.06473Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.2122Moderately InformativeInherited
Zebrafish Anatomy (ZA)blood vessel0.4788InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.1858Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.4204Least 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)multi-tissue structure0.000009747Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0001965Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.8446Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical direction0.00000001155InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.0000003026InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.000001454InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.00000157InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0001241InformativeDirect
Xenopus ANatomical entity (XAN)peripheral nervous system0.0007367InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.0008456InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.00103InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.9547InformativeInherited
Xenopus ANatomical entity (XAN)limb1InformativeInherited
Xenopus ANatomical entity (XAN)head mesenchyme0.00000000009372Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.000007255Highly InformativeDirect
Xenopus ANatomical entity (XAN)involuted dorsal mesoderm0.00001285Highly InformativeDirect
Xenopus ANatomical entity (XAN)neurogenic placode0.00001604Highly InformativeDirect
Xenopus ANatomical entity (XAN)circulatory system0.00001929Highly InformativeDirect
Xenopus ANatomical entity (XAN)head mesoderm0.0000239Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.00004006Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.00008105Highly InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.0001638Highly InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.000174Highly InformativeDirect
Xenopus ANatomical entity (XAN)animal hemisphere0.0002669Highly InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.002637Highly InformativeInherited
Xenopus ANatomical entity (XAN)branchial arch0.1547Highly InformativeInherited
Xenopus ANatomical entity (XAN)marginal zone0.9814Highly 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 23 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 23 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 ]