| Name | DoBISCUIT |
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| Aliases | Database Of BIoSynthesis clusters CUrated and InTegrated |
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| Description | Secondary metabolites such as those produced by bacteria have pharmacologically important activities and attract attentions as lead-compounds and/or candidates for drug development.Although we can find many INSDC entries describing either complete or partial sequences of such secondary metabolite biosynthetic gene clusters, gene descriptions in each entry varies wildly.DoBISCUIT enables easy access to comprehensive information related to biosynthesis clusters and browsing standardized up-to-date gene descriptions. DoBISCUIT will thus serve as a useful reference for the analysis of secondary metabolite synthesis. |
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| Type | DB |
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| Main Institutes of management | Biological Resource Center, National Institute of Technology and Evaluation (NITE) |
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| Country of the Institute | Japan |
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| URL of the site | https://www.nite.go.jp/nbrc/pks/ |
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| Interface | GUI |
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| Input example | [List menu]List:Click one in "Cluster List" on top page.[Search menu]Text:Click the "Text search" menu on the right side of top page. Input the keyword in the text box, push "Search" button.Blast:Click the "Blast search" menu on the right side of top page. Input the sequence in the text box, push "Search" button.Module:Click the "Module search" menu on the right side of top page. Select one check box in the domain list, push "Search" button. |
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| Keyword | bacteria | secondary metabolites | biosynthesis clusters |
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| Amount of the all data for download（Mbyte） | Method to obtain the all data. | 30|https://www.nite.go.jp/nbrc/pks/download/ |
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| External resources (databases) in building the product. | Genbank | Uniprot | NBRC | NCBI Taxonomy | Pubmed |
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| Data type | Annotation | secondary metabolite |
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| Biological species in the main concern | Pseudomonas fluorescens | Sorangium cellulosum | Stigmatella aurantiaca | Actinosporangium vitaminophilum ATCC 31673 [Taxonomy_id: 76728] | Amycolatopsis mediterranei S699 [Taxonomy_id: 33910] | Micromonospora megalomicea subsp. nigra NRRL 3275 [Taxonomy_id: 136926] | Mycobacterium ulcerans Agy99 [Taxonomy_id: 362242] | Nostoc sp. ATCC 53789 [Taxonomy_id: 76335] | Pseudomonas fluorescens Pf-5 [Taxonomy_id: 220664] | Saccharopolyspora spinosa NRRL 18538 [Taxonomy_id: 60894] | Sorangium cellulosum So ce26 [Taxonomy_id: 56] | Sorangium cellulosum So ce90 [Taxonomy_id: 56] | Stigmatella aurantiaca DW4/3-1 [Taxonomy_id: 378806] | Stigmatella aurantiaca Sga15 [Taxonomy_id: 41] | Streptomyces achromogenes var. rubradiris NRRL3061 [Taxonomy_id: 285531] | Streptomyces antibioticus ATCC 11891 [Taxonomy_id: 1890] | Streptomyces antibioticus DSM 40725 [Taxonomy_id: 1890] | Streptomyces antibioticus NRRL 8167 [Taxonomy_id: 1890] | Streptomyces aureofaciens T?117 [Taxonomy_id: 1894] | Streptomyces avermitilis ATCC 31267 [Taxonomy_id: 33903] | Streptomyces bikiniensis NRRL 2737 [Taxonomy_id: 1896] | Streptomyces caelestis NRRL 2821 [Taxonomy_id: 36816] | Streptomyces cinnamonensis ATCC 15413 [Taxonomy_id: 1900] | Streptomyces coelicolor A3 [Taxonomy_id: 100226] | Streptomyces collinus T?365 [Taxonomy_id: 42684] | Streptomyces cyanogenus S136 [Taxonomy_id: 80860] | Streptomyces diastaticus 108 [Taxonomy_id: 1956] | Streptomyces fradiae T?2717 [Taxonomy_id: 1906] | Streptomyces griseoflavus G? 3592 [Taxonomy_id: 35619] | Streptomyces griseoruber ATCC 15422 [Taxonomy_id: 1943] | Streptomyces griseus K-63 [Taxonomy_id: 1911] | Streptomyces halstedii HC34 [Taxonomy_id: 1944] | Streptomyces hygroscopicus AM 3672 [Taxonomy_id: 1912] | Streptomyces hygroscopicus NRRL 5491 [Taxonomy_id: 1912] | Streptomyces hygroscopicus subsp. ascomyceticus ATCC 14891 [Taxonomy_id: 132248] | Streptomyces lasaliensis ATCC 31180 [Taxonomy_id: 324833] | Streptomyces lydicus NRRL 2433 [Taxonomy_id: 47763] | Streptomyces nanchangensis NS3226 [Taxonomy_id: 204925] | Streptomyces natalensis ATCC 27448 [Taxonomy_id: 68242] | Streptomyces neyagawaensis ATCC 27749 [Taxonomy_id: 42238] | Streptomyces nodosus ATCC 14899 [Taxonomy_id: 40318] | Streptomyces noursei ATCC 11455 [Taxonomy_id: 316284] | Streptomyces parvulus T?4055 [Taxonomy_id: 146923] | Streptomyces platensis Mer-11107 [Taxonomy_id: 58346] | Streptomyces roseofulvus AK24158 [Taxonomy_id: 33902] | Streptomyces sp. AM-7161 [Taxonomy_id: 221710] | Streptomyces sp. CK4412 [Taxonomy_id: 404220] | Streptomyces sp. CM020 [Taxonomy_id: 569580] | Streptomyces sp. FR-008 [Taxonomy_id: 206662] | Streptomyces sp. HK803 [Taxonomy_id: 244967] | Streptomyces sp. NRRL 11266 [Taxonomy_id: 299254] | Streptomyces sp. R1128 [Taxonomy_id: 140437] | Streptomyces sp. SCC-2136 [Taxonomy_id: 264024] | Streptomyces spiroverticillatus [Taxonomy_id: 673666] | Streptomyces thioluteus HKI-227 [Taxonomy_id: 66431] | Streptomyces venezuelae ATCC 15439 [Taxonomy_id: 54571] | Streptomyces venezuelae ISP5230 [Taxonomy_id: 54571] | Streptomyces violaceoruber T?22 [Taxonomy_id: 1935] | Streptomyces violaceusniger [Taxonomy_id: 68280] | Streptomyces violaceusniger DSM 4137 [Taxonomy_id: 68280] | Streptomyces virginiae MAFF11-0615 [Taxonomy_id: 1961] |
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| Conditions of use | Creative Commons BY-ND 2.1 |
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| Frequency of updates (in last two years) | 2time/year |
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| Last date of updates (date of confirmation) | 2016-12-27 |
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| Main IDs used in the products | CDS ID |
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| How to make a link to get access to each IDs. | https://www.nite.go.jp/nbrc/pks/cds/01376/[CDS ID] |
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| external databases to which this database/tool have links | Genbank | Uniprot | NBRC | NCBI Taxonomy | Pubmed |
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| Published papers (PubMed IDs) | pmid:23185043 |
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| Operational Status | available |
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