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Protein

Two pore calcium channel protein 1

Gene

TPC1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Functions as a voltage-gated inward-rectifying Ca2+ channel (VDCC) across the vacuole membrane. Is one of the essential components of the slow vacuolar (SV) channel. Acts as the major ROS-responsive Ca2+ channel and is the possible target of Al-dependent inhibition. Involved in the regulation of germination and stomatal movement.2 Publications

Enzyme regulationi

Inhibited by Al3+.

GO - Molecular functioni

  • calcium ion binding Source: InterPro
  • voltage-gated calcium channel activity Source: TAIR

GO - Biological processi

  • calcium ion transport Source: TAIR
  • calcium-mediated signaling Source: TAIR
  • membrane depolarization during action potential Source: GO_Central
  • regulation of jasmonic acid biosynthetic process Source: TAIR
  • regulation of stomatal movement Source: TAIR
  • seed germination Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Calcium channel, Ion channel, Voltage-gated channel

Keywords - Biological processi

Calcium transport, Ion transport, Transport

Keywords - Ligandi

Calcium

Enzyme and pathway databases

ReactomeiR-ATH-2672351. Stimuli-sensing channels.

Protein family/group databases

TCDBi1.A.1.11.26. the voltage-gated ion channel (vic) superfamily.

Names & Taxonomyi

Protein namesi
Recommended name:
Two pore calcium channel protein 1
Alternative name(s):
Calcium channel protein 1
Short name:
AtCCH1
Fatty acid oxygenation up-regulated protein 2
Voltage-dependent calcium channel protein TPC1
Short name:
AtTPC1
Gene namesi
Name:TPC1
Synonyms:CCH1, FOU2
Ordered Locus Names:At4g03560
ORF Names:F9H3.19, T5L23.5
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G03560.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 7171CytoplasmicSequence analysisAdd
BLAST
Transmembranei72 – 9221Helical; Name=S1 of repeat ISequence analysisAdd
BLAST
Topological domaini93 – 12028VacuolarSequence analysisAdd
BLAST
Transmembranei121 – 14121Helical; Name=S2 of repeat ISequence analysisAdd
BLAST
Topological domaini142 – 15817CytoplasmicSequence analysisAdd
BLAST
Transmembranei159 – 17921Helical; Name=S3 of repeat ISequence analysisAdd
BLAST
Topological domaini180 – 1801VacuolarSequence analysis
Transmembranei181 – 19919Helical; Voltage-sensor; Name=S4 of repeat ISequence analysisAdd
BLAST
Topological domaini200 – 21819CytoplasmicSequence analysisAdd
BLAST
Transmembranei219 – 23921Helical; Name=S5 of repeat ISequence analysisAdd
BLAST
Topological domaini240 – 2456VacuolarSequence analysis
Intramembranei246 – 26015Pore-forming; Name=Pore-forming 1Add
BLAST
Topological domaini261 – 28222VacuolarSequence analysisAdd
BLAST
Transmembranei283 – 30321Helical; Name=S6 of repeat ISequence analysisAdd
BLAST
Topological domaini304 – 428125CytoplasmicSequence analysisAdd
BLAST
Transmembranei429 – 44921Helical; Name=S1 of repeat IISequence analysisAdd
BLAST
Topological domaini450 – 46516VacuolarSequence analysisAdd
BLAST
Transmembranei466 – 48621Helical; Name=S2 of repeat IISequence analysisAdd
BLAST
Topological domaini487 – 49812CytoplasmicSequence analysisAdd
BLAST
Transmembranei499 – 51921Helical; Name=S3 of repeat IISequence analysisAdd
BLAST
Topological domaini520 – 5289VacuolarSequence analysis
Transmembranei529 – 54618Helical; Voltage-sensor; Name=S4 of repeat IISequence analysisAdd
BLAST
Topological domaini547 – 55711CytoplasmicSequence analysisAdd
BLAST
Transmembranei558 – 57821Helical; Name=S5 of repeat IISequence analysisAdd
BLAST
Topological domaini579 – 61537VacuolarSequence analysisAdd
BLAST
Intramembranei616 – 63015Pore-forming; Name=Pore-forming 2Add
BLAST
Topological domaini631 – 65121VacuolarSequence analysisAdd
BLAST
Transmembranei652 – 67221Helical; Name=S6 of repeat IISequence analysisAdd
BLAST
Topological domaini673 – 73361CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • Golgi apparatus Source: TAIR
  • integral component of membrane Source: UniProtKB-KW
  • plant-type vacuole Source: TAIR
  • plasma membrane Source: TAIR
  • vacuolar membrane Source: TAIR
  • vacuole Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Vacuole

Pathology & Biotechi

Disruption phenotypei

Plants display an impairment of both the Ca2+ inhibition of stomatal guard cell opening and abscisic acid (ABA) inhibition of seed germination.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi454 – 4541D → N in fou2; shows elevated LOX and AOS activity levels and an increased resistance to B.cinerea. Strongly increases oxylipin biogenesis in response to wounding. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 733733Two pore calcium channel protein 1PRO_0000343169Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ94KI8.
PRIDEiQ94KI8.

PTM databases

SwissPalmiQ94KI8.

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

ExpressionAtlasiQ94KI8. baseline and differential.
GenevisibleiQ94KI8. AT.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi10969. 8 interactions.
IntActiQ94KI8. 1 interaction.
STRINGi3702.AT4G03560.1.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5DQQX-ray2.87A12-733[»]
5E1JX-ray3.31A1-733[»]
ProteinModelPortaliQ94KI8.
SMRiQ94KI8. Positions 427-674.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini322 – 35736EF-hand 1PROSITE-ProRule annotationAdd
BLAST
Domaini363 – 39836EF-hand 2PROSITE-ProRule annotationAdd
BLAST

Domaini

Each of the two internal repeats contains five hydrophobic transmembrane segments (S1, S2, S3, S5, S6) and one positively charged transmembrane segment (S4). S4 segments probably represent the voltage-sensor and are characterized by a series of positively charged amino acids (By similarity).By similarity

Sequence similaritiesi

Contains 2 EF-hand domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410INF7. Eukaryota.
ENOG410XZT8. LUCA.
HOGENOMiHOG000029959.
InParanoidiQ94KI8.
KOiK16900.
OMAiEKYPSFY.
PhylomeDBiQ94KI8.

Family and domain databases

Gene3Di1.10.238.10. 1 hit.
1.20.120.350. 1 hit.
InterProiIPR027359. Channel_four-helix_dom.
IPR011992. EF-hand-dom_pair.
IPR002048. EF_hand_dom.
IPR005821. Ion_trans_dom.
[Graphical view]
PfamiPF00520. Ion_trans. 2 hits.
[Graphical view]
SMARTiSM00054. EFh. 2 hits.
[Graphical view]
SUPFAMiSSF47473. SSF47473. 1 hit.
PROSITEiPS50222. EF_HAND_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q94KI8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEDPLIGRDS LGGGGTDRVR RSEAITHGTP FQKAAALVDL AEDGIGLPVE
60 70 80 90 100
ILDQSSFGES ARYYFIFTRL DLIWSLNYFA LLFLNFFEQP LWCEKNPKPS
110 120 130 140 150
CKDRDYYYLG ELPYLTNAES IIYEVITLAI LLVHTFFPIS YEGSRIFWTS
160 170 180 190 200
RLNLVKVACV VILFVDVLVD FLYLSPLAFD FLPFRIAPYV RVIIFILSIR
210 220 230 240 250
ELRDTLVLLS GMLGTYLNIL ALWMLFLLFA SWIAFVMFED TQQGLTVFTS
260 270 280 290 300
YGATLYQMFI LFTTSNNPDV WIPAYKSSRW SSVFFVLYVL IGVYFVTNLI
310 320 330 340 350
LAVVYDSFKE QLAKQVSGMD QMKRRMLEKA FGLIDSDKNG EIDKNQCIKL
360 370 380 390 400
FEQLTNYRTL PKISKEEFGL IFDELDDTRD FKINKDEFAD LCQAIALRFQ
410 420 430 440 450
KEEVPSLFEH FPQIYHSALS QQLRAFVRSP NFGYAISFIL IINFIAVVVE
460 470 480 490 500
TTLDIEESSA QKPWQVAEFV FGWIYVLEMA LKIYTYGFEN YWREGANRFD
510 520 530 540 550
FLVTWVIVIG ETATFITPDE NTFFSNGEWI RYLLLARMLR LIRLLMNVQR
560 570 580 590 600
YRAFIATFIT LIPSLMPYLG TIFCVLCIYC SIGVQVFGGL VNAGNKKLFE
610 620 630 640 650
TELAEDDYLL FNFNDYPNGM VTLFNLLVMG NWQVWMESYK DLTGTWWSIT
660 670 680 690 700
YFVSFYVITI LLLLNLVVAF VLEAFFTELD LEEEEKCQGQ DSQEKRNRRR
710 720 730
SAGSKSRSQR VDTLLHHMLG DELSKPECST SDT
Length:733
Mass (Da):84,873
Last modified:December 1, 2001 - v1
Checksum:i1CA978D6B8BFF445
GO

Sequence cautioni

The sequence AAD11598.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence AAD15312.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB77841.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti33 – 331K → R in BAB55460 (PubMed:11577183).Curated
Sequence conflicti256 – 2561Y → F in BAB55460 (PubMed:11577183).Curated
Sequence conflicti612 – 6121N → T in BAB55460 (PubMed:11577183).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB053952 mRNA. Translation: BAB55460.1.
AF360372 mRNA. Translation: AAK39554.1.
AC005142 Genomic DNA. Translation: AAD15312.1. Sequence problems.
AF071527 Genomic DNA. Translation: AAD11598.1. Sequence problems.
AL161497 Genomic DNA. Translation: CAB77841.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE82337.1.
PIRiB85045.
RefSeqiNP_567258.1. NM_116594.4.
UniGeneiAt.3957.

Genome annotation databases

EnsemblPlantsiAT4G03560.1; AT4G03560.1; AT4G03560.
GeneIDi825655.
GrameneiAT4G03560.1; AT4G03560.1; AT4G03560.
KEGGiath:AT4G03560.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB053952 mRNA. Translation: BAB55460.1.
AF360372 mRNA. Translation: AAK39554.1.
AC005142 Genomic DNA. Translation: AAD15312.1. Sequence problems.
AF071527 Genomic DNA. Translation: AAD11598.1. Sequence problems.
AL161497 Genomic DNA. Translation: CAB77841.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE82337.1.
PIRiB85045.
RefSeqiNP_567258.1. NM_116594.4.
UniGeneiAt.3957.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5DQQX-ray2.87A12-733[»]
5E1JX-ray3.31A1-733[»]
ProteinModelPortaliQ94KI8.
SMRiQ94KI8. Positions 427-674.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi10969. 8 interactions.
IntActiQ94KI8. 1 interaction.
STRINGi3702.AT4G03560.1.

Protein family/group databases

TCDBi1.A.1.11.26. the voltage-gated ion channel (vic) superfamily.

PTM databases

SwissPalmiQ94KI8.

Proteomic databases

PaxDbiQ94KI8.
PRIDEiQ94KI8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G03560.1; AT4G03560.1; AT4G03560.
GeneIDi825655.
GrameneiAT4G03560.1; AT4G03560.1; AT4G03560.
KEGGiath:AT4G03560.

Organism-specific databases

TAIRiAT4G03560.

Phylogenomic databases

eggNOGiENOG410INF7. Eukaryota.
ENOG410XZT8. LUCA.
HOGENOMiHOG000029959.
InParanoidiQ94KI8.
KOiK16900.
OMAiEKYPSFY.
PhylomeDBiQ94KI8.

Enzyme and pathway databases

ReactomeiR-ATH-2672351. Stimuli-sensing channels.

Miscellaneous databases

PROiQ94KI8.

Gene expression databases

ExpressionAtlasiQ94KI8. baseline and differential.
GenevisibleiQ94KI8. AT.

Family and domain databases

Gene3Di1.10.238.10. 1 hit.
1.20.120.350. 1 hit.
InterProiIPR027359. Channel_four-helix_dom.
IPR011992. EF-hand-dom_pair.
IPR002048. EF_hand_dom.
IPR005821. Ion_trans_dom.
[Graphical view]
PfamiPF00520. Ion_trans. 2 hits.
[Graphical view]
SMARTiSM00054. EFh. 2 hits.
[Graphical view]
SUPFAMiSSF47473. SSF47473. 1 hit.
PROSITEiPS50222. EF_HAND_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A putative two pore channel AtTPC1 mediates Ca(2+) flux in Arabidopsis leaf cells."
    Furuichi T., Cunningham K.W., Muto S.
    Plant Cell Physiol. 42:900-905(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], CHARACTERIZATION, TISSUE SPECIFICITY.
    Tissue: Leaf.
  2. "The vacuolar Ca(2+)-activated channel TPC1 regulates germination and stomatal movement."
    Peiter E., Maathuis F.J.M., Mills L.N., Knight H., Pelloux J., Hetherington A.M., Sanders D.
    Nature 434:404-408(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
  3. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Genes for calcium-permeable channels in the plasma membrane of plant root cells."
    White P.J., Bowen H.C., Demidchik V., Nichols C., Davies J.M.
    Biochim. Biophys. Acta 1564:299-309(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  6. Cited for: FUNCTION.
  7. "The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins."
    Carter C., Pan S., Zouhar J., Avila E.L., Girke T., Raikhel N.V.
    Plant Cell 16:3285-3303(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  8. "Large-scale characterization of integral proteins from Arabidopsis vacuolar membrane by two-dimensional liquid chromatography."
    Szponarski W., Sommerer N., Boyer J.-C., Rossignol M., Gibrat R.
    Proteomics 4:397-406(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  9. Cited for: REVIEW.
  10. "The fou2 gain-of-function allele and the wild-type allele of two pore channel 1 contribute to different extents or by different mechanisms to defense gene expression in Arabidopsis."
    Bonaventure G., Gfeller A., Rodriguez V.M., Armand F., Farmer E.E.
    Plant Cell Physiol. 48:1775-1789(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-454.
  11. "A gain-of-function allele of TPC1 activates oxylipin biogenesis after leaf wounding in Arabidopsis."
    Bonaventure G., Gfeller A., Proebsting W.M., Hoertensteiner S., Chetelat A., Martinoia E., Farmer E.E.
    Plant J. 49:889-898(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-454.
  12. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiTPC1_ARATH
AccessioniPrimary (citable) accession number: Q94KI8
Secondary accession number(s): Q948T1, Q9ZT83
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: December 1, 2001
Last modified: May 11, 2016
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.