{ "type": "genome", "identifier": "GCF_003675955.1", "organism": "Streptomyces rapamycinicus NRRL 5491", "title": "Streptomyces rapamycinicus NRRL 5491", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Novartis AG", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003675955.1", "bioproject": "PRJNA224116", "biosample": "SAMN02604192", "wgs_master": "QYCY00000000.1", "refseq_category": "na", "taxid": "1343740", "species_taxid": "1226757", "organism_name": "Streptomyces rapamycinicus NRRL 5491", "infraspecific_name": "strain=NRRL 5491", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/23", "asm_name": "ASM367595v1", "asm_submitter": "Novartis AG", "gbrs_paired_asm": "GCA_003675955.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/675/955/GCF_003675955.1_ASM367595v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "12663199", "genome_size_ungapped": "12663199", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003675955.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "10419", "protein_coding_gene_count": "9905", "non_coding_gene_count": "90", "pubmed_id": "30327433" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-23", "dateModified": "2018-10-23", "datePublished": "2018-10-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces rapamycinicus NRRL 5491" ], "sample_taxid": [ "1343740" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "3.364 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)": "12663199", "Number of Sequences": "4", "Longest Sequences (bp)": "6854462", "N50 (bp)": "6854462", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.0", "Number of CDSs": "10505", "Average Protein Length": "357.5", "Coding Ratio (%)": "89.0", "Number of rRNAs": "18", "Number of tRNAs": "91", "Number of CRISPRs": "7" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces rapamycinicus", "strain": "strain=NRRL 5491", "accession": "GCA_003675955.1", "taxid": 1226757, "species_taxid": 1226757, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 4217, "total_fragments": 4219, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Streptomyces rapamycinicus", "strain": "strain=DSM 41530", "accession": "GCA_014205315.1", "taxid": 1226757, "species_taxid": 1226757, "relation_to_type": "type", "validated": true, "ani": 99.996, "matched_fragments": 4191, "total_fragments": 4219, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Streptomyces rapamycinicus", "strain": "strain=NRRL 5491", "accession": "GCA_024298965.1", "taxid": 1226757, "species_taxid": 1226757, "relation_to_type": "type", "validated": true, "ani": 99.9916, "matched_fragments": 4155, "total_fragments": 4219, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Streptomyces rapamycinicus", "strain": "strain=NRRL 5491", "accession": "GCA_000418455.1", "taxid": 1226757, "species_taxid": 1226757, "relation_to_type": "type", "validated": true, "ani": 99.9027, "matched_fragments": 4167, "total_fragments": 4219, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Streptomyces iranensis", "strain": "strain=DSM 41954", "accession": "GCA_017874715.1", "taxid": 576784, "species_taxid": 576784, "relation_to_type": "type", "validated": true, "ani": 95.6427, "matched_fragments": 3231, "total_fragments": 4219, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Streptomyces javensis", "strain": "strain=DSM 41764", "accession": "GCA_016103505.1", "taxid": 114698, "species_taxid": 114698, "relation_to_type": "type", "validated": true, "ani": 94.5048, "matched_fragments": 2363, "total_fragments": 4219, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces paromomycinus", "strain": "strain=NBRC 15454", "accession": "GCA_003865155.1", "taxid": 92743, "species_taxid": 92743, "relation_to_type": "type", "validated": true, "ani": 80.9723, "matched_fragments": 1640, "total_fragments": 4219, "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": 80.9702, "matched_fragments": 1475, "total_fragments": 4219, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces rimosus subsp. rimosus", "strain": "strain=R7", "accession": "GCA_022760195.1", "taxid": 132474, "species_taxid": 1927, "relation_to_type": "type", "validated": true, "ani": 80.8882, "matched_fragments": 1618, "total_fragments": 4219, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces sennicomposti", "strain": "strain=RCPT1-4", "accession": "GCA_019890635.1", "taxid": 2873384, "species_taxid": 2873384, "relation_to_type": "type", "validated": true, "ani": 80.3335, "matched_fragments": 1345, "total_fragments": 4219, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003675955.1", "gtdb_species": "s__Streptomyces rapamycinicus", "ani": 100.0, "matched_fragments": 4217, "total_fragments": 4219, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.67, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_017874715.1", "gtdb_species": "s__Streptomyces iranensis", "ani": 95.6348, "matched_fragments": 3232, "total_fragments": 4219, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.67, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016741935.1", "gtdb_species": "s__Streptomyces sp016741935", "ani": 94.8284, "matched_fragments": 3184, "total_fragments": 4219, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0488, "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_018138715.1", "gtdb_species": "s__Streptomyces asiaticus", "ani": 94.753, "matched_fragments": 3173, "total_fragments": 4219, "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": "GCA_005405945.1", "gtdb_species": "s__Streptomyces violaceusniger", "ani": 94.1512, "matched_fragments": 3069, "total_fragments": 4219, "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_000968685.2", "gtdb_species": "s__Streptomyces antioxidans", "ani": 93.546, "matched_fragments": 2514, "total_fragments": 4219, "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": "-" } ] }, "_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": 8502949.0, "gc_content": 71.543, "coding_genes": 10002.0, "rRNA16S_genes": 6.155, "tRNA_genes": 67.804, "gram_stain": 1.0, "sporulation": 1.0, "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", "rapamycinicus", "NRRL", "5491" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }