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Protein

DNA-directed RNA polymerase II subunit rpb1

Gene

rpb1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single-stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing (By similarity).By similarity

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi69 – 691Zinc 1By similarity
Metal bindingi72 – 721Zinc 1By similarity
Metal bindingi79 – 791Zinc 1By similarity
Metal bindingi82 – 821Zinc 1By similarity
Metal bindingi109 – 1091Zinc 2By similarity
Metal bindingi112 – 1121Zinc 2By similarity
Metal bindingi150 – 1501Zinc 2By similarity
Metal bindingi175 – 1751Zinc 2By similarity
Metal bindingi487 – 4871Magnesium 1; catalyticBy similarity
Metal bindingi487 – 4871Magnesium 2; shared with RPB2By similarity
Metal bindingi489 – 4891Magnesium 1; catalyticBy similarity
Metal bindingi489 – 4891Magnesium 2; shared with RPB2By similarity
Metal bindingi491 – 4911Magnesium 1; catalyticBy similarity

GO - Molecular functioni

  • DNA binding Source: PomBase
  • DNA-directed RNA polymerase activity Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • transcription from RNA polymerase II promoter Source: PomBase
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi2.7.7.6. 5613.
ReactomeiR-SPO-113418. Formation of the Early Elongation Complex.
R-SPO-674695. RNA Polymerase II Pre-transcription Events.
R-SPO-6781823. Formation of TC-NER Pre-Incision Complex.
R-SPO-6782135. Dual incision in TC-NER.
R-SPO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SPO-72086. mRNA Capping.
R-SPO-72165. mRNA Splicing - Minor Pathway.
R-SPO-73776. RNA Polymerase II Promoter Escape.
R-SPO-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SPO-75953. RNA Polymerase II Transcription Initiation.
R-SPO-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SPO-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit rpb1 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit 1
Short name:
RNA polymerase II subunit B1
Alternative name(s):
DNA-directed RNA polymerase III largest subunit
Gene namesi
Name:rpb1
ORF Names:SPBC28F2.12
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC28F2.12.
PomBaseiSPBC28F2.12. rpb1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: PomBase
  • DNA-directed RNA polymerase II, core complex Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 17521752DNA-directed RNA polymerase II subunit rpb1PRO_0000073945Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1489 – 14891Phosphoserine1 Publication
Modified residuei1499 – 14991Phosphoserine1 Publication
Modified residuei1506 – 15061Phosphoserine1 Publication
Modified residuei1529 – 15291Phosphoserine1 Publication
Modified residuei1531 – 15311Phosphotyrosine1 Publication

Post-translational modificationi

The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapeptide repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatase, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP36594.

PTM databases

iPTMnetiP36594.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.By similarity

Protein-protein interaction databases

BioGridi276823. 33 interactions.
IntActiP36594. 9 interactions.
MINTiMINT-1214221.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65A/M1-1752[»]
4PZ6X-ray2.41P/Q1704-1724[»]
ProteinModelPortaliP36594.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36594.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati1558 – 156471
Repeati1578 – 158472
Repeati1585 – 159173
Repeati1592 – 159874
Repeati1599 – 160575
Repeati1606 – 161276; approximate
Repeati1613 – 161977
Repeati1620 – 162678
Repeati1627 – 163379
Repeati1634 – 1640710
Repeati1641 – 1647711
Repeati1648 – 1654712
Repeati1655 – 1661713
Repeati1662 – 1668714
Repeati1669 – 1675715
Repeati1676 – 1682716
Repeati1683 – 1689717
Repeati1690 – 1696718
Repeati1697 – 1703719
Repeati1704 – 1710720
Repeati1711 – 1717721
Repeati1718 – 1724722
Repeati1725 – 1731723
Repeati1732 – 1738724
Repeati1739 – 1745725
Repeati1746 – 1752726

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni816 – 82813Bridging helixAdd
BLAST
Regioni1558 – 1752195C-terminal domain (CTD); 26 X 7 AA approximate tandem repeats of Y-S-P-[TS]-S-P-SAdd
BLAST

Domaini

The C-terminal domain (CTD) serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.Curated

Sequence similaritiesi

Belongs to the RNA polymerase beta' chain family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

HOGENOMiHOG000222975.
InParanoidiP36594.
KOiK03006.
OMAiMGDSGYL.
OrthoDBiEOG780RVQ.
PhylomeDBiP36594.

Family and domain databases

InterProiIPR000722. RNA_pol_asu.
IPR000684. RNA_pol_II_repeat_euk.
IPR006592. RNA_pol_N.
IPR007080. RNA_pol_Rpb1_1.
IPR007066. RNA_pol_Rpb1_3.
IPR007083. RNA_pol_Rpb1_4.
IPR007081. RNA_pol_Rpb1_5.
IPR007075. RNA_pol_Rpb1_6.
IPR007073. RNA_pol_Rpb1_7.
[Graphical view]
PfamiPF04997. RNA_pol_Rpb1_1. 1 hit.
PF00623. RNA_pol_Rpb1_2. 1 hit.
PF04983. RNA_pol_Rpb1_3. 1 hit.
PF05000. RNA_pol_Rpb1_4. 1 hit.
PF04998. RNA_pol_Rpb1_5. 1 hit.
PF04992. RNA_pol_Rpb1_6. 1 hit.
PF04990. RNA_pol_Rpb1_7. 1 hit.
PF05001. RNA_pol_Rpb1_R. 19 hits.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 24 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P36594-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGIQFSPSS VPLRRVEEVQ FGILSPEEIR SMSVAKIEFP ETMDESGQRP
60 70 80 90 100
RVGGLLDPRL GTIDRQFKCQ TCGETMADCP GHFGHIELAK PVFHIGFLSK
110 120 130 140 150
IKKILECVCW NCGKLKIDSS NPKFNDTQRY RDPKNRLNAV WNVCKTKMVC
160 170 180 190 200
DTGLSAGSDN FDLSNPSANM GHGGCGAAQP TIRKDGLRLW GSWKRGKDES
210 220 230 240 250
DLPEKRLLSP LEVHTIFTHI SSEDLAHLGL NEQYARPDWM IITVLPVPPP
260 270 280 290 300
SVRPSISVDG TSRGEDDLTH KLSDIIKANA NVRRCEQEGA PAHIVSEYEQ
310 320 330 340 350
LLQFHVATYM DNEIAGQPQA LQKSGRPLKS IRARLKGKEG RLRGNLMGKR
360 370 380 390 400
VDFSARTVIT GDPNLSLDEL GVPRSIAKTL TYPETVTPYN IYQLQELVRN
410 420 430 440 450
GPDEHPGAKY IIRDTGERID LRYHKRAGDI PLRYGWRVER HIRDGDVVIF
460 470 480 490 500
NRQPSLHKMS MMGHRIRVMP YSTFRLNLSV TSPYNADFDG DEMNMHVPQS
510 520 530 540 550
EETRAEIQEI TMVPKQIVSP QSNKPVMGIV QDTLAGVRKF SLRDNFLTRN
560 570 580 590 600
AVMNIMLWVP DWDGILPPPV ILKPKVLWTG KQILSLIIPK GINLIRDDDK
610 620 630 640 650
QSLSNPTDSG MLIENGEIIY GVVDKKTVGA SQGGLVHTIW KEKGPEICKG
660 670 680 690 700
FFNGIQRVVN YWLLHNGFSI GIGDTIADAD TMKEVTRTVK EARRQVAECI
710 720 730 740 750
QDAQHNRLKP EPGMTLRESF EAKVSRILNQ ARDNAGRSAE HSLKDSNNVK
760 770 780 790 800
QMVAAGSKGS FINISQMSAC VGQQIVEGKR IPFGFKYRTL PHFPKDDDSP
810 820 830 840 850
ESRGFIENSY LRGLTPQEFF FHAMAGREGL IDTAVKTAET GYIQRRLVKA
860 870 880 890 900
MEDVMVRYDG TVRNAMGDII QFAYGEDGLD ATLVEYQVFD SLRLSTKQFE
910 920 930 940 950
KKYRIDLMED RSLSLYMENS IENDSSVQDL LDEEYTQLVA DRELLCKFIF
960 970 980 990 1000
PKGDARWPLP VNVQRIIQNA LQIFHLEAKK PTDLLPSDII NGLNELIAKL
1010 1020 1030 1040 1050
TIFRGSDRIT RDVQNNATLL FQILLRSKFA VKRVIMEYRL NKVAFEWIMG
1060 1070 1080 1090 1100
EVEARFQQAV VSPGEMVGTL AAQSIGEPAT QMTLNTFHYA GVSSKNVTLG
1110 1120 1130 1140 1150
VPRLKEILNV AKNIKTPSLT IYLMPWIAAN MDLAKNVQTQ IEHTTLSTVT
1160 1170 1180 1190 1200
SATEIHYDPD PQDTVIEEDK DFVEAFFAIP DEEVEENLYK QSPWLLRLEL
1210 1220 1230 1240 1250
DRAKMLDKKL SMSDVAGKIA ESFERDLFTI WSEDNADKLI IRCRIIRDDD
1260 1270 1280 1290 1300
RKAEDDDNMI EEDVFLKTIE GHMLESISLR GVPNITRVYM MEHKIVRQIE
1310 1320 1330 1340 1350
DGTFERADEW VLETDGINLT EAMTVEGVDA TRTYSNSFVE ILQILGIEAT
1360 1370 1380 1390 1400
RSALLKELRN VIEFDGSYVN YRHLALLCDV MTSRGHLMAI TRHGINRAET
1410 1420 1430 1440 1450
GALMRCSFEE TVEILMDAAA SGEKDDCKGI SENIMLGQLA PMGTGAFDIY
1460 1470 1480 1490 1500
LDQDMLMNYS LGTAVPTLAG SGMGTSQLPE GAGTPYERSP MVDSGFVGSP
1510 1520 1530 1540 1550
DAAAFSPLVQ GGSEGREGFG DYGLLGAASP YKGVQSPGYT SPFSSAMSPG
1560 1570 1580 1590 1600
YGLTSPSYSP SSPGYSTSPA YMPSSPSYSP TSPSYSPTSP SYSPTSPSYS
1610 1620 1630 1640 1650
PTSPSYSATS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP
1660 1670 1680 1690 1700
TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT
1710 1720 1730 1740 1750
SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS

PS
Length:1,752
Mass (Da):194,163
Last modified:June 1, 1994 - v1
Checksum:i15A4F0B59E60E570
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56564 Genomic DNA. Translation: CAA39916.1.
CU329671 Genomic DNA. Translation: CAB57941.1.
PIRiS26849.
RefSeqiNP_595673.1. NM_001021568.2.

Genome annotation databases

EnsemblFungiiSPBC28F2.12.1; SPBC28F2.12.1:pep; SPBC28F2.12.
GeneIDi2540292.
KEGGispo:SPBC28F2.12.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56564 Genomic DNA. Translation: CAA39916.1.
CU329671 Genomic DNA. Translation: CAB57941.1.
PIRiS26849.
RefSeqiNP_595673.1. NM_001021568.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65A/M1-1752[»]
4PZ6X-ray2.41P/Q1704-1724[»]
ProteinModelPortaliP36594.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi276823. 33 interactions.
IntActiP36594. 9 interactions.
MINTiMINT-1214221.

PTM databases

iPTMnetiP36594.

Proteomic databases

MaxQBiP36594.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPBC28F2.12.1; SPBC28F2.12.1:pep; SPBC28F2.12.
GeneIDi2540292.
KEGGispo:SPBC28F2.12.

Organism-specific databases

EuPathDBiFungiDB:SPBC28F2.12.
PomBaseiSPBC28F2.12. rpb1.

Phylogenomic databases

HOGENOMiHOG000222975.
InParanoidiP36594.
KOiK03006.
OMAiMGDSGYL.
OrthoDBiEOG780RVQ.
PhylomeDBiP36594.

Enzyme and pathway databases

BRENDAi2.7.7.6. 5613.
ReactomeiR-SPO-113418. Formation of the Early Elongation Complex.
R-SPO-674695. RNA Polymerase II Pre-transcription Events.
R-SPO-6781823. Formation of TC-NER Pre-Incision Complex.
R-SPO-6782135. Dual incision in TC-NER.
R-SPO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SPO-72086. mRNA Capping.
R-SPO-72165. mRNA Splicing - Minor Pathway.
R-SPO-73776. RNA Polymerase II Promoter Escape.
R-SPO-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SPO-75953. RNA Polymerase II Transcription Initiation.
R-SPO-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SPO-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

EvolutionaryTraceiP36594.
NextBioi20801422.
PROiP36594.

Family and domain databases

InterProiIPR000722. RNA_pol_asu.
IPR000684. RNA_pol_II_repeat_euk.
IPR006592. RNA_pol_N.
IPR007080. RNA_pol_Rpb1_1.
IPR007066. RNA_pol_Rpb1_3.
IPR007083. RNA_pol_Rpb1_4.
IPR007081. RNA_pol_Rpb1_5.
IPR007075. RNA_pol_Rpb1_6.
IPR007073. RNA_pol_Rpb1_7.
[Graphical view]
PfamiPF04997. RNA_pol_Rpb1_1. 1 hit.
PF00623. RNA_pol_Rpb1_2. 1 hit.
PF04983. RNA_pol_Rpb1_3. 1 hit.
PF05000. RNA_pol_Rpb1_4. 1 hit.
PF04998. RNA_pol_Rpb1_5. 1 hit.
PF04992. RNA_pol_Rpb1_6. 1 hit.
PF04990. RNA_pol_Rpb1_7. 1 hit.
PF05001. RNA_pol_Rpb1_R. 19 hits.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 24 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequence determination of the Schizosaccharomyces pombe rpb1 gene encoding the largest subunit of RNA polymerase II."
    Azuma Y., Yarnagishi M., Ueshima R., Ishihama A.
    Nucleic Acids Res. 19:461-468(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  3. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1489; SER-1499; SER-1506; SER-1529 AND TYR-1531, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiRPB1_SCHPO
AccessioniPrimary (citable) accession number: P36594
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: May 11, 2016
This is version 136 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucleotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  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.