{ "bcoid": "GLY_000427", "title": "SARS-CoV1 N-Glycosylation Sequon", "description": "The SARS coronavirus (SARS-CoV-1) N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif ...", "filename": "sarscov1_protein_glycosylation_motifs.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-1)", "molecule": "Protein", "tags": "N-Glycosylation Sequon", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P59596-1...", "4..." ], [ "P0C6U8-1...", "48..." ] ], "headers": [ "uniprotkb_ca...", "start_pos..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "motif" } ], [ "P59596-1", "4", "6", "NGT" ], [ "P0C6U8-1", "48", "50", "NGT" ], [ "P0C6U8-1", "389", "391", "NHS" ], [ "P0C6U8-1", "556", "558", "NHS" ], [ "P0C6U8-1", "916", "918", "NFS" ], [ "P0C6U8-1", "1628", "1630", "NHT" ], [ "P0C6U8-1", "1696", "1698", "NKT" ], [ "P0C6U8-1", "1899", "1901", "NAS" ], [ "P0C6U8-1", "2079", "2081", "NTS" ], [ "P0C6U8-1", "2249", "2251", "NSS" ], [ "P0C6U8-1", "2252", "2254", "NVT" ], [ "P0C6U8-1", "2507", "2509", "NNT" ], [ "P0C6U8-1", "2659", "2661", "NMT" ], [ "P0C6U8-1", "2685", "2687", "NVS" ], [ "P0C6U8-1", "3303", "3305", "NHS" ], [ "P0C6U8-1", "3359", "3361", "NGS" ], [ "P0C6U8-1", "3373", "3375", "NHT" ], [ "P0C6U8-1", "3382", "3384", "NGS" ], [ "P0C6U8-1", "3720", "3722", "NYS" ], [ "P0C6U8-1", "4150", "4152", "NNS" ], [ "P0C6U8-1", "4233", "4235", "NAT" ], [ "P0C6U8-1", "4240", "4242", "NST" ], [ "P59594-1", "29", "31", "NYT" ], [ "P59594-1", "65", "67", "NVT" ], [ "P59594-1", "73", "75", "NHT" ], [ "P59594-1", "109", "111", "NKS" ], [ "P59594-1", "118", "120", "NNS" ], [ "P59594-1", "119", "121", "NST" ], [ "P59594-1", "158", "160", "NCT" ], [ "P59594-1", "227", "229", "NIT" ], [ "P59594-1", "269", "271", "NGT" ], [ "P59594-1", "318", "320", "NIT" ], [ "P59594-1", "330", "332", "NAT" ], [ "P59594-1", "357", "359", "NST" ], [ "P59594-1", "589", "591", "NAS" ], [ "P59594-1", "602", "604", "NCT" ], [ "P59594-1", "691", "693", "NNT" ], [ "P59594-1", "699", "701", "NFS" ], [ "P59594-1", "783", "785", "NFS" ], [ "P59594-1", "1056", "1058", "NFT" ], [ "P59594-1", "1080", "1082", "NGT" ], [ "P59594-1", "1116", "1118", "NNT" ], [ "P59594-1", "1140", "1142", "NHT" ], [ "P59594-1", "1155", "1157", "NAS" ], [ "P59594-1", "1176", "1178", "NES" ], [ "P59595-1", "48", "50", "NNT" ], [ "P59595-1", "197", "199", "NST" ], [ "P59595-1", "270", "272", "NVT" ], [ "Q80H93-1", "43", "45", "NVT" ], [ "P59632-1", "22", "24", "NAS" ], [ "P59632-1", "227", "229", "NAT" ], [ "P59637-1", "48", "50", "NVS" ], [ "P59637-1", "66", "68", "NSS" ], [ "P59636-1", "4", "6", "NQT" ], [ "P0C6X7-1", "48", "50", "NGT" ], [ "P0C6X7-1", "389", "391", "NHS" ], [ "P0C6X7-1", "556", "558", "NHS" ], [ "P0C6X7-1", "916", "918", "NFS" ], [ "P0C6X7-1", "1628", "1630", "NHT" ], [ "P0C6X7-1", "1696", "1698", "NKT" ], [ "P0C6X7-1", "1899", "1901", "NAS" ], [ "P0C6X7-1", "2079", "2081", "NTS" ], [ "P0C6X7-1", "2249", "2251", "NSS" ], [ "P0C6X7-1", "2252", "2254", "NVT" ], [ "P0C6X7-1", "2507", "2509", "NNT" ], [ "P0C6X7-1", "2659", "2661", "NMT" ], [ "P0C6X7-1", "2685", "2687", "NVS" ], [ "P0C6X7-1", "3303", "3305", "NHS" ], [ "P0C6X7-1", "3359", "3361", "NGS" ], [ "P0C6X7-1", "3373", "3375", "NHT" ], [ "P0C6X7-1", "3382", "3384", "NGS" ], [ "P0C6X7-1", "3720", "3722", "NYS" ], [ "P0C6X7-1", "4150", "4152", "NNS" ], [ "P0C6X7-1", "4233", "4235", "NAT" ], [ "P0C6X7-1", "4240", "4242", "NST" ], [ "P0C6X7-1", "5016", "5018", "NLS" ], [ "P0C6X7-1", "5280", "5282", "NTS" ], [ "P0C6X7-1", "5403", "5405", "NVT" ], [ "P0C6X7-1", "5558", "5560", "NIS" ], [ "P0C6X7-1", "5650", "5652", "NST" ], [ "P0C6X7-1", "5905", "5907", "NVT" ], [ "P0C6X7-1", "6031", "6033", "NNT" ], [ "P0C6X7-1", "6130", "6132", "NHS" ], [ "P0C6X7-1", "6474", "6476", "NKT" ] ] }, "readme": "Name\n - SARS-CoV1 N-Glycosylation Sequon\n\nVersion\n - 1.8.24\n\nCreated on\n - 2020-04-03T00:35:31.181876\n\nModified on\n - 2020-04-09T18:43:07.886517\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 SARS coronavirus (SARS-CoV-1) N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif or consensus sequence for sarscov1 [taxid:694009] UniProtKB canonical sequences identified by the script. The script identifies the N-glycosylation sequon pattern - Asn-X-Ser/Thr , where X is any amino acid except proline (Pro) for UniProtKB accessions. The dataset is derived form 2020_01 UniprotKB release.\n\nDescription Domain\n Keywords\n - n-glycosylation sequon\n - NXS/T\n - n-glycosylation motif\n - n-glycosylation consensus sequence\n\n Pipeline Steps\n - Step-1: The script uses the PS Scan tool (accession- PS00001) from ProSite to extracts the N-glycosylation pattern/sequon/motif N-{P}-[ST]-{P} where P is not a proline from the UniProtKB canonical sequences. More info - https://prosite.expasy.org/PDOC00001, https://prosite.expasy.org/PS00001 and extracts as a csv.\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_canonicalsequences.fasta\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/sarscov1_protein_canonicalsequences.fasta\n Output Subdomain\n Name: sarscov1_protein_glycosylation_motifs.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/sarscov1_protein_glycosylation_motifs.csv\n Name: sarscov1_protein_glycosylation_motifs.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/sarscov1_protein_glycosylation_motifs.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-1.8.24/reviewed/sarscov1_protein_glycosylation_motifs.csv" }