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Protein

Signaling lymphocytic activation molecule

Gene

SLAMF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. SLAMF1-induced signal-transduction events in T-lymphocytes are different from those in B-cells. Two modes of SLAMF1 signaling seem to exist: one depending on SH2D1A (and perhaps SH2D1B) and another in which protein-tyrosine phosphatase 2C (PTPN11)-dependent signal transduction operates. Initially it has been proposed that association with SH2D1A prevents binding to inhibitory effectors including INPP5D/SHIP1 and PTPN11/SHP-2 (PubMed:11806999). However, signaling is also regulated by SH2D1A which can simultaneously interact with and recruit FYN which subsequently phosphorylates and activates SLAMF1 (PubMed:12458214). Mediates IL-2-independent proliferation of activated T-cells during immune responses and induces IFN-gamma production (By similarity). Downstreaming signaling involves INPP5D, DOK1 and DOK2 leading to inhibited IFN-gamma production in T-cells, and PRKCQ, BCL10 and NFKB1 leading to increased T-cell activation and Th2 cytokine production (By similarity). Promotes T-cell receptor-induced IL-4 secretion by CD4+ cells (By similarity). Inhibits antigen receptor-mediated production of IFN-gamma, but not IL-2, in CD4-/CD8- T-cells (By similarity). Required for IL-4 production by germinal centers T follicular helper (T(Fh))cells (By similarity). May inhibit CD40-induced signal transduction in monocyte-derived dendritic cells (PubMed:16317102). May play a role in a allergic responses and may regulate allergen-induced Th2 cytokine and Th1 cytokine secretion (By similarity). In conjunction with SLAMF6 controls the transition between positive selection and the subsequent expansion and differentiation of the thymocytic natural killer T (NKT) cell lineage. Involved in the peripheral differentiation of indifferent natural killer T (iNKT) cells toward a regulatory NKT2 type (By similarity). In macrophages involved in down-regulation of IL-12, TNF-alpha and nitric oxide in response to lipopolysaccharide (LPS) (By similarity). In B-cells activates the ERK signaling pathway independently of SH2D1A but implicating both, SYK and INPP5D, and activates Akt signaling dependent on SYK and SH2D1A (By similarity). In B-cells also activates p38 MAPK and JNK1 and JNK2 (PubMed:20231852). In conjunction with CD84/SLAMF5 and SLAMF6 may be a negative regulator of the humoral immune response (By similarity).By similarity2 Publications2 Publications
(Microbial infection) Acts as a receptor for measles virus; also including isoform 4 (PubMed:10972291, PubMed:25710480). Involved in innate immune response against Gram-negative bacteria in macrophages; probably recognizes OmpC and/or OmpF on the bacterial surface, regulates phagosome maturation and recruitment of the PI3K complex II (PI3KC3-C2) leading to accumulation of PdtIns3P and NOX2 activity in the phagosomes (PubMed:20818396).2 Publications

GO - Molecular functioni

  • antigen binding Source: ProtInc
  • transmembrane signaling receptor activity Source: ProtInc
  • virus receptor activity Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Host cell receptor for virus entry, Receptor

Keywords - Biological processi

Adaptive immunity, Cell adhesion, Host-virus interaction, Immunity, Innate immunity, Phagocytosis

Enzyme and pathway databases

BioCyciZFISH:ENSG00000117090-MONOMER.
SIGNORiQ13291.

Names & Taxonomyi

Protein namesi
Recommended name:
Signaling lymphocytic activation molecule
Alternative name(s):
CDw150
IPO-3
SLAM family member 1
CD_antigen: CD150
Gene namesi
Name:SLAMF1
Synonyms:SLAM
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:10903. SLAMF1.

