{
    "bcoid": "GLY_000471",
    "title": "SARS-CoV1 Protein PTM Annotation (UniProtKB)",
    "description": "The SARS coronavirus (SARS-CoV-1) Protein PTM Annotation (UniProtKB) dataset contains sarscov1 [taxid:694009] ...",
    "filename": "sarscov1_protein_ptm_annotation_uniprotkb.csv",
    "filetype": "csv",
    "categories": {
        "species": "SARS coronavirus (SARS-CoV-1)",
        "molecule": "Protein",
        "tags": "PTM annotation",
        "file_type": "csv",
        "status": "Reviewed",
        "scope": "internal"
    },
    "minitable": {
        "content": [
            [
                "P59594-1...",
                "protein_xref..."
            ],
            [
                "P59594-1...",
                "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"
                }
            ],
            [
                "P59594-1",
                "protein_xref_uniprotkb",
                "P59594",
                "ECO_0000269",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested by cathepsin CTSL within endosomes."
            ],
            [
                "P59594-1",
                "protein_xref_pubmed",
                "17134730",
                "ECO_0000269",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested by cathepsin CTSL within endosomes."
            ],
            [
                "P59594-1",
                "protein_xref_uniprotkb",
                "P59594",
                "ECO_0000255",
                "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host cell furin or another cellular protease to yield the mature S1 and S2 proteins. Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor."
            ],
            [
                "P59594-1",
                "protein_xref_pubmed",
                "MF_04099",
                "ECO_0000255",
                "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host cell furin or another cellular protease to yield the mature S1 and S2 proteins. Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor."
            ],
            [
                "P59594-1",
                "protein_xref_uniprotkb",
                "P59594",
                "ECO_0000255",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes."
            ],
            [
                "P59594-1",
                "protein_xref_pubmed",
                "MF_04099",
                "ECO_0000255",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes."
            ],
            [
                "P59595-1",
                "protein_xref_uniprotkb",
                "P59595",
                "ECO_0000255",
                "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "MF_04096",
                "ECO_0000255",
                "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection."
            ],
            [
                "P59595-1",
                "protein_xref_uniprotkb",
                "P59595",
                "ECO_0000269",
                "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "29199039",
                "ECO_0000269",
                "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection."
            ],
            [
                "P59595-1",
                "protein_xref_uniprotkb",
                "P59595",
                "ECO_0000255",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "MF_04096",
                "ECO_0000255",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_uniprotkb",
                "P59595",
                "ECO_0000269",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "24766657",
                "ECO_0000269",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "19106108",
                "ECO_0000269",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P0C6U8-1",
                "protein_xref_uniprotkb",
                "P0C6U8",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-11 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6U8-1",
                "protein_xref_pubmed",
                "15564471",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-11 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6U8-1",
                "protein_xref_pubmed",
                "15331731",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-11 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6U8-1",
                "protein_xref_pubmed",
                "16306590",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-11 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6U8-1",
                "protein_xref_pubmed",
                "12917450",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-11 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6U8-1",
                "protein_xref_pubmed",
                "32083638",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-11 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6X7-1",
                "protein_xref_uniprotkb",
                "P0C6X7",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-16 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6X7-1",
                "protein_xref_pubmed",
                "15331731",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-16 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6X7-1",
                "protein_xref_pubmed",
                "12917450",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-16 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6X7-1",
                "protein_xref_pubmed",
                "15564471",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-16 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6X7-1",
                "protein_xref_pubmed",
                "32083638",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-16 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P0C6X7-1",
                "protein_xref_pubmed",
                "16306590",
                "ECO_0000269",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins (PubMed:32083638, PubMed:16306590, PubMed:12917450, PubMed:15331731, PubMed:15564471). 3C-like proteinase nsp5 liberates nsps 6-16 from the polyprotein (PubMed:32083638). Papain-like and 3C-like proteinases are autocatalytically processed."
            ],
            [
                "P59632-1",
                "protein_xref_uniprotkb",
                "P59632",
                "ECO_0000269",
                "Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion."
            ],
            [
                "P59632-1",
                "protein_xref_pubmed",
                "16474139",
                "ECO_0000269",
                "Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion."
            ]
        ]
    },
    "readme": "Name\n   - SARS-CoV1 Protein PTM Annotation (UniProtKB)\n\nVersion\n   - 1.11.2\n\nCreated on\n  - 2020-04-19T11:41:41.632491\n\nModified on\n   - 2022-01-13T16:42:18.633188\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.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 SARS coronavirus (SARS-CoV-1) Protein PTM Annotation (UniProtKB) dataset contains sarscov1 [taxid:694009] PTM annotations for UniProtKB canonical accessions. The annotation is the curated statements of mainly about glycosylation and phosphorylation. The dataset is derived form 2020-01 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 sequences and 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: sarscov1_protein_masterlist.csv\n      URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/sarscov1_protein_masterlist.csv\n      Name: uniprot-proteome-sars-cov-2.nt\n      URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_ntdata.nt\n   Output Subdomain\n      Name: sarscov1_protein_ptm_annotation_uniprotkb.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/sarscov1_protein_ptm_annotation_uniprotkb.csv\n      Name: sarscov1_protein_ptm_annotation_uniprotkb.stat.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/sarscov1_protein_ptm_annotation_uniprotkb.stat.csv",
    "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/sarscov1_protein_ptm_annotation_uniprotkb.csv"
}