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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Bovine immunodeficiency virus (strain R29) (BIV) (Bovine immunodeficiency-like virus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Matrix protein p16 forms the outer shell of the core of the virus, lining the inner surface of the viral membrane.By similarity
Capsid protein p26 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex. Interaction between incoming particle-associated Gag proteins and host dynein allows intracellular microtubule-dependent virus transport toward the perinuclear region, prior to nucleus translocation and integration into host genome.1 Publication
The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.PROSITE-ProRule annotation
Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5'-end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity).By similarity
Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA (By similarity).By similarity

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei497PROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri403 – 420CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri421 – 438CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1199 – 1240Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1419 – 1465Integrase-typePROSITE-ProRule annotationAdd BLAST47

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

Cytoplasmic inwards viral transport, DNA integration, DNA recombination, Host-virus interaction, Microtubular inwards viral transport, Viral genome integration, Virion maturation, Virus entry into host cell, Virus exit from host cell

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, RNA-binding, Viral nucleoprotein, Zinc

Protein family/group databases

MEROPSiA02.005.

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Alternative name(s):
Pr170Gag-Pol
Cleaved into the following 8 chains:
Matrix protein p16
Short name:
MA
Capsid protein p26
Short name:
CA
Alternative name(s):
p11
Alternative name(s):
P119
Retropepsin
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
P72
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
Gene namesi
Name:gag-pol
OrganismiBovine immunodeficiency virus (strain R29) (BIV) (Bovine immunodeficiency-like virus)
Taxonomic identifieri417296 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusBovine lentivirus group
Virus hostiBos taurus (Bovine) [TaxID: 9913]

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Viral matrix protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002723241 – 1475Gag-Pol polyproteinAdd BLAST1475
ChainiPRO_00002723251 – 126Matrix protein p16Sequence analysisAdd BLAST126
PeptideiPRO_0000272326127 – 148p2LBy similarityAdd BLAST22
ChainiPRO_0000272327149 – 367Capsid protein p26Sequence analysisAdd BLAST219
PeptideiPRO_0000272328368 – 392p3By similarityAdd BLAST25
ChainiPRO_0000272329393 – 472Transframe peptideSequence analysisAdd BLAST80
ChainiPRO_0000038823473 – 562ProteaseSequence analysisAdd BLAST90
ChainiPRO_0000038824563 – 1193Reverse transcriptase/ribonuclease HSequence analysisAdd BLAST631
ChainiPRO_00000388251194 – 1475IntegraseSequence analysisAdd BLAST282

Post-translational modificationi

Specific enzymatic cleavages by the viral protease yield mature proteins. The protease is released by autocatalytic cleavage. The polyprotein is cleaved during and after budding, this process is termed maturation (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei126 – 127Cleavage; by viral proteaseSequence analysis2
Sitei148 – 149Cleavage; by viral proteaseSequence analysis2
Sitei367 – 368Cleavage; by viral proteaseBy similarity2
Sitei392 – 393Cleavage; by viral proteaseBy similarity2
Sitei472 – 473Cleavage; by viral proteaseSequence analysis2
Sitei562 – 563Cleavage; by viral proteaseSequence analysis2
Sitei1193 – 1194Cleavage; by viral proteaseSequence analysis2

Interactioni

Subunit structurei

Interacts with host light chain cytoplasmic dynein DYNLL1; this interaction is critical for intracellular microtubule-dependent viral genome transport.1 Publication

Structurei

Secondary structure

11475
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1257 – 1265Combined sources9
Beta strandi1268 – 1275Combined sources8
Turni1276 – 1278Combined sources3
Beta strandi1281 – 1289Combined sources9
Helixi1291 – 1304Combined sources14
Beta strandi1308 – 1312Combined sources5
Helixi1316 – 1319Combined sources4
Helixi1321 – 1329Combined sources9
Beta strandi1333 – 1338Combined sources6
Helixi1342 – 1362Combined sources21
Helixi1363 – 1365Combined sources3
Helixi1369 – 1382Combined sources14
Helixi1392 – 1401Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3KKRX-ray2.45A1257-1405[»]
3KKSX-ray2.20A/B1257-1405[»]
ProteinModelPortaliP19560.
SMRiP19560.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP19560.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini492 – 565Peptidase A2PROSITE-ProRule annotationAdd BLAST74
Domaini619 – 806Reverse transcriptasePROSITE-ProRule annotationAdd BLAST188
Domaini999 – 1119RNase HPROSITE-ProRule annotationAdd BLAST121
Domaini1248 – 1400Integrase catalyticPROSITE-ProRule annotationAdd BLAST153

Sequence similaritiesi

Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
Contains 1 integrase-type DNA-binding domain.PROSITE-ProRule annotation
Contains 1 integrase-type zinc finger.PROSITE-ProRule annotation
Contains 1 peptidase A2 domain.PROSITE-ProRule annotation
Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation
Contains 1 RNase H domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri403 – 420CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri421 – 438CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1199 – 1240Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
1.10.1200.30. 1 hit.
1.10.150.90. 1 hit.
1.10.375.10. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR012344. Matrix_HIV/RSV.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00607. Gag_p24. 1 hit.
PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF06817. RVT_thumb. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50175. ASP_PROT_RETROV. 1 hit.
PS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 2 hits.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]

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 ribosomal frameshifting. AlignAdd to basket

Note: This strategy of translation probably allows the virus to modulate the quantity of each viral protein.
Isoform Gag-Pol polyprotein (identifier: P19560-1) [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
MKRRELEKKL RKVRVTPQQD KYYTIGNLQW AIRMINLMGI KCVCDEECSA
60 70 80 90 100
AEVALIITQF SALDLENSPI RGKEEVAIKN TLKVFWSLLA GYKPESTETA
110 120 130 140 150
LGYWEAFTYR EREARADKEG EIKSIYPSLT QNTQNKKQTS NQTNTQSLPA
160 170 180 190 200
ITTQDGTPRF DPDLMKQLKI WSDATERNGV DLHAVNILGV ITANLVQEEI
210 220 230 240 250
KLLLNSTPKW RLDVQLIESK VREKENAHRT WKQHHPEAPK TDEIIGKGLS
260 270 280 290 300
SAEQATLISV ECRETFRQWV LQAAMEVAQA KHATPGPINI HQGPKEPYTD
310 320 330 340 350
FINRLVAALE GMAAPETTKE YLLQHLSIDH ANEDCQSILR PLGPNTPMEK
360 370 380 390 400
KLEACRVVGS QKSKMQFLVA AMKEMGIQSP IPAVLPHTPE AYASQTSGPE
410 420 430 440 450
DGRRCYGCGK TGHLKRNCKQ QKCYHCGKPG HQARNCRSKN REVLLCPLWA
460 470 480 490 500
EEPTTEQFSP EQHEFCDPIC TPSYIRLDKQ PFIKVFIGGR WVKGLVDTGA
510 520 530 540 550
DEVVLKNIHW DRIKGYPGTP IKQIGVNGVN VAKRKTHVEW RFKDKTGIID
560 570 580 590 600
VLFSDTPVNL FGRSLLRSIV TCFTLLVHTE KIEPLPVKVR GPGPKVPQWP
610 620 630 640 650
LTKEKYQALK EIVKDLLAEG KISEAAWDNP YNTPVFVIKK KGTGRWRMLM
660 670 680 690 700
DFRELNKITV KGQEFSTGLP YPPGIKECEH LTAIDIKDAY FTIPLHEDFR
710 720 730 740 750
PFTAFSVVPV NREGPIERFQ WNVLPQGWVC SPAIYQTTTQ KIIENIKKSH
760 770 780 790 800
PDVMLYQYMD DLLIGSNRDD HKQIVQEIRD KLGSYGFKTP DEKVQEERVK
810 820 830 840 850
WIGFELTPKK WRFQPRQLKI KNPLTVNELQ QLVGNCVWVQ PEVKIPLYPL
860 870 880 890 900
TDLLRDKTNL QEKIQLTPEA IKCVEEFNLK LKDPEWKDRI REGAELVIKI
910 920 930 940 950
QMVPRGIVFD LLQDGNPIWG GVKGLNYDHS NKIKKILRTM NELNRTVVIM
960 970 980 990 1000
TGREASFLLP GSSEDWEAAL QKEESLTQIF PVKFYRHSCR WTSICGPVRE
1010 1020 1030 1040 1050
NLTTYYTDGG KKGKTAAAVY WCEGRTKSKV FPGTNQQAEL KAICMALLDG
1060 1070 1080 1090 1100
PPKMNIITDS RYAYEGMREE PETWAREGIW LEIAKILPFK QYVGVGWVPA
1110 1120 1130 1140 1150
HKGIGGNTEA DEGVKKALEQ MAPCSPPEAI LLKPGEKQNL ETGIYMQGLR
1160 1170 1180 1190 1200
PQSFLPRADL PVAITGTMVD SELQLQLLNI GTEHIRIQKD EVFMTCFLEN
1210 1220 1230 1240 1250
IPSATEDHER WHTSPDILVR QFHLPKRIAK EIVARCQECK RTTTSPVRGT
1260 1270 1280 1290 1300
NPRGRFLWQM DNTHWNKTII WVAVETNSGL VEAQVIPEET ALQVALCILQ
1310 1320 1330 1340 1350
LIQRYTVLHL HSDNGPCFTA HRIENLCKYL GITKTTGIPY NPQSQGVVER
1360 1370 1380 1390 1400
AHRDLKDRLA AYQGDCETVE AALSLALVSL NKKRGGIGGH TPYEIYLESE
1410 1420 1430 1440 1450
HTKYQDQLEQ QFSKQKIEKW CYVRNRRKEW KGPYKVLWDG DGAAVIEEEG
1460 1470
KTALYPHRHM RFIPPPDSDI QDGSS
Note: Produced by -1 ribosomal frameshifting at the gag-pol genes boundary.
Length:1,475
Mass (Da):168,063
Last modified:January 23, 2007 - v2
Checksum:i4D249DCBB6158A78
GO
Isoform Gag polyprotein (identifier: P19558-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P19558.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.
Length:476
Mass (Da):53,440
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti17P → L in strain: Isolate R29-106 and Isolate R29-Nadin. 1
Natural varianti117D → E in strain: Isolate R29-106. 1
Natural varianti454T → I in strain: Isolate R29-Nadin. 1
Natural varianti577V → I in strain: Isolate R29-Nadin. 1
Natural varianti645R → K in strain: Isolate R29-Nadin. 1
Natural varianti729V → I in strain: Isolate R29-Nadin. 1
Natural varianti1095V → I in strain: Isolate R29-Nadin. 1
Natural varianti1226K → R in strain: Isolate R29-106 and Isolate R29-Nadin. 1
Natural varianti1244T → A in strain: Isolate R29-106 and Isolate R29-Nadin. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M32690 Genomic RNA. Translation: AAA91271.1. Sequence problems.
L04972 Genomic DNA. Translation: AAA42767.1. Sequence problems.
PIRiB34742. GNLJBT.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M32690 Genomic RNA. Translation: AAA91271.1. Sequence problems.
L04972 Genomic DNA. Translation: AAA42767.1. Sequence problems.
PIRiB34742. GNLJBT.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3KKRX-ray2.45A1257-1405[»]
3KKSX-ray2.20A/B1257-1405[»]
ProteinModelPortaliP19560.
SMRiP19560.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiA02.005.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP19560.

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
1.10.1200.30. 1 hit.
1.10.150.90. 1 hit.
1.10.375.10. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR012344. Matrix_HIV/RSV.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00607. Gag_p24. 1 hit.
PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF06817. RVT_thumb. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50175. ASP_PROT_RETROV. 1 hit.
PS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 2 hits.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOL_BIV29
AccessioniPrimary (citable) accession number: P19560
Secondary accession number(s): P19561, Q65593
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 132 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

The reverse transcriptase is an error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template switching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs (By similarity).By similarity
The sequence shown is that of isolate R29-127.

Keywords - Technical termi

3D-structure, Multifunctional enzyme

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  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.