{ "type": "genome", "identifier": "GCF_001514035.1", "organism": "Streptomyces yokosukanensis", "title": "Streptomyces yokosukanensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Bielefeld University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001514035.1", "bioproject": "PRJNA224116", "biosample": "SAMN04193343", "wgs_master": "LMWN00000000.1", "refseq_category": "reference genome", "taxid": "67386", "species_taxid": "67386", "organism_name": "Streptomyces yokosukanensis", "infraspecific_name": "strain=DSM 40224", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/01/13", "asm_name": "ASM151403v1", "asm_submitter": "Bielefeld University", "gbrs_paired_asm": "GCA_001514035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/514/035/GCF_001514035.1_ASM151403v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10159272", "genome_size_ungapped": "10107921", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "98", "contig_count": "188", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001514035.1-RS_2024_04_21", "annotation_date": "2024-04-21", "total_gene_count": "9122", "protein_coding_gene_count": "8757", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-01-13", "dateModified": "2016-01-13", "datePublished": "2016-01-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces yokosukanensis" ], "sample_taxid": [ "67386" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Yokosuka City" ], "sample_host_location_id": [], "data_size": "2.720 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 97.92, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "10159272", "Number of Sequences": "98", "Longest Sequences (bp)": "745504", "N50 (bp)": "463572", "Gap Ratio (%)": "0.505459", "GCcontent (%)": "71.3", "Number of CDSs": "9103", "Average Protein Length": "321.6", "Coding Ratio (%)": "86.4", "Number of rRNAs": "2", "Number of tRNAs": "87", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces yokosukanensis", "strain": "strain=DSM 40224", "accession": "GCA_001514035.1", "taxid": 67386, "species_taxid": 67386, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3329, "total_fragments": 3344, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces alanosinicus", "strain": "strain=JCM 4714", "accession": "GCA_014650595.1", "taxid": 68171, "species_taxid": 68171, "relation_to_type": "type", "validated": true, "ani": 91.1361, "matched_fragments": 2269, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces fodineus", "strain": "strain=TW1S1", "accession": "GCA_001735805.1", "taxid": 1904616, "species_taxid": 1904616, "relation_to_type": "type", "validated": true, "ani": 90.0005, "matched_fragments": 2219, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces barringtoniae", "strain": "strain=JA03", "accession": "GCA_020819595.1", "taxid": 2892029, "species_taxid": 2892029, "relation_to_type": "type", "validated": true, "ani": 89.801, "matched_fragments": 2144, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces filipinensis", "strain": "strain=JCM 4369", "accession": "GCA_014649495.1", "taxid": 66887, "species_taxid": 66887, "relation_to_type": "type", "validated": true, "ani": 89.6508, "matched_fragments": 2140, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces durhamensis", "strain": "strain=NRRL B-3309", "accession": "GCA_000725475.1", "taxid": 68194, "species_taxid": 68194, "relation_to_type": "type", "validated": true, "ani": 89.5917, "matched_fragments": 2133, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces broussonetiae", "strain": "strain=T44", "accession": "GCA_009796285.1", "taxid": 2686304, "species_taxid": 2686304, "relation_to_type": "type", "validated": true, "ani": 89.1726, "matched_fragments": 2211, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces monashensis", "strain": "strain=MUSC 1", "accession": "GCA_001866665.1", "taxid": 1678012, "species_taxid": 1678012, "relation_to_type": "type", "validated": true, "ani": 88.5753, "matched_fragments": 2186, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces cellostaticus", "strain": "strain=DSM 40189", "accession": "GCA_001513965.1", "taxid": 67285, "species_taxid": 67285, "relation_to_type": "type", "validated": true, "ani": 87.9441, "matched_fragments": 2187, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces spinosus", "strain": "strain=SBTS01", "accession": "GCA_020400655.1", "taxid": 2872623, "species_taxid": 2872623, "relation_to_type": "type", "validated": true, "ani": 87.7163, "matched_fragments": 1921, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces shenzhenensis subsp. oryzicola", "strain": "strain=W18L9", "accession": "GCA_013870495.1", "taxid": 2749088, "species_taxid": 943815, "relation_to_type": "type", "validated": true, "ani": 85.2492, "matched_fragments": 1397, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces lomondensis", "strain": "strain=DSM 41428", "accession": "GCA_021440105.1", "taxid": 68229, "species_taxid": 68229, "relation_to_type": "type", "validated": true, "ani": 84.5538, "matched_fragments": 1804, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces ferrugineus", "strain": "strain=CCTCC AA2014009", "accession": "GCA_015160855.1", "taxid": 1413221, "species_taxid": 1413221, "relation_to_type": "type", "validated": true, "ani": 84.4699, "matched_fragments": 1834, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces blattellae", "strain": "strain=TRM63209", "accession": "GCA_009709555.1", "taxid": 2569855, "species_taxid": 2569855, "relation_to_type": "type", "validated": true, "ani": 84.1981, "matched_fragments": 1595, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces acidicola", "strain": "strain=K1PN6", "accession": "GCA_009377235.1", "taxid": 2596892, "species_taxid": 2596892, "relation_to_type": "type", "validated": true, "ani": 83.036, "matched_fragments": 1619, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces tirandamycinicus", "strain": "strain=HNM0039", "accession": "GCA_003097515.1", "taxid": 2174846, "species_taxid": 2174846, "relation_to_type": "type", "validated": true, "ani": 81.2578, "matched_fragments": 1332, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glycomyces dulcitolivorans", "strain": "strain=SJ-25", "accession": "GCA_003265355.1", "taxid": 2200759, "species_taxid": 2200759, "relation_to_type": "type", "validated": true, "ani": 76.1453, "matched_fragments": 517, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glycomyces albidus", "strain": "strain=NEAU-7082", "accession": "GCA_009451885.1", "taxid": 2656774, "species_taxid": 2656774, "relation_to_type": "type", "validated": true, "ani": 76.0273, "matched_fragments": 540, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glycomyces sambucus", "strain": "strain=CGMCC 4.3147", "accession": "GCA_900102815.1", "taxid": 380244, "species_taxid": 380244, "relation_to_type": "type", "validated": true, "ani": 76.0166, "matched_fragments": 557, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glycomyces terrestris", "strain": "strain=YIM 121974", "accession": "GCA_003933745.1", "taxid": 2493553, "species_taxid": 2493553, "relation_to_type": "type", "validated": true, "ani": 76.0022, "matched_fragments": 574, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glycomyces artemisiae", "strain": "strain=CGMCC 4.7067", "accession": "GCA_003002955.1", "taxid": 1076443, "species_taxid": 1076443, "relation_to_type": "type", "validated": true, "ani": 75.8945, "matched_fragments": 576, "total_fragments": 3344, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 97.92, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001514035.1", "gtdb_species": "s__Streptomyces yokosukanensis", "ani": 100.0, "matched_fragments": 3329, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "conclusive" }, { "accession": "GCF_014650595.1", "gtdb_species": "s__Streptomyces alanosinicus", "ani": 91.1333, "matched_fragments": 2270, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001953885.1", "gtdb_species": "s__Streptomyces sp001953885", "ani": 91.0353, "matched_fragments": 2269, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000497445.1", "gtdb_species": "s__Streptomyces roseochromogenus", "ani": 91.0204, "matched_fragments": 2221, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001735805.1", "gtdb_species": "s__Streptomyces fodineus", "ani": 90.0105, "matched_fragments": 2217, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_009604455.1", "gtdb_species": "s__Streptomyces sp009604455", "ani": 89.7915, "matched_fragments": 2114, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001280015.1", "gtdb_species": "s__Streptomyces sp001280015", "ani": 89.2583, "matched_fragments": 2226, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_009796285.1", "gtdb_species": "s__Streptomyces broussonetiae", "ani": 89.1749, "matched_fragments": 2210, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001636945.1", "gtdb_species": "s__Streptomyces sp001636945", "ani": 89.0321, "matched_fragments": 2058, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_014650115.1", "gtdb_species": "s__Streptomyces olivaceoviridis", "ani": 87.588, "matched_fragments": 2006, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.78", "min_intra_species_ani": "96.54", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003634225.1", "gtdb_species": "s__Streptomyces sp003634225", "ani": 87.3309, "matched_fragments": 2143, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.82", "min_intra_species_ani": "99.82", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009650765.1", "gtdb_species": "s__Streptomyces sp003259585", "ani": 86.3642, "matched_fragments": 1857, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_015160855.1", "gtdb_species": "s__Streptomyces ferrugineus", "ani": 84.479, "matched_fragments": 1833, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001509475.1", "gtdb_species": "s__Streptomyces regalis", "ani": 84.267, "matched_fragments": 1800, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_014495685.1", "gtdb_species": "s__Streptomyces sp014495685", "ani": 84.2224, "matched_fragments": 1672, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_018638295.1", "gtdb_species": "s__Streptomyces sp018638295", "ani": 83.4708, "matched_fragments": 1532, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002214185.1", "gtdb_species": "s__Streptomyces capitiformicae", "ani": 82.9998, "matched_fragments": 1701, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009832925.1", "gtdb_species": "s__Streptomyces sp009832925", "ani": 81.1062, "matched_fragments": 1354, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_003265355.1", "gtdb_species": "s__Glycomyces dulcitolivorans", "ani": 76.1487, "matched_fragments": 516, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_009451885.1", "gtdb_species": "s__Glycomyces albidus", "ani": 76.0343, "matched_fragments": 537, "total_fragments": 3344, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.201, "cell_length": -0.05, "doubling_h": 0.103, "growth_tmp": 27.0, "optimum_tmp": 29.036, "optimum_ph": 7.341, "genome_size": 10159636.0, "gc_content": 70.89, "coding_genes": 7141.289, "rRNA16S_genes": 6.155, "tRNA_genes": 67.804, "gram_stain": 1.0, "sporulation": 0.958, "motility": 0.049, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.005, "aerobic_respiration": 0.994, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.208, "coccus_cell_shape": 0.032, "filament_cell_shape": 0.582, "coccobacillus_cell_shape": 0.098, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.076 }, "_genome_taxon": [ "Streptomyces", "yokosukanensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }