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Protein

Glutamate receptor ionotropic, NMDA 1

Gene

Grin1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Modulated by glycine. This protein plays a key role in synaptic plasticity, synaptogenesis, excitotoxicity, memory acquisition and learning. It mediates neuronal functions in glutamate neurotransmission. Is involved in the cell surface targeting of NMDA receptors (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei523 – 5231GlycineBy similarity
Binding sitei688 – 6881GlycineBy similarity
Binding sitei732 – 7321GlycineBy similarity

GO - Molecular functioni

  1. calcium channel activity Source: MGI
  2. calcium ion binding Source: MGI
  3. calmodulin binding Source: MGI
  4. cation channel activity Source: MGI
  5. extracellular-glutamate-gated ion channel activity Source: GO_Central
  6. glutamate binding Source: MGI
  7. glycine binding Source: UniProtKB
  8. neurotransmitter binding Source: Ensembl
  9. N-methyl-D-aspartate selective glutamate receptor activity Source: MGI
  10. receptor binding Source: MGI
  11. voltage-gated cation channel activity Source: Ensembl

GO - Biological processi

  1. adult locomotory behavior Source: MGI
  2. associative learning Source: MGI
  3. calcium ion homeostasis Source: MGI
  4. calcium ion transport Source: MGI
  5. cation transport Source: MGI
  6. cellular calcium ion homeostasis Source: MGI
  7. cellular response to manganese ion Source: Ensembl
  8. cerebral cortex development Source: MGI
  9. conditioned taste aversion Source: MGI
  10. ionotropic glutamate receptor signaling pathway Source: MGI
  11. learning Source: MGI
  12. learning or memory Source: MGI
  13. long-term memory Source: MGI
  14. male mating behavior Source: MGI
  15. memory Source: MGI
  16. negative regulation of neuron apoptotic process Source: MGI
  17. neuromuscular process Source: MGI
  18. olfactory learning Source: MGI
  19. pons maturation Source: MGI
  20. positive regulation of apoptotic process Source: MGI
  21. positive regulation of excitatory postsynaptic membrane potential Source: Ensembl
  22. positive regulation of transcription from RNA polymerase II promoter Source: MGI
  23. prepulse inhibition Source: MGI
  24. propylene metabolic process Source: BHF-UCL
  25. protein tetramerization Source: Ensembl
  26. regulation of axonogenesis Source: MGI
  27. regulation of cell communication Source: MGI
  28. regulation of dendrite morphogenesis Source: MGI
  29. regulation of excitatory postsynaptic membrane potential Source: MGI
  30. regulation of long-term neuronal synaptic plasticity Source: MGI
  31. regulation of membrane potential Source: MGI
  32. regulation of neuronal synaptic plasticity Source: MGI
  33. regulation of neuron apoptotic process Source: MGI
  34. regulation of respiratory gaseous exchange Source: MGI
  35. regulation of synapse assembly Source: MGI
  36. regulation of synaptic plasticity Source: MGI
  37. respiratory gaseous exchange Source: MGI
  38. response to amphetamine Source: MGI
  39. response to calcium ion Source: Ensembl
  40. response to ethanol Source: MGI
  41. response to fungicide Source: Ensembl
  42. response to morphine Source: MGI
  43. rhythmic process Source: Ensembl
  44. sensory perception of pain Source: MGI
  45. social behavior Source: MGI
  46. startle response Source: MGI
  47. suckling behavior Source: MGI
  48. synaptic transmission Source: MGI
  49. synaptic transmission, glutamatergic Source: MGI
  50. visual learning Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Ion channel, Ligand-gated ion channel, Receptor

Keywords - Biological processi

Ion transport, Transport

Keywords - Ligandi

Calcium, Magnesium

Enzyme and pathway databases

ReactomeiREACT_309838. CREB phosphorylation through the activation of CaMKII.
REACT_313804. EPHB-mediated forward signaling.
REACT_331187. Unblocking of NMDA receptor, glutamate binding and activation.
REACT_331823. Ras activation uopn Ca2+ infux through NMDA receptor.

