{
    "bcoid": "GLY_000364",
    "title": "HCV1b Protein PTM Annotation (UniProtKB)",
    "description": "The Hepatitis C virus (genotype 1b, isolate Japanese) Protein PTM Annotation (UniProtKB) dataset contains ...",
    "filename": "hcv1b_protein_ptm_annotation_uniprotkb.csv",
    "filetype": "csv",
    "categories": {
        "species": "Hepatitis C virus (genotype 1b, isolate Japanese)",
        "molecule": "Protein",
        "tags": "PTM annotation",
        "file_type": "csv",
        "status": "Reviewed",
        "scope": "internal"
    },
    "minitable": {
        "content": [
            [
                "P26662-1...",
                "..."
            ],
            [
                "P26662-1...",
                "..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "pmid..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "pmid"
                },
                {
                    "type": "string",
                    "label": "eco_id"
                },
                {
                    "type": "string",
                    "label": "ptm_annotation"
                }
            ],
            [
                "P26662-1",
                "",
                "",
                "Envelope E1 and E2 glycoproteins are highly N-glycosylated."
            ],
            [
                "P26662-1",
                "",
                "",
                "The N-terminus of a fraction of NS4B molecules seems to be relocated post-translationally from the cytoplasm to the ER lumen, with a 5th transmembrane segment. The C-terminus of NS2 may be lumenal with a fourth transmembrane segment (By similarity)."
            ],
            [
                "P26662-1",
                "",
                "",
                "NS4B is palmitoylated. This modification may play a role in its polymerization or in protein-protein interactions (By similarity)."
            ],
            [
                "P26662-1",
                "",
                "",
                "Core protein is phosphorylated by host PKC and PKA."
            ],
            [
                "P26662-1",
                "",
                "",
                "NS5A is phosphorylated in a basal form termed p56. p58 is a hyperphosphorylated form of p56. p56 and p58 coexist in the cell in roughly equivalent amounts. Hyperphosphorylation is dependent on the presence of NS4A. Human AKT1, RPS6KB1/p70S6K, MAP2K1/MEK1, MAP2K6/MKK6 and CSNK1A1/CKI-alpha kinases may be responsible for NS5A phosphorylation (By similarity)."
            ],
            [
                "P26662-1",
                "",
                "",
                "Core protein is ubiquitinated; mediated by UBE3A and leading to core protein subsequent proteasomal degradation."
            ],
            [
                "P26662-1",
                "",
                "",
                "Specific enzymatic cleavages in vivo yield mature proteins. The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases. The core protein is synthesized as a 21 kDa precursor which is retained in the ER membrane through the hydrophobic signal peptide. Cleavage by the signal peptidase releases the 19 kDa mature core protein. The other proteins (p7, NS2-3, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (By similarity)."
            ]
        ]
    },
    "readme": "Name\n   - HCV1b Protein PTM Annotation (UniProtKB)\n\nVersion\n   - 1.5.23\n\nCreated on\n  - 2020-03-14T15:26:35.442241\n\nModified on\n   - 2020-04-09T18:06:05.126892\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 1b, isolate Japanese) Protein PTM Annotation (UniProtKB) dataset contains hcv1b [taxid:11116] 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-1b.nt\n      URI: https://data.glygen.org/ln2wwwdata/reviewed/uniprot-proteome-hepatitis-c-virus-1b.nt\n      Name: hcv1b_protein_masterlist.csv\n      URI: https://data.glygen.org/ln2wwwdata/reviewed/hcv1b_protein_masterlist.csv\n   Output Subdomain\n      Name: hcv1b_protein_ptm_annotation_uniprotkb.csv\n      URI: http://data.glygen.org/ln2wwwdata/reviewed/hcv1b_protein_ptm_annotation_uniprotkb.csv\n      Name: hcv1b_protein_ptm_annotation_uniprotkb.stat.csv\n      URI: http://data.glygen.org/ln2wwwdata/reviewed/hcv1b_protein_ptm_annotation_uniprotkb.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n      Unique Values: \"1\"\n      Name: \"eco_id\"\n     Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n      Unique Values: \"1\"\n      Name: \"pmid\"\n     Description: \"NCBI PubMed database Identifier\"\n      Unique Values: \"1\"\n      Name: \"ptm_annotation\"\n     Description: \"The Post Translational Modifiaction (PTM) annotation in UniProtKB that provides more context and description about the PTMs occuring on a proein\"\n      Unique Values: \"7\"",
    "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/hcv1b_protein_ptm_annotation_uniprotkb.csv"
}