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Protein

DNA topoisomerase 2-alpha

Gene

Top2a

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

Functioni

Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Essential during mitosis and meiosis for proper segregation of daughter chromosomes. May play a role in regulating the period length of ARNTL/BMAL1 transcriptional oscillation (PubMed:24321095).2 Publications

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.PROSITE-ProRule annotation1 Publication

Cofactori

Mg2+PROSITE-ProRule annotation, Mn2+PROSITE-ProRule annotation, Ca2+PROSITE-ProRule annotationNote: Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca2+.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei90 – 901ATPBy similarity
Binding sitei119 – 1191ATPBy similarity
Metal bindingi460 – 4601Magnesium 1; catalyticPROSITE-ProRule annotation
Sitei488 – 4881Interaction with DNAPROSITE-ProRule annotation
Sitei491 – 4911Interaction with DNAPROSITE-ProRule annotation
Metal bindingi540 – 5401Magnesium 1; catalyticPROSITE-ProRule annotation
Metal bindingi540 – 5401Magnesium 2PROSITE-ProRule annotation
Metal bindingi542 – 5421Magnesium 2PROSITE-ProRule annotation
Sitei660 – 6601Interaction with DNAPROSITE-ProRule annotation
Sitei661 – 6611Interaction with DNAPROSITE-ProRule annotation
Sitei722 – 7221Interaction with DNAPROSITE-ProRule annotation
Sitei756 – 7561Interaction with DNAPROSITE-ProRule annotation
Sitei762 – 7621Interaction with DNAPROSITE-ProRule annotation
Sitei803 – 8031Transition state stabilizerBy similarity
Active sitei804 – 8041O-(5'-phospho-DNA)-tyrosine intermediateBy similarity
Sitei855 – 8551Important for DNA bending; intercalates between base pairs of target DNABy similarity
Sitei930 – 9301Interaction with DNAPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi147 – 1493ATPBy similarity
Nucleotide bindingi160 – 1678ATPBy similarity
Nucleotide bindingi375 – 3773ATPBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. chromatin binding Source: MGI
  3. DNA binding Source: MGI
  4. DNA binding, bending Source: UniProtKB
  5. DNA-dependent ATPase activity Source: MGI
  6. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: MGI
  7. drug binding Source: MGI
  8. enzyme binding Source: MGI
  9. histone deacetylase binding Source: MGI
  10. magnesium ion binding Source: UniProtKB
  11. poly(A) RNA binding Source: MGI
  12. protein C-terminus binding Source: MGI
  13. protein heterodimerization activity Source: MGI
  14. protein homodimerization activity Source: MGI
  15. protein kinase C binding Source: MGI
  16. ubiquitin binding Source: MGI

GO - Biological processi

  1. apoptotic chromosome condensation Source: MGI
  2. cellular response to DNA damage stimulus Source: MGI
  3. chromosome condensation Source: MGI
  4. chromosome segregation Source: MGI
  5. DNA ligation Source: MGI
  6. DNA topological change Source: MGI
  7. DNA unwinding involved in DNA replication Source: GO_Central
  8. embryonic cleavage Source: MGI
  9. hematopoietic progenitor cell differentiation Source: MGI
  10. mitotic DNA integrity checkpoint Source: GO_Central
  11. mitotic recombination Source: GO_Central
  12. positive regulation of apoptotic process Source: MGI
  13. positive regulation of single stranded viral RNA replication via double stranded DNA intermediate Source: MGI
  14. positive regulation of transcription from RNA polymerase II promoter Source: MGI
  15. positive regulation of viral genome replication Source: MGI
  16. regulation of circadian rhythm Source: UniProtKB
  17. resolution of meiotic recombination intermediates Source: GO_Central
  18. rhythmic process Source: UniProtKB-KW
  19. sister chromatid segregation Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Biological rhythms

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiREACT_274086. G0 and Early G1.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 2-alpha (EC:5.99.1.3)
Alternative name(s):
DNA topoisomerase II, alpha isozyme
Gene namesi
Name:Top2a
Synonyms:Top-2, Top2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:98790. Top2a.

Subcellular locationi

GO - Cellular componenti

  1. centriole Source: Ensembl
  2. condensed chromosome Source: MGI
  3. DNA topoisomerase complex (ATP-hydrolyzing) Source: MGI
  4. nuclear chromosome Source: Ensembl
  5. nucleolus Source: MGI
  6. nucleoplasm Source: MGI
  7. nucleus Source: MGI
  8. protein complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 15281528DNA topoisomerase 2-alphaPRO_0000145364Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity
Modified residuei4 – 41PhosphoserineBy similarity
Modified residuei281 – 2811PhosphothreonineBy similarity
Modified residuei1105 – 11051Phosphoserine; by CK1By similarity
Modified residuei1211 – 12111PhosphoserineBy similarity
Modified residuei1291 – 12911PhosphoserineBy similarity
Modified residuei1293 – 12931PhosphoserineBy similarity
Modified residuei1295 – 12951PhosphoserineBy similarity
Modified residuei1298 – 12981PhosphoserineBy similarity
Modified residuei1328 – 13281PhosphoserineBy similarity
Modified residuei1333 – 13331PhosphoserineBy similarity
Modified residuei1370 – 13701PhosphoserineBy similarity
Modified residuei1373 – 13731PhosphoserineBy similarity
Modified residuei1384 – 13841PhosphoserineBy similarity
Modified residuei1418 – 14181N6-acetyllysine1 Publication
Modified residuei1438 – 14381N6-acetyllysine1 Publication
Modified residuei1465 – 14651PhosphoserineBy similarity
Modified residuei1467 – 14671PhosphoserineBy similarity
Modified residuei1470 – 14701PhosphoserineBy similarity
Modified residuei1472 – 14721PhosphoserineBy similarity
Modified residuei1521 – 15211PhosphoserineBy similarity

Post-translational modificationi

Phosphorylation has no effect on catalytic activity. However, phosphorylation at Ser-1105 by CSNK1D/CK1 promotes DNA cleavable complex formation (By similarity).By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ01320.
PRIDEiQ01320.

PTM databases

PhosphoSiteiQ01320.

Expressioni

Gene expression databases

BgeeiQ01320.
CleanExiMM_TOP2A.
ExpressionAtlasiQ01320. baseline and differential.
GenevestigatoriQ01320.

Interactioni

Subunit structurei

Homodimer. Interacts with COPS5. Interacts with RECQL5; this stimulates DNA decatenation. Interacts with SETMAR; stimulates the topoisomerase activity.By similarity

Protein-protein interaction databases

DIPiDIP-40621N.
IntActiQ01320. 8 interactions.
MINTiMINT-1712967.

Structurei

3D structure databases

ProteinModelPortaliQ01320.
SMRiQ01320. Positions 28-404, 433-1187.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini454 – 571118ToprimPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni341 – 3433Interaction with DNABy similarity
Regioni989 – 99810Interaction with DNABy similarity

Sequence similaritiesi

Belongs to the type II topoisomerase family.Curated
Contains 1 Toprim domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0187.
GeneTreeiENSGT00390000016222.
HOGENOMiHOG000216693.
HOVERGENiHBG052998.
InParanoidiQ01320.
KOiK03164.
OMAiGKAGEMK.
OrthoDBiEOG73JKTM.
TreeFamiTF105282.

Family and domain databases

Gene3Di1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
3.90.199.10. 1 hit.
InterProiIPR024946. Arg_repress_C-like.
IPR012542. DTHCT.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR028466. Top2a.
IPR001241. Topo_IIA.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR10169:SF33. PTHR10169:SF33. 1 hit.
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00521. DNA_topoisoIV. 1 hit.
PF08070. DTHCT. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q01320-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELSPLQPVN ENMLMNKKKN EDGKKRLSIE RIYQKKTQLE HILLRPDTYI
60 70 80 90 100
GSVELVTQQM WVYDEDVGIN YREVTFVPGL YKIFDEILVN AADNKQRDPK
110 120 130 140 150
MSCIRVTIDP ENNVISIWNN GKGIPVVEHK VEKIYVPALI FGQLLTSSNY
160 170 180 190 200
DDDEKKVTGG RNGYGAKLCN IFSTKFTVET ASREYKKMFK QTWMDNMGRA
210 220 230 240 250
GDMELKPFSG EDYTCITFQP DLSKFKMQSL DKDIVALMVR RAYDIAGSTK
260 270 280 290 300
DVKVFLNGNS LPVKGFRSYV DLYLKDKVDE TGNSLKVIHE QVNPRWEVCL
310 320 330 340 350
TMSERGFQQI SFVNSIATSK GGRHVDYVAD QIVSKLVDVV KKKNKGGVAV
360 370 380 390 400
KAHQVKNHMW IFVNALIENP TFDSQTKENM TLQAKSFGST CQLSEKFIKA
410 420 430 440 450
AIGCGIVESI LNWVKFKAQI QLNKKCSAVK HTKIKGIPKL DDANDAGSRN
460 470 480 490 500
STECTLILTE GDSAKTLAVS GLGVVGRDKY GVFPLRGKIL NVREASHKQI
510 520 530 540 550
MENAEINNII KIVGLQYKKN YEDEDSLKTL RYGKIMIMTD QDQDGSHIKG
560 570 580 590 600
LLINFIHHNW PSLLRHRFLE EFITPIVKVS KNKQEIAFYS LPEFEEWKSS
610 620 630 640 650
TPNHKKWKVK YYKGLGTSTS KEAKEYFADM KRHRIQFKYS GPEDDAAISL
660 670 680 690 700
AFSKKQVDDR KEWLTNFMED RRQRKLLGLP EDYLYGQSTS YLTYNDFINK
710 720 730 740 750
ELILFSNSDN ERSIPSMVDG LKPGQRKVLF TCFKRNDKRE VKVAQLAGSV
760 770 780 790 800
AEMSSYHHGE MSLMMTIINL AQNFVGSNNL NLLQPIGQFG TRLHGGKDSA
810 820 830 840 850
SPRYIFTMLS PLARLLFPPK DDHTLRFLYD DNQRVEPEWY IPIIPMVLIN
860 870 880 890 900
GAEGIGTGWS CKIPNFDVRE VVNNIRRLLD GEEPLPMLPS YKNFKGTIEE
910 920 930 940 950
LASNQYVING EVAILDSTTI EISELPIRTW TQTYKEQVLE PMLNGTEKTP
960 970 980 990 1000
SLITDYREYH TDTTVKFVIK MTEEKLAEAE RVGLHKVFKL QSSLTCNSMV
1010 1020 1030 1040 1050
LFDHVGCLKK YDTVLDILRD FFELRLKYYG LRKEWLLGML GAESSKLNNQ
1060 1070 1080 1090 1100
ARFILEKIDG KIVIENKPKK ELIKVLIQRG YDSDPVKAWK EAQQKVPDEE
1110 1120 1130 1140 1150
ENEESDTETS TSDSAAEAGP TFNYLLDMPL WYLTKEKKDE LCKQRNEKEQ
1160 1170 1180 1190 1200
ELNTLKQKSP SDLWKEDLAV FIEELEVVEA KEKQDEQVGL PGKAGKAKGK
1210 1220 1230 1240 1250
KAQMCADVLP SPRGKRVIPQ VTVEMKAEAE KKIRKKIKSE NVEGTPAEDG
1260 1270 1280 1290 1300
AEPGSLRQRI EKKQKKEPGA KKQTTLPFKP VKKGRKKNPW SDSESDVSSN
1310 1320 1330 1340 1350
ESNVDVPPRQ KEQRSAAAKA KFTVDLDSDE DFSGLDEKDE DEDFLPLDAT
1360 1370 1380 1390 1400
PPKAKIPPKN TKKALKTQGS SMSVVDLESD VKDSVPASPG VPAADFPAET
1410 1420 1430 1440 1450
EQSKPSKKTV GVKKTATKSQ SSVSTAGTKK RAAPKGTKSD SALSARVSEK
1460 1470 1480 1490 1500
PAPAKAKNSR KRKPSSSDSS DSDFERAISK GATSKKAKGE EQDFPVDLED
1510 1520
TIAPRAKSDR ARKPIKYLEE SDDDDDLF
Length:1,528
Mass (Da):172,790
Last modified:December 14, 2011 - v2
Checksum:i63CBF8F649D103C7
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti184 – 1841E → A in BAA02076 (PubMed:1331984).Curated
Sequence conflicti260 – 2601S → M in BAA02076 (PubMed:1331984).Curated
Sequence conflicti640 – 6401S → P in BAA02076 (PubMed:1331984).Curated
Sequence conflicti841 – 8411I → N in BAA02076 (PubMed:1331984).Curated
Sequence conflicti844 – 8452IP → NT in BAA02076 (PubMed:1331984).Curated
Sequence conflicti1316 – 13161A → R in BAA02076 (PubMed:1331984).Curated
Sequence conflicti1316 – 13161A → R in AAC52135 (PubMed:8261398).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D12513 mRNA. Translation: BAA02076.1.
AL591067 Genomic DNA. No translation available.
U01915 mRNA. Translation: AAC52135.1.
CCDSiCCDS25370.1.
PIRiJS0703.
RefSeqiNP_035753.2. NM_011623.2.
XP_006533216.1. XM_006533153.1.
UniGeneiMm.4237.

Genome annotation databases

EnsembliENSMUST00000068031; ENSMUSP00000068896; ENSMUSG00000020914.
GeneIDi21973.
KEGGimmu:21973.
UCSCiuc007lid.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D12513 mRNA. Translation: BAA02076.1.
AL591067 Genomic DNA. No translation available.
U01915 mRNA. Translation: AAC52135.1.
CCDSiCCDS25370.1.
PIRiJS0703.
RefSeqiNP_035753.2. NM_011623.2.
XP_006533216.1. XM_006533153.1.
UniGeneiMm.4237.

3D structure databases

ProteinModelPortaliQ01320.
SMRiQ01320. Positions 28-404, 433-1187.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-40621N.
IntActiQ01320. 8 interactions.
MINTiMINT-1712967.

Chemistry

ChEMBLiCHEMBL3586.
GuidetoPHARMACOLOGYi2637.

PTM databases

PhosphoSiteiQ01320.

Proteomic databases

PaxDbiQ01320.
PRIDEiQ01320.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000068031; ENSMUSP00000068896; ENSMUSG00000020914.
GeneIDi21973.
KEGGimmu:21973.
UCSCiuc007lid.1. mouse.

Organism-specific databases

CTDi7153.
MGIiMGI:98790. Top2a.

Phylogenomic databases

eggNOGiCOG0187.
GeneTreeiENSGT00390000016222.
HOGENOMiHOG000216693.
HOVERGENiHBG052998.
InParanoidiQ01320.
KOiK03164.
OMAiGKAGEMK.
OrthoDBiEOG73JKTM.
TreeFamiTF105282.

Enzyme and pathway databases

ReactomeiREACT_274086. G0 and Early G1.

Miscellaneous databases

ChiTaRSiTop2a. mouse.
NextBioi301670.
PROiQ01320.
SOURCEiSearch...

Gene expression databases

BgeeiQ01320.
CleanExiMM_TOP2A.
ExpressionAtlasiQ01320. baseline and differential.
GenevestigatoriQ01320.

Family and domain databases

Gene3Di1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
3.90.199.10. 1 hit.
InterProiIPR024946. Arg_repress_C-like.
IPR012542. DTHCT.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR028466. Top2a.
IPR001241. Topo_IIA.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR10169:SF33. PTHR10169:SF33. 1 hit.
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00521. DNA_topoisoIV. 1 hit.
PF08070. DTHCT. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of cDNA encoding the mouse DNA topoisomerase II that can complement the budding yeast top2 mutation."
    Adachi N., Miyaike M., Ikeda H., Kikuchi A.
    Nucleic Acids Res. 20:5297-5303(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, FUNCTION.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "Characterization of a DNA topoisomerase IIalpha gene rearrangement in adriamycin-resistant P388 leukemia: expression of a fusion messenger RNA transcript encoding topoisomerase IIalpha and the retinoic acid receptor alpha locus."
    McPherson J., Brown G.A., Goldenberg G.J.
    Cancer Res. 53:5885-5889(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1254-1528.
    Tissue: Lymphoma.
  4. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-1418 AND LYS-1438, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.
  5. "Shikonin shortens the circadian period: possible involvement of Top2 inhibition."
    Ogawa Y., Kawano Y., Yamazaki Y., Onishi Y.
    Biochem. Biophys. Res. Commun. 443:339-343(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiTOP2A_MOUSE
AccessioniPrimary (citable) accession number: Q01320
Secondary accession number(s): E9PX08
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: December 14, 2011
Last modified: April 1, 2015
This is version 150 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Eukaryotic topoisomerase I and II can relax both negative and positive supercoils, whereas prokaryotic enzymes relax only negative supercoils.

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.