{ "type": "genome", "identifier": "GCF_001969965.1", "organism": "Streptomyces sparsogenes DSM 40356", "title": "Streptomyces sparsogenes DSM 40356", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Department of Chemistry - University of Basel", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001969965.1", "bioproject": "PRJNA224116", "biosample": "SAMN06251500", "wgs_master": "ASQP00000000.1", "refseq_category": "na", "taxid": "1331668", "species_taxid": "67365", "organism_name": "Streptomyces sparsogenes DSM 40356", "infraspecific_name": "strain=DSM 40356", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/23", "asm_name": "Sparso1.0", "asm_submitter": "Department of Chemistry - University of Basel", "gbrs_paired_asm": "GCA_001969965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/969/965/GCF_001969965.1_Sparso1.0", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9699678", "genome_size_ungapped": "9699678", "gc_percent": "72.000000", "replicon_count": "0", "scaffold_count": "646", "contig_count": "646", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001969965.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "8942", "protein_coding_gene_count": "8335", "non_coding_gene_count": "74", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-23", "dateModified": "2017-01-23", "datePublished": "2017-01-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces sparsogenes DSM 40356" ], "sample_taxid": [ "1331668" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "2.609 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9699678", "Number of Sequences": "646", "Longest Sequences (bp)": "238727", "N50 (bp)": "28947", "Gap Ratio (%)": "0.000031", "GCcontent (%)": "72.2", "Number of CDSs": "8238", "Average Protein Length": "316.3", "Coding Ratio (%)": "80.6", "Number of rRNAs": "4", "Number of tRNAs": "84", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces sparsogenes", "strain": "strain=DSM 40356", "accession": "GCA_001969965.1", "taxid": 67365, "species_taxid": 67365, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2886, "total_fragments": 2912, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces sparsogenes", "strain": "strain=ATCC 25498", "accession": "GCA_001704635.1", "taxid": 67365, "species_taxid": 67365, "relation_to_type": "type", "validated": true, "ani": 99.7959, "matched_fragments": 2507, "total_fragments": 2912, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces milbemycinicus", "strain": "strain=NRRL 5739", "accession": "GCA_002154605.1", "taxid": 476552, "species_taxid": 476552, "relation_to_type": "type", "validated": true, "ani": 89.311, "matched_fragments": 1844, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces hygroscopicus subsp. hygroscopicus", "strain": "strain=NBRC 13472", "accession": "GCA_001553455.1", "taxid": 68042, "species_taxid": 1912, "relation_to_type": "type", "validated": true, "ani": 85.0603, "matched_fragments": 1646, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces rapamycinicus", "strain": "strain=NRRL 5491", "accession": "GCA_003675955.1", "taxid": 1226757, "species_taxid": 1226757, "relation_to_type": "type", "validated": true, "ani": 84.6364, "matched_fragments": 1867, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces rapamycinicus", "strain": "strain=NRRL 5491", "accession": "GCA_024298965.1", "taxid": 1226757, "species_taxid": 1226757, "relation_to_type": "type", "validated": true, "ani": 84.6264, "matched_fragments": 1856, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces yatensis", "strain": "strain=DSM 41771", "accession": "GCA_018069625.1", "taxid": 155177, "species_taxid": 155177, "relation_to_type": "type", "validated": true, "ani": 84.5869, "matched_fragments": 1775, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces sabulosicollis", "strain": "strain=PRKS01-29", "accession": "GCA_016103465.1", "taxid": 2715963, "species_taxid": 2715963, "relation_to_type": "type", "validated": true, "ani": 84.5715, "matched_fragments": 1568, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces javensis", "strain": "strain=DSM 41764", "accession": "GCA_016103505.1", "taxid": 114698, "species_taxid": 114698, "relation_to_type": "type", "validated": true, "ani": 84.5461, "matched_fragments": 1491, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces palmae", "strain": "strain=JCM 31289", "accession": "GCA_004684805.1", "taxid": 1701085, "species_taxid": 1701085, "relation_to_type": "type", "validated": true, "ani": 82.7104, "matched_fragments": 1224, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces albireticuli", "strain": "strain=NRRL B1670", "accession": "GCA_021228125.1", "taxid": 1940, "species_taxid": 1940, "relation_to_type": "type", "validated": true, "ani": 81.5554, "matched_fragments": 1286, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces huiliensis", "strain": "strain=SCA2-4", "accession": "GCA_020037025.1", "taxid": 2876027, "species_taxid": 2876027, "relation_to_type": "type", "validated": true, "ani": 81.113, "matched_fragments": 1133, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces thermoviolaceus subsp. apingens", "strain": "strain=JCM 4312", "accession": "GCA_014649255.1", "taxid": 66859, "species_taxid": 1952, "relation_to_type": "type", "validated": true, "ani": 80.9371, "matched_fragments": 1067, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces thermodiastaticus", "strain": "strain=DSM 40573", "accession": "GCA_021394575.1", "taxid": 44061, "species_taxid": 44061, "relation_to_type": "type", "validated": true, "ani": 80.9208, "matched_fragments": 1108, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces thermoviolaceus subsp. thermoviolaceus", "strain": "strain=NBRC 13905", "accession": "GCA_012034235.1", "taxid": 66860, "species_taxid": 1952, "relation_to_type": "type", "validated": true, "ani": 80.8308, "matched_fragments": 1056, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces thermoviolaceus subsp. thermoviolaceus", "strain": "strain=JCM 4843", "accession": "GCA_014650975.1", "taxid": 66860, "species_taxid": 1952, "relation_to_type": "type", "validated": true, "ani": 80.8149, "matched_fragments": 1071, "total_fragments": 2912, "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": 80.719, "matched_fragments": 1349, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces panaciradicis", "strain": "strain=NBRC 109811", "accession": "GCA_023516615.1", "taxid": 1470261, "species_taxid": 1470261, "relation_to_type": "type", "validated": true, "ani": 80.622, "matched_fragments": 1320, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces nymphaeiformis", "strain": "strain=SFB5A", "accession": "GCA_014203895.1", "taxid": 2663842, "species_taxid": 2663842, "relation_to_type": "type", "validated": true, "ani": 80.5608, "matched_fragments": 1291, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura macra", "strain": "strain=NBRC 14102", "accession": "GCA_001552215.1", "taxid": 46164, "species_taxid": 46164, "relation_to_type": "type", "validated": true, "ani": 76.4356, "matched_fragments": 686, "total_fragments": 2912, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001704635.1", "gtdb_species": "s__Streptomyces sparsogenes", "ani": 99.8089, "matched_fragments": 2506, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.81", "min_intra_species_ani": "99.81", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_002224125.1", "gtdb_species": "s__Streptomyces sp002224125", "ani": 89.9054, "matched_fragments": 2191, "total_fragments": 2912, "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_002154605.1", "gtdb_species": "s__Streptomyces milbemycinicus", "ani": 89.301, "matched_fragments": 1845, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001553455.1", "gtdb_species": "s__Streptomyces hygroscopicus", "ani": 85.043, "matched_fragments": 1648, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.24", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001417735.1", "gtdb_species": "s__Streptomyces sp001417735", "ani": 85.0236, "matched_fragments": 1707, "total_fragments": 2912, "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": "GCA_005405945.1", "gtdb_species": "s__Streptomyces violaceusniger", "ani": 84.6919, "matched_fragments": 1857, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.67", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018138715.1", "gtdb_species": "s__Streptomyces asiaticus", "ani": 84.5254, "matched_fragments": 1864, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.17", "min_intra_species_ani": "95.36", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.81", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_013364155.1", "gtdb_species": "s__Streptomyces sp013364155", "ani": 84.3206, "matched_fragments": 1627, "total_fragments": 2912, "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_000147815.2", "gtdb_species": "s__Streptomyces violaceusniger_A", "ani": 84.3143, "matched_fragments": 1789, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.3301, "mean_intra_species_ani": "95.69", "min_intra_species_ani": "95.54", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.80", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000158915.1", "gtdb_species": "s__Streptomyces himastatinicus", "ani": 84.2766, "matched_fragments": 1773, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.59", "min_intra_species_ani": "95.41", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_016741875.1", "gtdb_species": "s__Streptomyces coffeae", "ani": 84.1367, "matched_fragments": 1617, "total_fragments": 2912, "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_007595705.1", "gtdb_species": "s__Streptomyces sp007595705", "ani": 82.7993, "matched_fragments": 1388, "total_fragments": 2912, "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_000931445.1", "gtdb_species": "s__Streptomyces cyaneogriseus", "ani": 80.9352, "matched_fragments": 1282, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 96.603, "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_002155905.1", "gtdb_species": "s__Streptomyces tricolor", "ani": 80.7483, "matched_fragments": 1197, "total_fragments": 2912, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.72", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_008704425.1", "gtdb_species": "s__Streptomyces fradiae", "ani": 80.5442, "matched_fragments": 1168, "total_fragments": 2912, "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": "99.37", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 5, "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": 9699678.0, "gc_content": 72.2, "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": 0.98, "thermophilic_range_tmp": 0.019, "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", "sparsogenes", "DSM", "40356" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }