{ "type": "genome", "identifier": "GCF_014649875.1", "organism": "Streptomyces rubiginosohelvolus", "title": "Streptomyces rubiginosohelvolus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014649875.1", "bioproject": "PRJNA224116", "biosample": "SAMD00245448", "wgs_master": "BMTW00000000.1", "refseq_category": "reference genome", "taxid": "67362", "species_taxid": "67362", "organism_name": "Streptomyces rubiginosohelvolus", "infraspecific_name": "strain=JCM 4415", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/12", "asm_name": "ASM1464987v1", "asm_submitter": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "gbrs_paired_asm": "GCA_014649875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/649/875/GCF_014649875.1_ASM1464987v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7548572", "genome_size_ungapped": "7547769", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "40", "contig_count": "40", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014649875.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "6838", "protein_coding_gene_count": "6652", "non_coding_gene_count": "71", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-12", "dateModified": "2020-09-12", "datePublished": "2020-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces rubiginosohelvolus" ], "sample_taxid": [ "67362" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "2.023 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 9.38, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7548572", "Number of Sequences": "40", "Longest Sequences (bp)": "1555311", "N50 (bp)": "350824", "Gap Ratio (%)": "0.010638", "GCcontent (%)": "71.7", "Number of CDSs": "6840", "Average Protein Length": "328.3", "Coding Ratio (%)": "89.2", "Number of rRNAs": "2", "Number of tRNAs": "82", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces parvus", "strain": "strain=JCM 4069", "accession": "GCA_014648875.1", "taxid": 66428, "species_taxid": 66428, "relation_to_type": "type", "validated": true, "ani": 95.2155, "matched_fragments": 2136, "total_fragments": 2495, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces parvus", "strain": "strain=NRRL B-1455", "accession": "GCA_008632535.1", "taxid": 66428, "species_taxid": 66428, "relation_to_type": "type", "validated": true, "ani": 95.0932, "matched_fragments": 1926, "total_fragments": 2495, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces sindenensis", "strain": "strain=JCM 4164", "accession": "GCA_014649035.1", "taxid": 67363, "species_taxid": 67363, "relation_to_type": "type", "validated": true, "ani": 94.5756, "matched_fragments": 2028, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces badius", "strain": "strain=JCM 4350", "accession": "GCA_014649415.1", "taxid": 1941, "species_taxid": 1941, "relation_to_type": "type", "validated": true, "ani": 94.4191, "matched_fragments": 2027, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces anulatus", "strain": "strain=JCM 4721", "accession": "GCA_014650675.1", "taxid": 1892, "species_taxid": 1892, "relation_to_type": "type", "validated": true, "ani": 92.3775, "matched_fragments": 2134, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces griseus", "strain": "strain=DSM 40236", "accession": "GCA_900105705.1", "taxid": 1911, "species_taxid": 1911, "relation_to_type": "type", "validated": true, "ani": 91.9294, "matched_fragments": 2088, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces californicus", "strain": "strain=FDAARGOS_1209", "accession": "GCA_016906185.1", "taxid": 67351, "species_taxid": 67351, "relation_to_type": "type", "validated": true, "ani": 90.7456, "matched_fragments": 2024, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces microflavus", "strain": "strain=JCM 4496", "accession": "GCA_014650075.1", "taxid": 1919, "species_taxid": 1919, "relation_to_type": "type", "validated": true, "ani": 89.8665, "matched_fragments": 2017, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces rhizosphaericola", "strain": "strain=1AS2c", "accession": "GCA_004794175.1", "taxid": 2564098, "species_taxid": 2564098, "relation_to_type": "type", "validated": true, "ani": 89.1495, "matched_fragments": 1580, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Kitasatospora] papulosa", "strain": "strain=NRRL B-16504", "accession": "GCA_000717245.1", "taxid": 1464011, "species_taxid": 1464011, "relation_to_type": "type", "validated": true, "ani": 84.8028, "matched_fragments": 1596, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces lichenis", "strain": "strain=LCR6-01", "accession": "GCA_023218175.1", "taxid": 2306967, "species_taxid": 2306967, "relation_to_type": "type", "validated": true, "ani": 82.7581, "matched_fragments": 1372, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces genisteinicus", "strain": "strain=CRPJ-33", "accession": "GCA_014489615.1", "taxid": 2768068, "species_taxid": 2768068, "relation_to_type": "type", "validated": true, "ani": 82.551, "matched_fragments": 1484, "total_fragments": 2495, "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": 81.3278, "matched_fragments": 1208, "total_fragments": 2495, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 9.38, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014649875.1", "gtdb_species": "s__Streptomyces rubiginosohelvolus", "ani": 100.0, "matched_fragments": 2493, "total_fragments": 2495, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 96.2941, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "96.67", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 22, "status": "conclusive" }, { "accession": "GCA_014649555.1", "gtdb_species": "s__Streptomyces globisporus", "ani": 96.2784, "matched_fragments": 2225, "total_fragments": 2495, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 96.2941, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "97.57", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_003501885.1", "gtdb_species": "s__Streptomyces globisporus_D", "ani": 95.5696, "matched_fragments": 1926, "total_fragments": 2495, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.6693, "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_014648875.1", "gtdb_species": "s__Streptomyces parvus", "ani": 95.225, "matched_fragments": 2135, "total_fragments": 2495, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.2347, "mean_intra_species_ani": "97.39", "min_intra_species_ani": "96.11", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.79", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_000718455.1", "gtdb_species": "s__Streptomyces globisporus_A", "ani": 95.2151, "matched_fragments": 2036, "total_fragments": 2495, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.2621, "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_001687325.1", "gtdb_species": "s__Streptomyces sp001687325", "ani": 94.9891, "matched_fragments": 2094, "total_fragments": 2495, "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_014649035.1", "gtdb_species": "s__Streptomyces sindenensis", "ani": 94.5737, "matched_fragments": 2028, "total_fragments": 2495, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0775, "mean_intra_species_ani": "95.83", "min_intra_species_ani": "95.78", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.84", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_018866325.1", "gtdb_species": "s__Streptomyces sp001895105", "ani": 93.761, "matched_fragments": 2031, "total_fragments": 2495, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.85", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002551355.1", "gtdb_species": "s__Streptomyces sp002551355", "ani": 93.4479, "matched_fragments": 2101, "total_fragments": 2495, "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_002154345.1", "gtdb_species": "s__Streptomyces fimicarius", "ani": 92.6729, "matched_fragments": 1751, "total_fragments": 2495, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.88", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.81", "num_clustered_genomes": 11, "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": 8292419.302, "gc_content": 71.543, "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", "rubiginosohelvolus" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }