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Entry version 168 (11 Dec 2019)
Sequence version 1 (01 Nov 1996)
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Protein
Submitted name:

Pol polyprotein

Gene

pol

Organism
Simian immunodeficiency virus (SIV)
Status
Unreviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

  • 3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.SAAS annotation EC:3.1.13.2
  • 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.SAAS annotation EC:3.1.26.13

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi990 – 1037Integrase-typePROSITE-ProRule annotationAdd BLAST48

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionAspartyl proteaseUniRule annotationSAAS annotation, DNA-bindingSAAS annotation, EndonucleaseSAAS annotation, Hydrolase, Multifunctional enzymeSAAS annotation, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymeraseSAAS annotation, Transferase
Biological processDNA integration, DNA recombinationSAAS annotation, Viral genome integrationSAAS annotation, Virus entry into host cell
LigandMetal-binding, Zinc

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Submitted name:
Pol polyproteinImported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:polImported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSimian immunodeficiency virus (SIV)Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri11723 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiVirusesOrterviralesRetroviridaeOrthoretrovirinaeLentivirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiCercopithecidae (Old World monkeys) [TaxID: 9527]
Pan troglodytes (Chimpanzee) [TaxID: 9598]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000005623 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Chemistry databases

Drug and drug target database

More...
DrugBanki
DB07722 3-(4-NITRO-PHENOXY)-PROPAN-1-OL

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

Protein interaction database and analysis system

More...
IntActi
Q88016, 1 interactor

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q88016

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
Q88016

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini129 – 198Peptidase A2InterPro annotationAdd BLAST70
Domaini252 – 442Reverse transcriptaseInterPro annotationAdd BLAST191
Domaini641 – 764RNase HInterPro annotationAdd BLAST124
Domaini770 – 811Integrase-typeInterPro annotationAdd BLAST42
Domaini820 – 971Integrase catalyticInterPro annotationAdd BLAST152
Domaini990 – 1037Integrase-typeInterPro annotationAdd BLAST48

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni46 – 78DisorderedSequence analysisAdd BLAST33
Regioni1038 – 1060DisorderedSequence analysisAdd BLAST23

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and domains’ section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili78 – 98Sequence analysisAdd BLAST21
Coiled coili922 – 942Sequence analysisAdd BLAST21

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the retroviral Pol polyprotein family.UniRule annotation

Keywords - Domaini

Coiled coilSequence analysis, Zinc-fingerPROSITE-ProRule annotationSAAS annotation

Family and domain databases

Conserved Domains Database

More...
CDDi
cd05482 HIV_retropepsin_like, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.10.200, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
3.30.420.10, 2 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR017856 Integrase-like_N
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR034170 Retropepsin-like_cat_dom
IPR018061 Retropepsins
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010659 RVT_connect
IPR010661 RVT_thumb

Pfam protein domain database

More...
Pfami
View protein in Pfam
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
PF06815 RVT_connect, 1 hit
PF06817 RVT_thumb, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF46919 SSF46919, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF53098 SSF53098, 2 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50175 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
PS50876 ZF_INTEGRASE, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Fragment.

Q88016-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
VLELWERGTL CKAMQSPKKT GMLEMWKNGP CYGQMPRQTG GFFRPWSMGK
60 70 80 90 100
EAPQFPHGSS ASGADANCSP RGPSCGSAKE LHAVGQAAER KAERKQREAL
110 120 130 140 150
QGGDRGFAAP QFSLWRRPVV TAHIEGQPVE VLLDTGADDS IVTGIELGPH
160 170 180 190 200
YTPKIVGGIG GFINTKEYKN VEIEVLGKRI KGTIMTGDTP INIFGRNLLT
210 220 230 240 250
ALGMSLNFPI AKVEPVKVAL KPGKDGPKLK QWPLSKEKIV ALREICEKME
260 270 280 290 300
KDGQLEEAPP TNPYNTPTFA IKKKDKNKWR MLIDFRELNR VTQDFTEVQL
310 320 330 340 350
GIPHPAGLAK RKRITVLDIG DAYFSIPLDE EFRQYTAFTL PSVNNAEPGK
360 370 380 390 400
RYIYKVLPQG WKGSPAIFQY TMRHVLEPFR KANPDVTLVQ YMDDILIASD
410 420 430 440 450
RTDLEHDRVV LQSKELLNSI GFSTPEEKFQ KDPPFQWMGY ELWPTKWKLQ
460 470 480 490 500
KIELPQRETW TVNDIQKLVG VLNWAAQIYP GIKTKHLCRL IRGKMTLTEE
510 520 530 540 550
VQWTEMAEAE YEENKIILSQ EQEGCYYQEG KPLEATVIKS QDNQWSYKIH
560 570 580 590 600
QEDKILKVGK FAKIKNTHTN GVRLLAHVIQ KIGKEAIVIW GQVPKFHLPV
610 620 630 640 650
EKDVWEQWWT DYWQVTWIPE WDFISTPPLV RLVFNLVKDP IEGEETYYTD
660 670 680 690 700
GSCNKQSKEG KAGYITDRGK DKVKVLEQTT NQQAELEAFL MALTDSGPKA
710 720 730 740 750
NIIVDSQYVM GIITGCPTES ESRLVNQIIE EMIKKSEIYV AWVPAHKGIG
760 770 780 790 800
GNQEIDHLVS QGIRQVLFLE KIEPAQEEHD KYHSNVKELV FKFGLPRIVA
810 820 830 840 850
RQIVDTCDKC HQKGEAIHGQ ANSDLGTWQM DCTHLEGKII IVAVHVASGF
860 870 880 890 900
IEAEVIPQET GRQTALFLLK LAGRWPITHL HTDNGANFAS QEVKMVAWWA
910 920 930 940 950
GIEHTFGVPY NPQSQGVVEA MNHHLKNQID RIREQANSVE TIVLMAVHCM
960 970 980 990 1000
NFKRRGGIGD MTPAERLINM ITTEQEIQFQ QSKNSKFKNF RVYYREGRDQ
1010 1020 1030 1040 1050
LWKGPGELLW KGEGAVILKV GTDIKVVPRR KAKIIKDYGG GKEVDSSSHM
1060
EDTGEAREVA
Length:1,060
Mass (Da):120,105
Last modified:November 1, 1996 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i0A1265BBD12C3483
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section is used for sequence fragments to indicate that the residue at the extremity of the sequence is not the actual terminal residue in the complete protein sequence.<p><a href='/help/non_ter' target='_top'>More...</a></p>Non-terminal residuei1Imported1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
M33262 Genomic RNA Translation: AAA47633.2

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33262 Genomic RNA Translation: AAA47633.2

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1C6VX-ray3.00A/B/C/D817-980[»]
X980-1060[»]
1SIPX-ray2.30A110-208[»]
SMRiQ88016
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

IntActiQ88016, 1 interactor

Chemistry databases

DrugBankiDB07722 3-(4-NITRO-PHENOXY)-PROPAN-1-OL

Miscellaneous databases

EvolutionaryTraceiQ88016

Family and domain databases

CDDicd05482 HIV_retropepsin_like, 1 hit
Gene3Di1.10.10.200, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
3.30.420.10, 2 hits
InterProiView protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR017856 Integrase-like_N
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR034170 Retropepsin-like_cat_dom
IPR018061 Retropepsins
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010659 RVT_connect
IPR010661 RVT_thumb
PfamiView protein in Pfam
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
PF06815 RVT_connect, 1 hit
PF06817 RVT_thumb, 1 hit
SUPFAMiSSF46919 SSF46919, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF53098 SSF53098, 2 hits
PROSITEiView protein in PROSITE
PS50175 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
PS50876 ZF_INTEGRASE, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiQ88016_SIV
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q88016
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/TrEMBL: November 1, 1996
Last sequence update: November 1, 1996
Last modified: December 11, 2019
This is version 168 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiUnreviewed (UniProtKB/TrEMBL)

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources
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