Names & Taxonomyi

Protein namesi
Recommended name:
Glutamate receptor ionotropic, NMDA 1
Short name:
GluN1
Alternative name(s):
Glutamate [NMDA] receptor subunit zeta-1
N-methyl-D-aspartate receptor subunit NR1
Short name:
NMD-R1
Gene namesi
Name:Grin1
Synonyms:Glurz1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:95819. Grin1.

Subcellular locationi

Cell membrane By similarity; Multi-pass membrane protein By similarity. Cell junctionsynapsepostsynaptic cell membrane By similarity. Cell junctionsynapsepostsynaptic cell membranepostsynaptic density By similarity
Note: Enriched in postsynaptic plasma membrane and postsynaptic densities.By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini19 – 559541ExtracellularSequence AnalysisAdd
BLAST
Transmembranei560 – 58021HelicalSequence AnalysisAdd
BLAST
Topological domaini581 – 63656CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei637 – 65721HelicalSequence AnalysisAdd
BLAST
Topological domaini658 – 812155ExtracellularSequence AnalysisAdd
BLAST
Transmembranei813 – 83321HelicalSequence AnalysisAdd
BLAST
Topological domaini834 – 938105CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. cell junction Source: UniProtKB-KW
  2. cell surface Source: BHF-UCL
  3. cytoplasm Source: MGI
  4. dendrite Source: MGI
  5. dendrite membrane Source: Ensembl
  6. dendritic spine Source: MGI
  7. endoplasmic reticulum Source: MGI
  8. excitatory synapse Source: Ensembl
  9. growth cone Source: UniProtKB
  10. integral component of plasma membrane Source: MGI
  11. membrane Source: MGI
  12. neuronal postsynaptic density Source: MGI
  13. N-methyl-D-aspartate selective glutamate receptor complex Source: MGI
  14. plasma membrane Source: Reactome
  15. postsynaptic density Source: MGI
  16. postsynaptic membrane Source: MGI
  17. synapse Source: MGI
  18. synaptic cleft Source: Ensembl
  19. synaptic vesicle Source: MGI
  20. terminal bouton Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane, Postsynaptic cell membrane, Synapse

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1818Sequence AnalysisAdd
BLAST
Chaini19 – 938920Glutamate receptor ionotropic, NMDA 1PRO_0000011588Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi61 – 611N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi79 – 79InterchainBy similarity
Glycosylationi203 – 2031N-linked (GlcNAc...)Sequence Analysis
Glycosylationi239 – 2391N-linked (GlcNAc...)Sequence Analysis
Glycosylationi276 – 2761N-linked (GlcNAc...)Sequence Analysis
Glycosylationi300 – 3001N-linked (GlcNAc...)Sequence Analysis
Glycosylationi350 – 3501N-linked (GlcNAc...)Sequence Analysis
Glycosylationi368 – 3681N-linked (GlcNAc...)Sequence Analysis
Glycosylationi440 – 4401N-linked (GlcNAc...)Sequence Analysis
Glycosylationi471 – 4711N-linked (GlcNAc...)Sequence Analysis
Glycosylationi491 – 4911N-linked (GlcNAc...)Sequence Analysis
Modified residuei889 – 8891Phosphoserine; by PKCBy similarity
Modified residuei890 – 8901PhosphoserineBy similarity
Modified residuei896 – 8961Phosphoserine; by PKCBy similarity
Modified residuei897 – 8971Phosphoserine; by PKCBy similarity

Post-translational modificationi

NMDA is probably regulated by C-terminal phosphorylation of an isoform of NR1 by PKC. Dephosphorylated on Ser-897 probably by protein phosphatase 2A (PPP2CB). Its phosphorylated state is influenced by the formation of the NMDAR-PPP2CB complex and the NMDAR channel activity (By similarity).By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

MaxQBiP35438.
PaxDbiP35438.
PRIDEiP35438.

PTM databases

PhosphoSiteiP35438.

Expressioni

Gene expression databases

BgeeiP35438.
CleanExiMM_GRIN1.
ExpressionAtlasiP35438. baseline and differential.
GenevestigatoriP35438.

Interactioni

Subunit structurei

Forms heteromeric channel of a zeta subunit (GRIN1), a epsilon subunit (GRIN2A, GRIN2B, GRIN2C or GRIN2D) and a third subunit (GRIN3A or GRIN3B); disulfide-linked. Found in a complex with GRIN2A or GRIN2B and GRIN3B. Found in a complex with GRIN2A or GRIN2B, GRIN3A and PPP2CB. Interacts with DLG4 and MPDZ (By similarity). Interacts with LRFN1 and LRFN2 (By similarity). Interacts with MYZAP. Interacts with SNX27 (via PDZ domain); the interaction is required for recycling to the plasma membrane when endocytosed and prevent degradation in lysosomes.By similarity4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Dlg4Q6210810EBI-400084,EBI-300895
Lrp8Q924X64EBI-400084,EBI-432319

Protein-protein interaction databases

BioGridi200067. 82 interactions.
DIPiDIP-31577N.
IntActiP35438. 124 interactions.
MINTiMINT-135802.

Structurei

3D structure databases

ProteinModelPortaliP35438.
SMRiP35438. Positions 24-833.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni516 – 5183Glycine bindingBy similarity

Sequence similaritiesi

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG282132.
GeneTreeiENSGT00760000119186.
HOGENOMiHOG000231491.
HOVERGENiHBG052638.
InParanoidiP35438.
KOiK05208.
TreeFamiTF351405.

Family and domain databases

InterProiIPR001828. ANF_lig-bd_rcpt.
IPR018882. CaM-bd_C0_NMDA_rcpt_NR1.
IPR019594. Glu/Gly-bd.
IPR001508. Iono_rcpt_met.
IPR001320. Iontro_rcpt.
IPR028082. Peripla_BP_I.
[Graphical view]
PfamiPF01094. ANF_receptor. 1 hit.
PF10562. CaM_bdg_C0. 1 hit.
PF00060. Lig_chan. 1 hit.
[Graphical view]
PRINTSiPR00177. NMDARECEPTOR.
SMARTiSM00918. Lig_chan-Glu_bd. 1 hit.
SM00079. PBPe. 1 hit.
[Graphical view]
SUPFAMiSSF53822. SSF53822. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P35438-1) [UniParc]FASTAAdd to basket

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
MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN
60 70 80 90 100
KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYAI LVSHPPTPND
110 120 130 140 150
HFTPTPVSYT AGFYRIPVLG LTTRMSIYSD KSIHLSFLRT VPPYSHQSSV
160 170 180 190 200
WFEMMRVYNW NHIILLVSDD HEGRAAQKRL ETLLEERESK AEKVLQFDPG
210 220 230 240 250
TKNVTALLME ARDLEARVII LSASEDDAAT VYRAAAMLNM TGSGYVWLVG
260 270 280 290 300
EREISGNALR YAPDGIIGLQ LINGKNESAH ISDAVGVVAQ AVHELLEKEN
310 320 330 340 350
ITDPPRGCVG NTNIWKTGPL FKRVLMSSKY ADGVTGRVEF NEDGDRKFAN
360 370 380 390 400
YSIMNLQNRK LVQVGIYNGT HVIPNDRKII WPGGETEKPR GYQMSTRLKI
410 420 430 440 450
VTIHQEPFVY VKPTMSDGTC KEEFTVNGDP VKKVICTGPN DTSPGSPRHT
460 470 480 490 500
VPQCCYGFCV DLLIKLARTM NFTYEVHLVA DGKFGTQERV NNSNKKEWNG
510 520 530 540 550
MMGELLSGQA DMIVAPLTIN NERAQYIEFS KPFKYQGLTI LVKKEIPRST
560 570 580 590 600
LDSFMQPFQS TLWLLVGLSV HVVAVMLYLL DRFSPFGRFK VNSEEEEEDA
610 620 630 640 650
LTLSSAMWFS WGVLLNSGIG EGAPRSFSAR ILGMVWAGFA MIIVASYTAN
660 670 680 690 700
LAAFLVLDRP EERITGINDP RLRNPSDKFI YATVKQSSVD IYFRRQVELS
710 720 730 740 750
TMYRHMEKHN YESAAEAIQA VRDNKLHAFI WDSAVLEFEA SQKCDLVTTG
760 770 780 790 800
ELFFRSGFGI GMRKDSPWKQ NVSLSILKSH ENGFMEDLDK TWVRYQECDS
810 820 830 840 850
RSNAPATLTF ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDARRKQMQL
860 870 880 890 900
AFAAVNVWRK NLQDRKSGRA EPDPKKKATF RAITSTLASS FKRRRSSKDT
910 920 930
STGGGRGALQ NQKDTVLPRR AIEREEGQLQ LCSRHRES
Length:938
Mass (Da):105,481
Last modified:June 1, 1994 - v1
Checksum:iC610632DD3E06171
GO
Isoform 2 (identifier: P35438-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     864-885: DRKSGRAEPDPKKKATFRAITS → QYHPTDITGPLNLSDPSVSTVV
     886-938: Missing.

