{ "bcoid": "GLY_000363", "title": "HCV1a Protein PTM Annotation (UniProtKB)", "description": "The Hepatitis C virus (genotype 1a, isolate H) Protein PTM Annotation (UniProtKB) dataset contains hcv1a ...", "filename": "hcv1a_protein_ptm_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Hepatitis C virus (genotype 1a, isolate H)", "molecule": "Protein", "tags": "PTM annotation", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P27958-1...", "protein_xref..." ], [ "P27958-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "ptm_annotation" } ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000250", "Phosphorylated by host PKC and PKA." ], [ "P27958-1", "protein_xref_pubmed", "Q01403", "ECO_0000250", "Phosphorylated by host PKC and PKA." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000269", "Palmitoylation is required for NS2/3 autoprocessing and E2 recruitment to membranes." ], [ "P27958-1", "protein_xref_pubmed", "31597774", "ECO_0000269", "Palmitoylation is required for NS2/3 autoprocessing and E2 recruitment to membranes." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000269", "Highly N-glycosylated." ], [ "P27958-1", "protein_xref_pubmed", "18187336", "ECO_0000269", "Highly N-glycosylated." ], [ "P27958-1", "protein_xref_pubmed", "14990718", "ECO_0000269", "Highly N-glycosylated." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000269", "Palmitoylated. This modification may play a role in its polymerization or in protein-protein interactions." ], [ "P27958-1", "protein_xref_pubmed", "16731940", "ECO_0000269", "Palmitoylated. This modification may play a role in its polymerization or in protein-protein interactions." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000250", "Cleaved by host caspases which are probably activated by the viral infection." ], [ "P27958-1", "protein_xref_pubmed", "P26662", "ECO_0000250", "Cleaved by host caspases which are probably activated by the viral infection." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000250", "Tyrosine phosphorylation is essential for the interaction with host SRC." ], [ "P27958-1", "protein_xref_pubmed", "Q99IB8", "ECO_0000250", "Tyrosine phosphorylation is essential for the interaction with host SRC." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000269", "Ubiquitinated (PubMed:27194766). Ubiquitination, most probably at Lys-2350, mediated by host IFI27 and SKP2 leads to proteasomal degradation, restricting viral infection (PubMed:27194766)." ], [ "P27958-1", "protein_xref_pubmed", "27194766", "ECO_0000269", "Ubiquitinated (PubMed:27194766). Ubiquitination, most probably at Lys-2350, mediated by host IFI27 and SKP2 leads to proteasomal degradation, restricting viral infection (PubMed:27194766)." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000250", "Phosphorylated on serines in a basal form termed p56 (By similarity). p58 is a hyperphosphorylated form of p56 (By similarity). p56 and p58 coexist in the cell in roughly equivalent amounts (By similarity). Hyperphosphorylation is dependent on the presence of NS4A (By similarity). Host CSNK1A1/CKI-alpha, PI4KA or RPS6KB1 kinases may be responsible for NS5A phosphorylation (By similarity). Phosphorylated NS5A is involved in viral replication (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "P26663", "ECO_0000250", "Phosphorylated on serines in a basal form termed p56 (By similarity). p58 is a hyperphosphorylated form of p56 (By similarity). p56 and p58 coexist in the cell in roughly equivalent amounts (By similarity). Hyperphosphorylation is dependent on the presence of NS4A (By similarity). Host CSNK1A1/CKI-alpha, PI4KA or RPS6KB1 kinases may be responsible for NS5A phosphorylation (By similarity). Phosphorylated NS5A is involved in viral replication (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "P26662", "ECO_0000250", "Phosphorylated on serines in a basal form termed p56 (By similarity). p58 is a hyperphosphorylated form of p56 (By similarity). p56 and p58 coexist in the cell in roughly equivalent amounts (By similarity). Hyperphosphorylation is dependent on the presence of NS4A (By similarity). Host CSNK1A1/CKI-alpha, PI4KA or RPS6KB1 kinases may be responsible for NS5A phosphorylation (By similarity). Phosphorylated NS5A is involved in viral replication (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "Q99IB8", "ECO_0000250", "Phosphorylated on serines in a basal form termed p56 (By similarity). p58 is a hyperphosphorylated form of p56 (By similarity). p56 and p58 coexist in the cell in roughly equivalent amounts (By similarity). Hyperphosphorylation is dependent on the presence of NS4A (By similarity). Host CSNK1A1/CKI-alpha, PI4KA or RPS6KB1 kinases may be responsible for NS5A phosphorylation (By similarity). Phosphorylated NS5A is involved in viral replication (By similarity)." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000250", "Ubiquitinated; mediated by UBE3A and leading to core protein subsequent proteasomal degradation." ], [ "P27958-1", "protein_xref_pubmed", "Q03463", "ECO_0000250", "Ubiquitinated; mediated by UBE3A and leading to core protein subsequent proteasomal degradation." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000269", "The N-terminus is phosphorylated by host PRK2/PKN2." ], [ "P27958-1", "protein_xref_pubmed", "15364941", "ECO_0000269", "The N-terminus is phosphorylated by host PRK2/PKN2." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000250", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "Q99IB8", "ECO_0000250", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_uniprotkb", "P27958", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "15247249", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "8386278", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "15722527", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "8189513", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "7679746", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "P26663", "ECO_0000250", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "8035505", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ], [ "P27958-1", "protein_xref_pubmed", "P26664", "ECO_0000250", "Specific enzymatic cleavages in vivo yield mature proteins (PubMed:8189513, PubMed:15722527, PubMed:8035505, PubMed:8386278). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (PubMed:15247249). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (PubMed:15247249, PubMed:7679746, PubMed:8189513, PubMed:8035505, PubMed:8386278). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity)." ] ] }, "readme": "Name\n - HCV1a Protein PTM Annotation (UniProtKB)\n\nVersion\n - 1.8.25\n\nCreated on\n - 2020-03-14T15:22:20.601417\n\nModified on\n - 2020-04-09T17:38:19.494458\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Hepatitis C virus (genotype 1a, isolate H) Protein PTM Annotation (UniProtKB) dataset contains hcv1a [taxid:11108] PTM annotations for UniProtKB canonical accessions. The annotation is the curated statements of mainly about glycosylation and phosphorylation. The dataset is derived form 2019-09 UniprotKB release. If you use this dataset please give proper attribution to UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - ptm annotation\n - glycosylation\n - phosphorylation\n\n Pipeline Steps\n - Step-1: The script extracts the ptm annotation strings from the triplestore for the UniProtKB canonical sequnces asnd extracts as a dataset in a csv format\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: uniprot-proteome-hepatitis-c-virus-1a.nt\n URI: https://data.glygen.org/ln2wwwdata/reviewed/uniprot-proteome-hepatitis-c-virus-1a.nt\n Name: hcv1a_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/hcv1a_protein_masterlist.csv\n Output Subdomain\n Name: hcv1a_protein_ptm_annotation_uniprotkb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/hcv1a_protein_ptm_annotation_uniprotkb.csv\n Name: hcv1a_protein_ptm_annotation_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/hcv1a_protein_ptm_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/hcv1a_protein_ptm_annotation_uniprotkb.csv" }