SUPERFAMILY 1.75 HMM library and genome assignments server

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Cytokine superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   beta-Trefoil [ 50352] (8)
Superfamily:   Cytokine [ 50353] (2)
Families:   Fibroblast growth factors (FGF) [ 50354] (9)
  Interleukin-1 (IL-1) [ 50362] (5)


Superfamily statistics
Genomes (149) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 2,549 6,821 61
Proteins 2,494 6,688 61


Functional annotation
General category Processes_EC
Detailed category Immune response

Document:
Function annotation of SCOP domain superfamilies

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.4928Least InformativeInherited
Disease Ontology (DO)skin disease0.0007937Moderately InformativeDirect
Disease Ontology (DO)lower respiratory tract disease0.02945Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.04386Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1029Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.1874Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.2079Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.501Moderately InformativeInherited
Disease Ontology (DO)periodontal disease0.00001112InformativeDirect
Disease Ontology (DO)physical disorder0.00002179InformativeDirect
Disease Ontology (DO)bullous pemphigoid0.00009262InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.001274InformativeInherited
Disease Ontology (DO)female reproductive system disease0.001654InformativeInherited
Disease Ontology (DO)parasitic protozoa infectious disease0.006546InformativeInherited
Disease Ontology (DO)interstitial lung disease0.02485InformativeInherited
Disease Ontology (DO)purpura0.0001123Highly InformativeDirect
Disease Ontology (DO)Behcet's disease0.0001417Highly InformativeDirect
Disease Ontology (DO)obstructive lung disease0.0001429Highly InformativeDirect
Disease Ontology (DO)primary open angle glaucoma0.0002982Highly InformativeDirect
Disease Ontology (DO)endometriosis0.0004511Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.8572Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.4331Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.2343InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.03965Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.3951Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9624Least InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.001134Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.01573Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.07072Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.2771Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.8141Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.01333InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.1519InformativeInherited
Mammalian Phenotype (MP)abnormal coat appearance1InformativeInherited
Mammalian Phenotype (MP)abnormal right subclavian artery morphology0.0002683Highly InformativeDirect
Mammalian Phenotype (MP)abnormal heart atrium morphology0.0006339Highly InformativeDirect
Mammalian Phenotype (MP)abnormal body temperature homeostasis0.0008147Highly InformativeDirect
Mammalian Phenotype (MP)abnormal aortic arch morphology0.005403Highly InformativeInherited
Mammalian Phenotype (MP)abnormal forelimb morphology0.06631Highly InformativeInherited
Mammalian Phenotype (MP)abnormal hair growth0.1858Highly InformativeInherited

Document: MP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)cell number defective0InformativeDirect
Fly Phenotype (FP)cell migration defective0Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)organism subdivision0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)embryo0Moderately InformativeDirect
Fly Anatomy (FA)central nervous system0Moderately InformativeDirect
Fly Anatomy (FA)abdominal segment0InformativeDirect
Fly Anatomy (FA)extended germ band embryo0InformativeDirect
Fly Anatomy (FA)dorsal closure embryo0InformativeDirect
Fly Anatomy (FA)primordium0InformativeDirect
Fly Anatomy (FA)CNS glial cell0Highly InformativeDirect
Fly Anatomy (FA)late extended germ band embryo0Highly InformativeDirect
Fly Anatomy (FA)early extended germ band embryo0Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0.3058Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.5203Least InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.3834Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.763Moderately InformativeInherited
Zebrafish Anatomy (ZA)skeletal system0.007094InformativeInherited
Zebrafish Anatomy (ZA)surface structure0.01154InformativeInherited
Zebrafish Anatomy (ZA)pectoral fin0.0001613Highly InformativeDirect
Zebrafish Anatomy (ZA)olfactory region0.0009129Highly InformativeDirect
Zebrafish Anatomy (ZA)bone element0.1827Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0.301Least InformativeInherited
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0000003357Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.000001004Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.003125Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.08471Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.13Moderately InformativeInherited
Xenopus ANatomical entity (XAN)eye0.000000002703InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.0000007824InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000008729InformativeDirect
Xenopus ANatomical entity (XAN)neural crest0.00001844InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00003891InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.0001018InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.0002849InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.0003061InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.0009979InformativeDirect
Xenopus ANatomical entity (XAN)peripheral nervous system0.00103InformativeInherited
Xenopus ANatomical entity (XAN)mesenchyme0.001179InformativeInherited
Xenopus ANatomical entity (XAN)tail0.002016InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.1236InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.181InformativeInherited
Xenopus ANatomical entity (XAN)limb0.7907InformativeInherited
Xenopus ANatomical entity (XAN)neural tube0.0000000365Highly InformativeDirect
Xenopus ANatomical entity (XAN)neurogenic placode0.000001571Highly InformativeDirect
Xenopus ANatomical entity (XAN)pelvic appendage0.000008323Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.00001556Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.00002191Highly InformativeDirect
Xenopus ANatomical entity (XAN)presomitic mesoderm0.00002426Highly InformativeDirect
Xenopus ANatomical entity (XAN)ganglion0.00006683Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.0001532Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.0004686Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail bud0.0009121Highly InformativeDirect
Xenopus ANatomical entity (XAN)limb bud0.001736Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.02532Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.5896InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 400.00002451Highly InformativeDirect

Document: XA annotation of SCOP domains

InterPro annotation
Cross references IPR008996 SSF50353 Protein matches
Abstract

Human basic fibroblast growth factor (hFGF-2)1 is a globular single chain heparin-binding polypeptide synthesized by different cell types and is involved in processes associated with proliferation and differentiation of cells. The determination of the three-dimensional structure of hFGF-2 by x-ray crystallography revealed a complex all beta-sheet protein without any disulphide bond. The overall structure shows strong homology with the fold of interleukin-1 and can be described as a trigonal pyramid with three topological units consisting each of four anti-parallel beta-sheets, giving the molecules internal pseudo three-fold symmetry. Both proteins share only 10-13% sequence identity, but superposition of their carbon backbone involves 9 of the 12 beta-sheet strands, including the anti-parallel beta-sheet incorporating the N- and C-terminal regions of the molecules [PubMed10567376].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · 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 33 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 Cytokine 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 33 hidden Markov models representing the Cytokine 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 · InterPro annotation · PDBeMotif links · Functional annotation · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Internal database links ]