Show »
Length:885
Mass (Da):99,423
Checksum:i283AA14096E81558
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti936 – 9361R → T.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei864 – 88522DRKSG…RAITS → QYHPTDITGPLNLSDPSVST VV in isoform 2. 1 PublicationVSP_014222Add
BLAST
Alternative sequencei886 – 93853Missing in isoform 2. 1 PublicationVSP_014223Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D10028 mRNA. Translation: BAA00920.1.
AL732309 Genomic DNA. Translation: CAM14685.1.
AL732309 Genomic DNA. Translation: CAM14688.1.
BC039157 mRNA. Translation: AAH39157.1.
CCDSiCCDS15764.1. [P35438-1]
CCDS50528.1. [P35438-2]
PIRiS21104.
RefSeqiNP_001171127.1. NM_001177656.2.
NP_001171128.1. NM_001177657.2. [P35438-2]
NP_032195.1. NM_008169.3. [P35438-1]
UniGeneiMm.278672.

Genome annotation databases

EnsembliENSMUST00000028335; ENSMUSP00000028335; ENSMUSG00000026959. [P35438-1]
ENSMUST00000114312; ENSMUSP00000109951; ENSMUSG00000026959. [P35438-2]
GeneIDi14810.
KEGGimmu:14810.
UCSCiuc008iri.2. mouse. [P35438-2]
uc008irk.2. mouse. [P35438-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D10028 mRNA. Translation: BAA00920.1.
AL732309 Genomic DNA. Translation: CAM14685.1.
AL732309 Genomic DNA. Translation: CAM14688.1.
BC039157 mRNA. Translation: AAH39157.1.
CCDSiCCDS15764.1. [P35438-1]
CCDS50528.1. [P35438-2]
PIRiS21104.
RefSeqiNP_001171127.1. NM_001177656.2.
NP_001171128.1. NM_001177657.2. [P35438-2]
NP_032195.1. NM_008169.3. [P35438-1]
UniGeneiMm.278672.

3D structure databases

ProteinModelPortaliP35438.
SMRiP35438. Positions 24-833.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi200067. 82 interactions.
DIPiDIP-31577N.
IntActiP35438. 124 interactions.
MINTiMINT-135802.

Chemistry

GuidetoPHARMACOLOGYi455.

PTM databases

PhosphoSiteiP35438.

Proteomic databases

MaxQBiP35438.
PaxDbiP35438.
PRIDEiP35438.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000028335; ENSMUSP00000028335; ENSMUSG00000026959. [P35438-1]
ENSMUST00000114312; ENSMUSP00000109951; ENSMUSG00000026959. [P35438-2]
GeneIDi14810.
KEGGimmu:14810.
UCSCiuc008iri.2. mouse. [P35438-2]
uc008irk.2. mouse. [P35438-1]

Organism-specific databases

CTDi2902.
MGIiMGI:95819. Grin1.

