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 0 61
Proteins 2,494 0 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 disease0.494Least InformativeInherited
Disease Ontology (DO)skin disease0.0007845Moderately InformativeDirect
Disease Ontology (DO)lower respiratory tract disease0.02932Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.04368Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1026Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.1867Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.2077Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.4999Moderately InformativeInherited
Disease Ontology (DO)periodontal disease0.00001094InformativeDirect
Disease Ontology (DO)physical disorder0.00002243InformativeDirect
Disease Ontology (DO)bullous pemphigoid0.00009143InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.001265InformativeInherited
Disease Ontology (DO)female reproductive system disease0.001663InformativeInherited
Disease Ontology (DO)parasitic protozoa infectious disease0.006509InformativeInherited
Disease Ontology (DO)interstitial lung disease0.02475InformativeInherited
Disease Ontology (DO)purpura0.0001113Highly InformativeDirect
Disease Ontology (DO)Behcet's disease0.0001404Highly InformativeDirect
Disease Ontology (DO)obstructive lung disease0.0001416Highly InformativeDirect
Disease Ontology (DO)primary open angle glaucoma0.0002948Highly InformativeDirect
Disease Ontology (DO)endometriosis0.0004563Highly 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 system0.7031Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.4051Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.1692InformativeInherited
Phenotypic Abnormality (PA)Renal hypoplasia/aplasia0.004839Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.0399Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.397Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9621Least InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.001134Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.01569Moderately InformativeInherited
Mammalian Phenotype (MP)limbs/digits/tail phenotype0.03839Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.07048Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.2766Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.814Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.01337InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.152InformativeInherited
Mammalian Phenotype (MP)abnormal coat appearance1InformativeInherited
Mammalian Phenotype (MP)abnormal right subclavian artery morphology0.0002684Highly InformativeDirect
Mammalian Phenotype (MP)abnormal heart atrium morphology0.000635Highly InformativeDirect
Mammalian Phenotype (MP)abnormal body temperature homeostasis0.0008194Highly InformativeDirect
Mammalian Phenotype (MP)abnormal aortic arch morphology0.005418Highly InformativeInherited
Mammalian Phenotype (MP)abnormal forelimb morphology0.06619Highly InformativeInherited
Mammalian Phenotype (MP)abnormal hair growth0.1868Highly 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 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)embryo0Least InformativeDirect
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)somatic cell0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)developing embryonic structure0Moderately InformativeDirect
Fly Anatomy (FA)central nervous system0Moderately InformativeDirect
Fly Anatomy (FA)late embryo0Moderately 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)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)compound organ0.445Least InformativeInherited
Zebrafish Anatomy (ZA)organism subdivision0.5523Least InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.1009Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.5898Moderately InformativeInherited
Zebrafish Anatomy (ZA)skeletal element0.001463InformativeInherited
Zebrafish Anatomy (ZA)surface structure0.02577InformativeInherited
Zebrafish Anatomy (ZA)cranium0.02831InformativeInherited
Zebrafish Anatomy (ZA)pectoral fin0.000179Highly InformativeDirect
Zebrafish Anatomy (ZA)intramembranous bone0.0003017Highly InformativeDirect

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 organ0.2964Least InformativeInherited
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.0000000491Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0.0000001203Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0.07448Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.1315Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.3344Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)eye0.0000000008948InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.0000000652InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.000000942InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.00003199InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.00004107InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0.0001262InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0004057InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.0005302InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.000688InformativeDirect
Xenopus ANatomical entity (XAN)peripheral nervous system0.005453InformativeInherited
Xenopus ANatomical entity (XAN)tail0.006922InformativeInherited
Xenopus ANatomical entity (XAN)vestibuloauditory system0.0701InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.1709InformativeInherited
Xenopus ANatomical entity (XAN)limb0.794InformativeInherited
Xenopus ANatomical entity (XAN)neurogenic placode0.000000766Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail tip0.000001524Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindlimb0.000006433Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.000008178Highly InformativeDirect
Xenopus ANatomical entity (XAN)notochord0.00005704Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastema0.00009293Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0002228Highly InformativeDirect
Xenopus ANatomical entity (XAN)otic vesicle0.0002427Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranium0.0003739Highly InformativeDirect
Xenopus ANatomical entity (XAN)tail bud0.000499Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0005657Highly InformativeDirect
Xenopus ANatomical entity (XAN)ganglion0.005766Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.02147Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.5705InformativeInherited

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processImmunity0.0000002041Moderately InformativeDirect
Biological processAngiogenesis0InformativeDirect
Biological processInflammatory response0InformativeDirect
Biological processInnate immunity0.0000000007779InformativeDirect
Biological processNeurogenesis0.00002658InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentLysosome0InformativeDirect
DiseaseProto-oncogene0.00002396Moderately InformativeDirect
DomainSignal0Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationHeparin-binding0InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationGrowth factor0Highly InformativeDirect
Post-translational modificationMitogen0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

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 18 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 18 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) · UniProtKB KeyWords (KW) · Internal database links ]