Subcellular locationi

  • Cell membrane 1 Publication; Single-pass type I membrane protein

  • Note: Present on the surface of B-cells and T-cells. Located at the plasma membrane contacts between neighboring T-cells (PubMed:11806999).1 Publication
Isoform 3 :
Isoform 4 :

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini21 – 237ExtracellularSequence analysisAdd BLAST217
Transmembranei238 – 258HelicalSequence analysisAdd BLAST21
Topological domaini259 – 335CytoplasmicSequence analysisAdd BLAST77

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane, Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi269Y → F: No effect on interaction with INPP5D/SHIP-1, PTPN11/SHP-2 and SH2D1A. 1 Publication1
Mutagenesisi279T → A: Disrupts interaction with SH2D1A; when associated with A-325. 1 Publication1
Mutagenesisi281Y → F: Disrupts interaction with INPP5D/SHIP-1 and PTPN11/SHP-2, no effect on interaction with SH2D1A. 2 Publications1
Mutagenesisi281Y → F: Disrupts interaction with SH2D1A; when associated with F-327. 1 Publication1
Mutagenesisi307Y → F: No effect on interaction with PTPN11/SHP-2 and SH2D1A. 1 Publication1
Mutagenesisi325T → A: Disrupts interaction with SH2D1A; when associated with A-279. 1 Publication1
Mutagenesisi327Y → F: Disrupts interaction with INPP5D/SHIP-1 and PTPN11/SHP-2, no effect on interaction with SH2D1A. 2 Publications1
Mutagenesisi327Y → F: Disrupts interaction with SH2D1A; when associated with F-281. 1 Publication1

Organism-specific databases

DisGeNETi6504.
OpenTargetsiENSG00000117090.
PharmGKBiPA35803.

Polymorphism and mutation databases

BioMutaiSLAMF1.
DMDMi9297047.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 20Sequence analysisAdd BLAST20
ChainiPRO_000001495921 – 335Signaling lymphocytic activation moleculeAdd BLAST315

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi53N-linked (GlcNAc...)Sequence analysis1
Glycosylationi57N-linked (GlcNAc...)Sequence analysis1
Glycosylationi102N-linked (GlcNAc...)Sequence analysis1
Glycosylationi125N-linked (GlcNAc...)Sequence analysis1
Glycosylationi150N-linked (GlcNAc...)Sequence analysis1
Glycosylationi155N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi158 ↔ 228PROSITE-ProRule annotation
Disulfide bondi164 ↔ 209PROSITE-ProRule annotation
Glycosylationi189N-linked (GlcNAc...)Sequence analysis1
Glycosylationi217N-linked (GlcNAc...)Sequence analysis1
Modified residuei281Phosphotyrosine; by FYN2 Publications1
Modified residuei307Phosphotyrosine; by FYN1 Publication1
Modified residuei327Phosphotyrosine; by FYN1 Publication1

Post-translational modificationi

Phosphorylated on tyrosine residues by FYN.2 Publications

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiQ13291.
PeptideAtlasiQ13291.
PRIDEiQ13291.

PTM databases

iPTMnetiQ13291.
PhosphoSitePlusiQ13291.

Expressioni

Tissue specificityi

Constitutively expressed on peripheral blood memory T-cells, T-cell clones, immature thymocytes and a proportion of B-cells, and is rapidly induced on naive T-cells after activation (PubMed:7617038). Activated B-cells express isoform 1, isoform 3 and a cytoplasmic isoform (PubMed:9091591). Isoform 4 is expressed in B-cells, primary T-cells, dendritic cells and macrophages. Isoform 4 is expressed in tumors of the central nervous system (PubMed:25710480).3 Publications

Gene expression databases

BgeeiENSG00000117090.
CleanExiHS_SLAMF1.
ExpressionAtlasiQ13291. baseline and differential.
GenevisibleiQ13291. HS.

Organism-specific databases

HPAiCAB002438.

Interactioni

Subunit structurei

Interacts (via cytoplasmic domain) with SH2D1A and SH2D1B; SH2D1A mediates association with FYN; SH2D1A binds to phosphorylated and not phosphorylated ITSM 1 (PubMed:9774102, PubMed:11313386, PubMed:11806999, PubMed:12458214). Interacts (via cytoplasmic domain phosphorylated on tyrosine residues) with INPP5D and PTPN11; presence of SH2D1A facilitates binding to INPP5D (PubMed:11313386, PubMed:12458214). Interacts with MAP4K1 (PubMed:20231852). Interacts with PIK3C3, BECN1 and UVRAG; indicative for an association with PI3K complex II (PI3KC3-C2) (PubMed:20818396).9 Publications
(Microbial infection) Interacts with measles hemagglutinin protein.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
HQ786F22EBI-4315002,EBI-5323300From a different organism.
MAP4K1Q929183EBI-4315002,EBI-881
SH2D1AO6088012EBI-4315002,EBI-6983382

Protein-protein interaction databases

BioGridi112395. 112 interactors.
DIPiDIP-40767N.
IntActiQ13291. 9 interactors.
MINTiMINT-113752.
STRINGi9606.ENSP00000306190.

Structurei

Secondary structure

1335
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi278 – 281Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1D4TX-ray1.10B276-286[»]
1D4WX-ray1.80C/D276-286[»]
1I3ZX-ray2.15B273-286[»]
1KA6NMR-B275-282[»]
1KA7NMR-B275-286[»]
1M27X-ray2.50B276-286[»]
2DZFmodel-@1-335[»]
2IE9model-@1-335[»]
2IFLmodel-@3-335[»]
2IG5model-@1-335[»]
ProteinModelPortaliQ13291.
SMRiQ13291.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13291.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 138Ig-like V-typeAdd BLAST110
Domaini144 – 223Ig-like C2-typeAdd BLAST80

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi279 – 284ITSM 11 Publication6
Motifi307 – 312SH2-bindingSequence analysis6
Motifi325 – 330ITSM 22 Publications6

Domaini

The ITSMs (immunoreceptor tyrosine-based switch motifs) with the consensus sequence T-X-Y-X-X-[VI] present in SLAM family receptors have overlapping specificity for activating and inhibitory SH2 domain-containing binding partners. Especially they mediate the interaction with the SH2 domain of SH2D1A and SH2D1B. For SLAMF1 a 'two-out-of-three-pronged' mechanism is proposed involving threonine (position -2), phosphorylated tyrosine (position 0) and valine/isoleucine (position +3). SH2D1A binding is mediated by either three 'prongs' (for high affinity binding involving ITSM 1) or a combination of any two also including non-phosphorylated Tyr-281 of ITSM 1 thus providing a positive feedback loop implicating SH2D1A-dependent recruitment of activating FYN. ITSM 2 needs to be phosphorylated on Tyr-327 for SH2D1A binding.1 Publication2 Publications

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IFKK. Eukaryota.
ENOG4111DAM. LUCA.
GeneTreeiENSGT00510000048858.
HOGENOMiHOG000125310.
HOVERGENiHBG054224.
InParanoidiQ13291.
KOiK06536.
OMAiRIVVTMA.
OrthoDBiEOG091G0EOO.
PhylomeDBiQ13291.
TreeFamiTF334964.

Family and domain databases

InterProiIPR007110. Ig-like_dom.
IPR010407. Sig_lymph_act_molc_N.
[Graphical view]
PfamiPF06214. SLAM. 1 hit.
[Graphical view]
ProDomiPD090491. Sig_lymph_act_molc_N. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF48726. SSF48726. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: Q13291-1) [UniParc]FASTAAdd to basket
Also known as: Long, mCD150

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MDPKGLLSLT FVLFLSLAFG ASYGTGGRMM NCPKILRQLG SKVLLPLTYE
60 70 80 90 100
RINKSMNKSI HIVVTMAKSL ENSVENKIVS LDPSEAGPPR YLGDRYKFYL
110 120 130 140 150
ENLTLGIRES RKEDEGWYLM TLEKNVSVQR FCLQLRLYEQ VSTPEIKVLN
160 170 180 190 200
KTQENGTCTL ILGCTVEKGD HVAYSWSEKA GTHPLNPANS SHLLSLTLGP
210 220 230 240 250
QHADNIYICT VSNPISNNSQ TFSPWPGCRT DPSETKPWAV YAGLLGGVIM
260 270 280 290 300
ILIMVVILQL RRRGKTNHYQ TTVEKKSLTI YAQVQKPGPL QKKLDSFPAQ
310 320 330
DPCTTIYVAA TEPVPESVQE TNSITVYASV TLPES
Length:335
Mass (Da):37,231
Last modified:November 1, 1996 - v1
Checksum:iBFB0F27EA31D8C04
GO
Isoform 2 (identifier: Q13291-2) [UniParc]FASTAAdd to basket
Also known as: Short, SURslam2, vmSLAM

The sequence of this isoform differs from the canonical sequence as follows:
     289-298: PLQKKLDSFP → DTHHQTSDLF
     299-335: Missing.

Show »
Length:298
Mass (Da):33,365
Checksum:iDCE97AC03ACDC045
GO
Isoform 3 (identifier: Q13291-3) [UniParc]FASTAAdd to basket
Also known as: Secreted, SECslam, sSLAM

The sequence of this isoform differs from the canonical sequence as follows:
     234-263: Missing.

Show »
Length:305
Mass (Da):33,839
Checksum:iF5CBDC25B2E19967
GO
Isoform 4 (identifier: Q13291-4) [UniParc]FASTAAdd to basket
Also known as: nCD150

The sequence of this isoform differs from the canonical sequence as follows:
     264-335: GKTNHYQTTV...VYASVTLPES → ATLTTTNQYW...KQIPSQSMLV

Show »
Length:357
Mass (Da):40,292
Checksum:iDA43C3AE974A5013
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02192411F → L.Corresponds to variant rs2295612dbSNPEnsembl.1
Natural variantiVAR_03552481L → F in a breast cancer sample; somatic mutation. 1 Publication1
Natural variantiVAR_021925333P → T.Corresponds to variant rs3796504dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_002567234 – 263Missing in isoform 3. 1 PublicationAdd BLAST30
Alternative sequenceiVSP_058033264 – 335GKTNH…TLPES → ATLTTTNQYWSQNVLTQDQE RCPGCLPMVKRTITRQQWKK KALRSMPKSRNQVLFRRNLT PSQLRTLAPPYMLLPQSLSQ SLSRKQIPSQSMLV in isoform 4. 1 PublicationAdd BLAST72
Alternative sequenceiVSP_002568289 – 298PLQKKLDSFP → DTHHQTSDLF in isoform 2. 1 Publication10
Alternative sequenceiVSP_002569299 – 335Missing in isoform 2. 1 PublicationAdd BLAST37

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U33017 mRNA. Translation: AAA75380.1.
KF471075 mRNA. Translation: AHF72732.1.
AL121985, AL138930 Genomic DNA. Translation: CAH73505.1.
AL138930, AL121985 Genomic DNA. Translation: CAI15154.1.
CH471121 Genomic DNA. Translation: EAW52706.1.
BC132792 mRNA. Translation: AAI32793.1.
AF252305 Genomic DNA. Translation: AAG10434.1.
CCDSiCCDS1207.1. [Q13291-1]
CCDS81389.1. [Q13291-4]
PIRiS58892.
RefSeqiNP_001317683.1. NM_001330754.1.
NP_003028.1. NM_003037.4. [Q13291-1]
XP_005245513.1. XM_005245456.3. [Q13291-3]
UniGeneiHs.523660.

Genome annotation databases

EnsembliENST00000302035; ENSP00000306190; ENSG00000117090. [Q13291-1]
ENST00000538290; ENSP00000438406; ENSG00000117090. [Q13291-4]
GeneIDi6504.
KEGGihsa:6504.
UCSCiuc001fwl.6. human. [Q13291-1]
uc031vca.2. human.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U33017 mRNA. Translation: AAA75380.1.
KF471075 mRNA. Translation: AHF72732.1.
AL121985, AL138930 Genomic DNA. Translation: CAH73505.1.
AL138930, AL121985 Genomic DNA. Translation: CAI15154.1.
CH471121 Genomic DNA. Translation: EAW52706.1.
BC132792 mRNA. Translation: AAI32793.1.
AF252305 Genomic DNA. Translation: AAG10434.1.
CCDSiCCDS1207.1. [Q13291-1]
CCDS81389.1. [Q13291-4]
PIRiS58892.
RefSeqiNP_001317683.1. NM_001330754.1.
NP_003028.1. NM_003037.4. [Q13291-1]
XP_005245513.1. XM_005245456.3. [Q13291-3]
UniGeneiHs.523660.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1D4TX-ray1.10B276-286[»]
1D4WX-ray1.80C/D276-286[»]
1I3ZX-ray2.15B273-286[»]
1KA6NMR-B275-282[»]
1KA7NMR-B275-286[»]
1M27X-ray2.50B276-286[»]
2DZFmodel-@1-335[»]
2IE9model-@1-335[»]
2IFLmodel-@3-335[»]
2IG5model-@1-335[»]
ProteinModelPortaliQ13291.
SMRiQ13291.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112395. 112 interactors.
DIPiDIP-40767N.
IntActiQ13291. 9 interactors.
MINTiMINT-113752.
STRINGi9606.ENSP00000306190.

PTM databases

iPTMnetiQ13291.
PhosphoSitePlusiQ13291.

Polymorphism and mutation databases

BioMutaiSLAMF1.
DMDMi9297047.

Proteomic databases

PaxDbiQ13291.
PeptideAtlasiQ13291.
PRIDEiQ13291.

Protocols and materials databases

DNASUi6504.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000302035; ENSP00000306190; ENSG00000117090. [Q13291-1]
ENST00000538290; ENSP00000438406; ENSG00000117090. [Q13291-4]
GeneIDi6504.
KEGGihsa:6504.
UCSCiuc001fwl.6. human. [Q13291-1]
uc031vca.2. human.

Organism-specific databases

CTDi6504.
DisGeNETi6504.
GeneCardsiSLAMF1.
HGNCiHGNC:10903. SLAMF1.
HPAiCAB002438.
MIMi603492. gene.
neXtProtiNX_Q13291.
OpenTargetsiENSG00000117090.
PharmGKBiPA35803.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IFKK. Eukaryota.
ENOG4111DAM. LUCA.
GeneTreeiENSGT00510000048858.
HOGENOMiHOG000125310.
HOVERGENiHBG054224.
InParanoidiQ13291.
KOiK06536.
OMAiRIVVTMA.
OrthoDBiEOG091G0EOO.
PhylomeDBiQ13291.
TreeFamiTF334964.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000117090-MONOMER.
SIGNORiQ13291.

Miscellaneous databases

ChiTaRSiSLAMF1. human.
EvolutionaryTraceiQ13291.
GeneWikiiSLAMF1.
GenomeRNAii6504.
PROiQ13291.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000117090.
CleanExiHS_SLAMF1.
ExpressionAtlasiQ13291. baseline and differential.
GenevisibleiQ13291. HS.

Family and domain databases

InterProiIPR007110. Ig-like_dom.
IPR010407. Sig_lymph_act_molc_N.
[Graphical view]
PfamiPF06214. SLAM. 1 hit.
[Graphical view]
ProDomiPD090491. Sig_lymph_act_molc_N. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF48726. SSF48726. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSLAF1_HUMAN
AccessioniPrimary (citable) accession number: Q13291
Secondary accession number(s): Q5W172, Q9HBE8, W0HKK7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1996
Last modified: November 30, 2016
This is version 159 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  2. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.