Phylogenomic databases

eggNOGiNOG282132.
GeneTreeiENSGT00760000119186.
HOGENOMiHOG000231491.
HOVERGENiHBG052638.
InParanoidiP35438.
KOiK05208.
TreeFamiTF351405.

Enzyme and pathway databases

ReactomeiREACT_309838. CREB phosphorylation through the activation of CaMKII.
REACT_313804. EPHB-mediated forward signaling.
REACT_331187. Unblocking of NMDA receptor, glutamate binding and activation.
REACT_331823. Ras activation uopn Ca2+ infux through NMDA receptor.

Miscellaneous databases

NextBioi286995.
PROiP35438.
SOURCEiSearch...

Gene expression databases

BgeeiP35438.
CleanExiMM_GRIN1.
ExpressionAtlasiP35438. baseline and differential.
GenevestigatoriP35438.

Family and domain databases

InterProiIPR001828. ANF_lig-bd_rcpt.
IPR018882. CaM-bd_C0_NMDA_rcpt_NR1.
IPR019594. Glu/Gly-bd.
IPR001508. Iono_rcpt_met.
IPR001320. Iontro_rcpt.
IPR028082. Peripla_BP_I.
[Graphical view]
PfamiPF01094. ANF_receptor. 1 hit.
PF10562. CaM_bdg_C0. 1 hit.
PF00060. Lig_chan. 1 hit.
[Graphical view]
PRINTSiPR00177. NMDARECEPTOR.
SMARTiSM00918. Lig_chan-Glu_bd. 1 hit.
SM00079. PBPe. 1 hit.
[Graphical view]
SUPFAMiSSF53822. SSF53822. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, expression and modulation of a mouse NMDA receptor subunit."
    Yamazaki M., Mori H., Araki K., Mori K.J., Mishina M.
    FEBS Lett. 300:39-45(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Eye.
  4. "Cloning and characterization of a novel NMDA receptor subunit NR3B: a dominant subunit that reduces calcium permeability."
    Matsuda K., Kamiya Y., Matsuda S., Yuzaki M.
    Brain Res. Mol. Brain Res. 100:43-52(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A COMPLEX WITH GRIN2A OR GRIN2B AND GRIN3B.
  5. "Specific assembly with the NMDA receptor 3B subunit controls surface expression and calcium permeability of NMDA receptors."
    Matsuda K., Fletcher M., Kamiya Y., Yuzaki M.
    J. Neurosci. 23:10064-10073(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, IDENTIFICATION IN A COMPLEX WITH GRIN2A OR GRIN2B AND GRIN3B.
  6. "GRINL1A colocalizes with N-methyl D-aspartate receptor NR1 subunit and reduces N-methyl D-aspartate toxicity."
    Roginski R.S., Goubaeva F., Mikami M., Fried-Cassorla E., Nair M.R., Yang J.
    NeuroReport 19:1721-1726(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH MYZAP.
  7. "Loss of sorting nexin 27 contributes to excitatory synaptic dysfunction by modulating glutamate receptor recycling in Down's syndrome."
    Wang X., Zhao Y., Zhang X., Badie H., Zhou Y., Mu Y., Loo L.S., Cai L., Thompson R.C., Yang B., Chen Y., Johnson P.F., Wu C., Bu G., Mobley W.C., Zhang D., Gage F.H., Ranscht B.
    , Zhang Y.W., Lipton S.A., Hong W., Xu H.
    Nat. Med. 19:473-480(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SNX27.

Entry informationi

Entry nameiNMDZ1_MOUSE
AccessioniPrimary (citable) accession number: P35438
Secondary accession number(s): A2AI15, A2AI18, Q8CFS4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: April 1, 2015
This is version 163 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.