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Entry version 117 (07 Oct 2020)
Sequence version 2 (28 Feb 2018)
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Protein

Gag-Pro-Pol polyprotein

Gene

pol

Organism
Sheep pulmonary adenomatosis virus (Jaagsiekte sheep retrovirus) (JSRV)
Status
Reviewed-Annotation score:

Annotation score:5 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>
-Protein inferred from homologyi <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

Matrix protein.By similarity
Nucleocapsid protein p14: Nucleocapsid protein.By similarity
Capsid protein.By similarity
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 annotationBy similarity
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 annotationBy similarity
Enhances the activity of the reverse transcriptase. May be part of the mature RT.By similarity
RT is a multifunctional enzyme that converts the viral dimeric 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 perfom 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 perfom 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 primers. 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.PROSITE-ProRule annotation
Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.1 Publication

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 swiching 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.PROSITE-ProRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+PROSITE-ProRule annotationNote: The RT polymerase active site binds 2 magnesium ions.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei739Protease; shared with dimeric partnerPROSITE-ProRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi976Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1051Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1052Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1322Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1351Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1371Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1436MagnesiumPROSITE-ProRule annotation1
Metal bindingi1511Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1568Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1604Magnesium; catalytic; for integrase activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri507 – 524CCHC-typePROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1446 – 1487Integrase-typePROSITE-ProRule annotationAdd BLAST42
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 bindingi1665 – 1714Integrase-typePROSITE-ProRule annotationAdd BLAST50

<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 protease, DNA-binding, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein
Biological processDNA integration, DNA recombination, Viral genome integration, Virus entry into host cell
LigandMagnesium, Metal-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%5Fand%5Ftaxonomy%5Fsection">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
Recommended name:
Gag-Pro-Pol polyprotein
Cleaved into the following 10 chains:
Nucleocapsid protein-dUTPase (EC:3.6.1.23By similarity)
Short name:
NC-dUTPase
Protease 17 kDaBy similarity (EC:3.4.23.-PROSITE-ProRule annotation)
Protease 13 kDaBy similarity (EC:3.4.23.-PROSITE-ProRule annotation)
G-patch peptideBy similarity
Reverse transcriptase/ribonuclease H (EC:2.7.7.49PROSITE-ProRule annotation, EC:2.7.7.7PROSITE-ProRule annotation, EC:3.1.26.4PROSITE-ProRule annotation)
Short name:
RT
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:pol
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiSheep pulmonary adenomatosis virus (Jaagsiekte sheep retrovirus) (JSRV)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri11746 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiVirusesRiboviriaPararnaviraeArtverviricotaRevtraviricetesOrterviralesRetroviridaeOrthoretrovirinaeBetaretrovirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 hostiOvis aries (Sheep) [TaxID: 9940]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000007215 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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 location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Viral matrix protein, Virion

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved; by hostBy similarity
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001254902 – 1726Gag-Pro-Pol polyproteinAdd BLAST1725
ChainiPRO_00004431302 – 99Matrix protein p10Add BLAST98
ChainiPRO_0000443131100 – 167Phosphorylated proteinAdd BLAST68
ChainiPRO_0000443132168 – 256p12Add BLAST89
ChainiPRO_0000443133257 – 477Capsid protein p27Add BLAST221
ChainiPRO_0000443134478 – 713Nucleocapsid protein-dUTPaseAdd BLAST236
ChainiPRO_0000443135714 – 865Protease 17 kDaAdd BLAST152
ChainiPRO_0000443136714 – 831Protease 13 kDaAdd BLAST118
<p>This subsection of the 'PTM / Processing' section describes the position and length of an active peptide in the mature protein.<p><a href='/help/peptide' target='_top'>More...</a></p>PeptideiPRO_0000443137832 – 865G-patch peptideAdd BLAST34
ChainiPRO_0000434769866 – 1446Reverse transcriptase/ribonuclease HAdd BLAST581
ChainiPRO_00004347701447 – 1726IntegraseAdd BLAST280

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section specifies the position(s) and the type of covalently attached lipid group(s).<p><a href='/help/lipid' target='_top'>More...</a></p>Lipidationi2N-myristoyl glycine; by hostBy similarity1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Released by autocatalytic processing. The protease can undergo further autoprocessing to yield 2 shorter but enzymatically active forms of 12 kDa and 13 kDa.By similarity
Myristoylated. Myristoylation of the matrix (MA) domain mediates the transport and binding of Gag polyproteins to the host plasma membrane and is required for the assembly of viral particles.By similarity
Specific enzymatic cleavages in vivo yield mature proteins.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei99 – 100Cleavage; by viral proteaseBy similarity2
Sitei256 – 257Cleavage; by viral proteaseBy similarity2
Sitei477 – 478Cleavage; by viral proteaseBy similarity2
Sitei713 – 714Cleavage; by viral proteaseBy similarity2
Sitei831 – 832Cleavage; by viral proteaseBy similarity2
Sitei865 – 866Cleavage; by viral proteaseBy similarity2
Sitei1446 – 1447Cleavage; by viral proteaseBy similarity2

Keywords - PTMi

Lipoprotein, Myristate

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

By similarity

Interacts with the G-patch peptide.

By similarity

Interacts with the reverse transcriptase/ribonuclease H.

By similarity

Homotrimer.

By similarity

<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
P31623

Database of comparative protein structure models

More...
ModBasei
Search...

<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%5Fand%5Fdomains%5Fsection">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>Domaini734 – 810Peptidase A2PROSITE-ProRule annotationAdd BLAST77
Domaini821 – 866G-patchPROSITE-ProRule annotationAdd BLAST46
Domaini911 – 1099Reverse transcriptasePROSITE-ProRule annotationAdd BLAST189
Domaini1313 – 1444RNase HPROSITE-ProRule annotationAdd BLAST132
Domaini1500 – 1659Integrase catalyticPROSITE-ProRule annotationAdd BLAST160

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi202 – 205PTAP/PSAP motifCurated4
Motifi208 – 211PPXY motifCurated4
Motifi287 – 290PTAP/PSAP motifBy similarity4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi121 – 127Poly-ProSequence analysis7
Compositional biasi202 – 228Pro-richPROSITE-ProRule annotationAdd BLAST27

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Gag polyprotein: Late-budding domains (L domains) are short sequence motifs essential for viral particle release. They can occur individually or in close proximity within structural proteins. They interacts with sorting cellular proteins of the multivesicular body (MVB) pathway. Most of these proteins are class E vacuolar protein sorting factors belonging to ESCRT-I, ESCRT-II or ESCRT-III complexes. Gag-p12 contains two L domains: a PTAP/PSAP motif which interacts with the UEV domain of TSG101, and a PPXY motif which binds to the WW domains of the ubiquitin ligase NEDD4. Gag-p27 contains one L domain: a PTAP/PSAP motif which interacts with the UEV domain of TSG101.By similarity
The glycine-rich G-patch domain (GPD) is present at the C-terminus of the protease from which it is then detached by the protease itself.By similarity

<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.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri507 – 524CCHC-typePROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1446 – 1487Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Repeat, Zinc-finger

Family and domain databases

Conserved Domains Database

More...
CDDi
cd05482, HIV_retropepsin_like, 1 hit
cd07557, trimeric_dUTPase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.150.490, 1 hit
1.10.375.10, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
2.70.40.10, 1 hit
3.30.420.10, 2 hits
3.30.70.270, 2 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001969, Aspartic_peptidase_AS
IPR003322, B_retro_matrix
IPR038124, B_retro_matrix_sf
IPR043502, DNA/RNA_pol_sf
IPR029054, dUTPase-like
IPR036157, dUTPase-like_sf
IPR033704, dUTPase_trimeric
IPR000467, G_patch_dom
IPR000721, Gag_p24
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
IPR008916, Retrov_capsid_C
IPR008919, Retrov_capsid_N
IPR010999, Retrovr_matrix
IPR043128, Rev_trsase/Diguanyl_cyclase
IPR012337, RNaseH-like_sf
IPR002156, RNaseH_domain
IPR036397, RNaseH_sf
IPR000477, RT_dom
IPR010661, RVT_thumb
IPR001878, Znf_CCHC
IPR036875, Znf_CCHC_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00692, dUTPase, 1 hit
PF01585, G-patch, 1 hit
PF02337, Gag_p10, 1 hit
PF00607, 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, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00443, G_patch, 1 hit
SM00343, ZnF_C2HC, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF46919, SSF46919, 1 hit
SSF47836, SSF47836, 1 hit
SSF47943, SSF47943, 1 hit
SSF50122, SSF50122, 1 hit
SSF50630, SSF50630, 1 hit
SSF51283, SSF51283, 1 hit
SSF53098, SSF53098, 2 hits
SSF56672, SSF56672, 1 hit
SSF57756, SSF57756, 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
PS50174, G_PATCH, 1 hit
PS50994, INTEGRASE, 1 hit
PS51027, INTEGRASE_DBD, 1 hit
PS50879, RNASE_H, 1 hit
PS50878, RT_POL, 1 hit
PS50158, ZF_CCHC, 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%5Flength">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>Sequences (3)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 <p>This subsection of the 'Sequence' section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform. This section is only present in reviewed entries, i.e. in UniProtKB/Swiss-Prot.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by ribosomal frameshifting. AlignAdd to basket
Isoform Gag-Pro-Pol polyprotein (identifier: P31623-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali 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
MGHTHSRQLF VHMLSVMLKH RGITVSKTKL INFLSFIEEV CPWFPREGTV
60 70 80 90 100
NLETWKKVGE QIRTHYTLHG PEKVPVETLS FWTLIRDCLD FDNDELKRLG
110 120 130 140 150
NLLKQEEDPL HTPDSVPSYD PPPPPPPSLK MHPSDNDDSL SSTDEAELDE
160 170 180 190 200
EAAKYHQEDW GFLAQEKGAL TSKDELVECF KNLTIALQNA GIQLPSNNNT
210 220 230 240 250
FPSAPPFPPA YTPTVMAGLD PPPGFPPPSK HMSPLQKALR QAQRLGEVVS
260 270 280 290 300
DFSLAFPVFE NNNQRYYESL PFKQLKELKI ACSQYGPTAP FTIAMIESLG
310 320 330 340 350
TQALPPNDWK QTARACLSGG DYLLWKSEFF EQCARIADVN RQQGIQTSYE
360 370 380 390 400
MLIGEGPYQA TDTQLNFLPG AYAQISNAAR QAWKKLPSSS TKTEDLSKVR
410 420 430 440 450
QGPDEPYQDF VARLLDTIGK IMSDEKAGMV LAKQLAFENA NSACQAALRP
460 470 480 490 500
YRKKGDLSDF IRICADIGPS YMQGIAMAAA LQGKSIKEVL FQQQARNKKG
510 520 530 540 550
LQKSGNSGCF VCGQPGHRAA VCPQKHQTSV NTPNLCPRCK KGKHWARDCR
560 570 580 590 600
SKTDVQGNPL PPVSGNLGEG PAPGPETMLW GNTAGSKRTI ADLCRATRGS
610 620 630 640 650
AGLDLCATSY TVLTPEMGVQ TLATGVFGPL PPGTVGLLLG RSSASLKGIL
660 670 680 690 700
IHPGVIDSDY TGEIKILASA PNKIIVINAG QRIAQLLLVP LVIQGKTINR
710 720 730 740 750
DRQDKGFGSS DAYWVQNVTE ARPELELRIN ANFFRGVLDT GADISVISDK
760 770 780 790 800
YWPTTWPKQM AISTLQGIGQ TTNPEQSSSL LTWKDKDGHT GQFKPYILPY
810 820 830 840 850
LPVNLWGRDI LSKMGVYLYS PSPTVTDLML DQGLLPNQGL GKQHQGIILP
860 870 880 890 900
LDLKPNQDRK GLGCFPLGTS DSPVTHADPI DWKSEEPVWV DQWPLTQEKL
910 920 930 940 950
SAAQQLVQEQ LRLGHIEPST SAWNSPIFVI KKKSGKWRLL QDLRKVNETM
960 970 980 990 1000
MHMGALQPGL PTPSAIPDKS YIIVIDLKDC FYTIPLAPQD CKRFAFSLPS
1010 1020 1030 1040 1050
VNFKEPMQRY QWRVLPQGMT NSPTLCQKFV ATAIAPVRQR FPQLYLVHYM
1060 1070 1080 1090 1100
DDILLAHTDE HLLYQAFSIL KQHLSLNGLV IADEKIQTHF PYNYLGFSLY
1110 1120 1130 1140 1150
PRVYNTQLVK LQTDHLKTLN DFQKLLGDIN WIRPYLKLPT YTLQPLFDIL
1160 1170 1180 1190 1200
KGDSDPASPR TLSLEGRTAL QSIEEAIRQQ QITYCDYQRS WGLYILPTPR
1210 1220 1230 1240 1250
APTGVLYQDK PLRWIYLSAT PTKHLLPYYE LVAKIIAKGR HEAIQYFGME
1260 1270 1280 1290 1300
PPFICVPYAL EQQDWLFQFS DNWSIAFANY PGQITHHYPS DKLLQFASSH
1310 1320 1330 1340 1350
AFIFPKIVRR QPIPEATLIF TDGSSNGTAA LIINHQTYYA QTSFSSAQVV
1360 1370 1380 1390 1400
ELFAVHQALL TVPTSFNLFT DSSYVVGALQ MIETVPIIGT TSPEVLNLFT
1410 1420 1430 1440 1450
LIQQVLHCRQ HPCFFGHIRA HSTLPGALVQ GNHTADVLTK QVFFQSAIDA
1460 1470 1480 1490 1500
ARKSHDLHHQ NSHSLRLQFK ISREAARQIV KSCSTCPQFF VLPQYGVNPR
1510 1520 1530 1540 1550
GLRPNHLWQT DVTHIPQFGR LKYVHVSIDT FSNFLMASLH TGESTRHCIQ
1560 1570 1580 1590 1600
HLLFCFSTSG IPQTLKTDNG PGYTSRSFQR FCLSFQIHHK TGIPYNPQGQ
1610 1620 1630 1640 1650
GIVERAHQRI KHQLLKQKKG NELYSPSPHN ALNHALYVLN FLTLDTEGNS
1660 1670 1680 1690 1700
AAQRFWGERS SCKKPLVRWK DPLTNLWYGP DPVLIWGRGH VCVFPQDAEA
1710 1720
PRWIPERLVR AAEELPDASD ATHDPE
Note: Produced by -1 ribosomal frameshiftings between gag-pro and pro-pol.1 Publication
Length:1,726
Mass (Da):193,421
Last modified:February 28, 2018 - v2
<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:iACA8108A7C6A1A5B
GO
Isoform Gag-Pro polyprotein (identifier: P31625-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P31625.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:866
Mass (Da):95,245
GO
Isoform Gag polyprotein (identifier: P31622-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P31622.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:612
Mass (Da):68,089
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAA89182 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
M80216 Genomic RNA Translation: AAA89182.1 Different initiation.

Protein sequence database of the Protein Information Resource

More...
PIRi
C42740, GNMVJA

NCBI Reference Sequences

More...
RefSeqi
NP_041186.1, NC_001494.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
1490020

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
vg:1490020

Keywords - Coding sequence diversityi

Ribosomal frameshifting

<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
M80216 Genomic RNA Translation: AAA89182.1 Different initiation.
PIRiC42740, GNMVJA
RefSeqiNP_041186.1, NC_001494.1

3D structure databases

SMRiP31623
ModBaseiSearch...

Genome annotation databases

GeneIDi1490020
KEGGivg:1490020

Family and domain databases

CDDicd05482, HIV_retropepsin_like, 1 hit
cd07557, trimeric_dUTPase, 1 hit
Gene3Di1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.150.490, 1 hit
1.10.375.10, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
2.70.40.10, 1 hit
3.30.420.10, 2 hits
3.30.70.270, 2 hits
InterProiView protein in InterPro
IPR001969, Aspartic_peptidase_AS
IPR003322, B_retro_matrix
IPR038124, B_retro_matrix_sf
IPR043502, DNA/RNA_pol_sf
IPR029054, dUTPase-like
IPR036157, dUTPase-like_sf
IPR033704, dUTPase_trimeric
IPR000467, G_patch_dom
IPR000721, Gag_p24
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
IPR008916, Retrov_capsid_C
IPR008919, Retrov_capsid_N
IPR010999, Retrovr_matrix
IPR043128, Rev_trsase/Diguanyl_cyclase
IPR012337, RNaseH-like_sf
IPR002156, RNaseH_domain
IPR036397, RNaseH_sf
IPR000477, RT_dom
IPR010661, RVT_thumb
IPR001878, Znf_CCHC
IPR036875, Znf_CCHC_sf
PfamiView protein in Pfam
PF00692, dUTPase, 1 hit
PF01585, G-patch, 1 hit
PF02337, Gag_p10, 1 hit
PF00607, 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, 1 hit
SMARTiView protein in SMART
SM00443, G_patch, 1 hit
SM00343, ZnF_C2HC, 2 hits
SUPFAMiSSF46919, SSF46919, 1 hit
SSF47836, SSF47836, 1 hit
SSF47943, SSF47943, 1 hit
SSF50122, SSF50122, 1 hit
SSF50630, SSF50630, 1 hit
SSF51283, SSF51283, 1 hit
SSF53098, SSF53098, 2 hits
SSF56672, SSF56672, 1 hit
SSF57756, SSF57756, 2 hits
PROSITEiView protein in PROSITE
PS50175, ASP_PROT_RETROV, 1 hit
PS00141, ASP_PROTEASE, 1 hit
PS50174, G_PATCH, 1 hit
PS50994, INTEGRASE, 1 hit
PS51027, INTEGRASE_DBD, 1 hit
PS50879, RNASE_H, 1 hit
PS50878, RT_POL, 1 hit
PS50158, ZF_CCHC, 1 hit
PS50876, ZF_INTEGRASE, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

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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 nameiPOL_JSRV
<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: P31623
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: February 28, 2018
Last modified: October 7, 2020
This is version 117 of the entry and version 2 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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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