{ "bcoid": "GLY_000755", "title": "Yeast N-Glycosylation Sequon", "description": "The Yeast N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif or consensus sequence ...", "filename": "yeast_protein_glycosylation_motifs.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "N-Glycosylation Sequon" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P30619-1...", "51..." ], [ "P30619-1...", "347..." ] ], "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" } ], [ "P30619-1", "51", "53", "NVT" ], [ "P30619-1", "347", "349", "NTT" ], [ "P30619-1", "396", "398", "NLS" ], [ "P30619-1", "558", "560", "NTS" ], [ "P30619-1", "562", "564", "NSS" ], [ "P39970-1", "259", "261", "NSS" ], [ "P39970-1", "278", "280", "NQS" ], [ "P39970-1", "295", "297", "NNS" ], [ "P39970-1", "304", "306", "NIS" ], [ "P39970-1", "319", "321", "NLT" ], [ "P39970-1", "373", "375", "NNT" ], [ "P39970-1", "457", "459", "NNS" ], [ "P39971-1", "200", "202", "NRS" ], [ "P39976-1", "75", "77", "NST" ], [ "P39977-1", "27", "29", "NFT" ], [ "P39977-1", "31", "33", "NTS" ], [ "P39977-1", "54", "56", "NWT" ], [ "P39974-1", "10", "12", "NAT" ], [ "P39974-1", "43", "45", "NVS" ], [ "P39974-1", "50", "52", "NET" ], [ "P39975-1", "18", "20", "NSS" ], [ "P39975-1", "154", "156", "NYS" ], [ "P25379-1", "6", "8", "NKT" ], [ "P25379-1", "216", "218", "NTS" ], [ "P25379-1", "244", "246", "NQT" ], [ "P25378-1", "10", "12", "NST" ], [ "P17121-1", "3", "5", "NNT" ], [ "P17121-1", "14", "16", "NVS" ], [ "P17121-1", "40", "42", "NIT" ], [ "P17121-1", "258", "260", "NKT" ], [ "P17121-1", "262", "264", "NVT" ], [ "P17121-1", "324", "326", "NDT" ], [ "P17121-1", "469", "471", "NSS" ], [ "P17121-1", "572", "574", "NRS" ], [ "P17121-1", "578", "580", "NST" ], [ "P17121-1", "581", "583", "NSS" ], [ "P25374-1", "46", "48", "NFS" ], [ "P25374-1", "383", "385", "NGS" ], [ "P25374-1", "395", "397", "NVS" ], [ "P17123-1", "47", "49", "NES" ], [ "P17122-1", "29", "31", "NTS" ], [ "P17122-1", "83", "85", "NFT" ], [ "P25371-1", "50", "52", "NDT" ], [ "P25371-1", "114", "116", "NDT" ], [ "P25371-1", "165", "167", "NVT" ], [ "P25371-1", "221", "223", "NTS" ], [ "P25371-1", "388", "390", "NIT" ], [ "P25371-1", "580", "582", "NRT" ], [ "P25371-1", "657", "659", "NIS" ], [ "P25371-1", "815", "817", "NVS" ], [ "P25371-1", "935", "937", "NNS" ], [ "P25371-1", "960", "962", "NIT" ], [ "P25371-1", "971", "973", "NFS" ], [ "P25370-1", "13", "15", "NGS" ], [ "P25370-1", "49", "51", "NGT" ], [ "P25370-1", "227", "229", "NGT" ], [ "P25370-1", "526", "528", "NRT" ], [ "P25372-1", "32", "34", "NLT" ], [ "Q03049-1", "51", "53", "NLT" ], [ "Q03049-1", "216", "218", "NTS" ], [ "Q03049-1", "231", "233", "NAS" ], [ "Q06567-1", "52", "54", "NDT" ], [ "Q06567-1", "88", "90", "NKS" ], [ "Q06567-1", "180", "182", "NKT" ], [ "Q06567-1", "259", "261", "NFT" ], [ "Q06567-1", "412", "414", "NIT" ], [ "Q06567-1", "535", "537", "NLT" ], [ "Q06563-1", "151", "153", "NFS" ], [ "Q00539-1", "18", "20", "NDS" ], [ "Q00539-1", "32", "34", "NNS" ], [ "Q00539-1", "33", "35", "NSS" ], [ "Q00539-1", "46", "48", "NVS" ], [ "Q00539-1", "89", "91", "NNT" ], [ "Q00539-1", "94", "96", "NGS" ], [ "Q00539-1", "151", "153", "NNS" ], [ "Q00539-1", "162", "164", "NCS" ], [ "Q00539-1", "173", "175", "NVT" ], [ "Q00539-1", "254", "256", "NRS" ], [ "Q00539-1", "311", "313", "NNT" ], [ "Q00539-1", "312", "314", "NTT" ], [ "Q00539-1", "432", "434", "NVS" ], [ "Q00539-1", "445", "447", "NYS" ], [ "Q00539-1", "460", "462", "NFS" ], [ "Q00539-1", "468", "470", "NAT" ] ] }, "readme": "Name\n - Yeast N-Glycosylation Sequon\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2022-08-30T16:10:07.494670\n\nModified on\n - 2023-09-11T19:06:05\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@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 Yeast N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif or consensus sequence for yeast [taxid:559292] 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. \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/glygener/glygen-backend-integration/blob/master/dataset-maker/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: yeast_protein_canonicalsequences.fasta\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_canonicalsequences.fasta\n Name: prosite.dat\n URI: https:/data.glygen.org/ln2downloads/prosite/prosite.dat\n Output Subdomain\n Name: yeast_protein_glycosylation_motifs.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_glycosylation_motifs.csv\n Name: yeast_protein_glycosylation_motifs.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_glycosylation_motifs.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"5009\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1802\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1802\"\n Name: \"motif\"\n Description: \"Glycan motif\"\n Unique Values: \"38\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/yeast_protein_glycosylation_motifs.csv" }