{ "type": "genome", "identifier": "GCF_003074055.1", "organism": "Streptomyces nigra", "title": "Streptomyces nigra", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zhejiang university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003074055.1", "bioproject": "PRJNA224116", "biosample": "SAMN08957528", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1827580", "species_taxid": "1827580", "organism_name": "Streptomyces nigra", "infraspecific_name": "strain=452", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/30", "asm_name": "ASM307405v1", "asm_submitter": "Zhejiang university", "gbrs_paired_asm": "GCA_003074055.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/074/055/GCF_003074055.1_ASM307405v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7641029", "genome_size_ungapped": "7641029", "gc_percent": "72.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003074055.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "6985", "protein_coding_gene_count": "6738", "non_coding_gene_count": "92", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-30", "dateModified": "2018-04-30", "datePublished": "2018-04-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces nigra" ], "sample_taxid": [ "1827580" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Zhangzhou city, Fujian province" ], "sample_host_location_id": [], "data_size": "2.039 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 5.21, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7641029", "Number of Sequences": "1", "Longest Sequences (bp)": "7641029", "N50 (bp)": "7641029", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.9", "Number of CDSs": "7047", "Average Protein Length": "320.9", "Coding Ratio (%)": "88.8", "Number of rRNAs": "18", "Number of tRNAs": "81", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces nigra", "strain": "strain=452", "accession": "GCA_003074055.1", "taxid": 1827580, "species_taxid": 1827580, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2547, "total_fragments": 2547, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces chartreusis", "strain": "strain=ATCC 14922", "accession": "GCA_008704715.1", "taxid": 1969, "species_taxid": 1969, "relation_to_type": "suspected-type", "validated": true, "ani": 87.6339, "matched_fragments": 2039, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces chartreusis", "strain": "strain=JCM 4570", "accession": "GCA_014650315.1", "taxid": 1969, "species_taxid": 1969, "relation_to_type": "suspected-type", "validated": true, "ani": 87.5819, "matched_fragments": 2037, "total_fragments": 2547, "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": 87.3887, "matched_fragments": 1936, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces zinciresistens", "strain": "strain=K42", "accession": "GCA_000225525.2", "taxid": 1073330, "species_taxid": 1073330, "relation_to_type": "type", "validated": true, "ani": 87.2912, "matched_fragments": 1662, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces curacoi", "strain": "strain=DSM 40107", "accession": "GCA_001513975.1", "taxid": 146536, "species_taxid": 146536, "relation_to_type": "type", "validated": true, "ani": 87.2573, "matched_fragments": 1818, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces caeruleatus", "strain": "strain=NRRL B-24802", "accession": "GCA_001514235.1", "taxid": 661399, "species_taxid": 661399, "relation_to_type": "type", "validated": true, "ani": 87.1811, "matched_fragments": 1923, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces lanatus", "strain": "strain=JCM 4588", "accession": "GCA_014655715.1", "taxid": 66900, "species_taxid": 66900, "relation_to_type": "type", "validated": true, "ani": 87.1332, "matched_fragments": 1962, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces cyaneochromogenes", "strain": "strain=MK-45", "accession": "GCA_003963535.1", "taxid": 2496836, "species_taxid": 2496836, "relation_to_type": "type", "validated": true, "ani": 87.0857, "matched_fragments": 1975, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces justiciae", "strain": "strain=3R004", "accession": "GCA_015163075.1", "taxid": 2780140, "species_taxid": 2780140, "relation_to_type": "type", "validated": true, "ani": 85.3279, "matched_fragments": 1842, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces calvus", "strain": "strain=CECT 3271", "accession": "GCA_014138735.1", "taxid": 67282, "species_taxid": 67282, "relation_to_type": "type", "validated": true, "ani": 85.3109, "matched_fragments": 1680, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces calvus", "strain": "strain=JCM 4326", "accession": "GCA_014649315.1", "taxid": 67282, "species_taxid": 67282, "relation_to_type": "type", "validated": true, "ani": 85.3073, "matched_fragments": 1697, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces solaniscabiei", "strain": "strain=FS70", "accession": "GCA_020312315.1", "taxid": 2683255, "species_taxid": 2683255, "relation_to_type": "type", "validated": true, "ani": 85.2737, "matched_fragments": 1663, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces griseicoloratus", "strain": "strain=TRM S81-3", "accession": "GCA_014534645.1", "taxid": 2752516, "species_taxid": 2752516, "relation_to_type": "type", "validated": true, "ani": 85.2668, "matched_fragments": 1669, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces plumbidurans", "strain": "strain=KC 17012", "accession": "GCA_019857225.1", "taxid": 2814589, "species_taxid": 2814589, "relation_to_type": "type", "validated": true, "ani": 85.1923, "matched_fragments": 1721, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces viridiviolaceus", "strain": "strain=JCM 4855", "accession": "GCA_014650995.1", "taxid": 68282, "species_taxid": 68282, "relation_to_type": "type", "validated": true, "ani": 85.1859, "matched_fragments": 1696, "total_fragments": 2547, "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": 85.1772, "matched_fragments": 1774, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces viridosporus", "strain": "strain=NRRL 2414", "accession": "GCA_002078235.1", "taxid": 67581, "species_taxid": 67581, "relation_to_type": "type", "validated": true, "ani": 85.1221, "matched_fragments": 1334, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces malachitofuscus", "strain": "strain=JCM 4493", "accession": "GCA_014650055.1", "taxid": 67322, "species_taxid": 67322, "relation_to_type": "type", "validated": true, "ani": 85.1142, "matched_fragments": 1689, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces harenosi", "strain": "strain=PRKS01-65", "accession": "GCA_011008945.1", "taxid": 2697029, "species_taxid": 2697029, "relation_to_type": "type", "validated": true, "ani": 85.0179, "matched_fragments": 1387, "total_fragments": 2547, "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": 85.0107, "matched_fragments": 1621, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces griseoflavus", "strain": "strain=JCM 4479", "accession": "GCA_014649995.1", "taxid": 35619, "species_taxid": 35619, "relation_to_type": "type", "validated": true, "ani": 84.9718, "matched_fragments": 1612, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces pilosus", "strain": "strain=JCM 4403", "accession": "GCA_014649835.1", "taxid": 28893, "species_taxid": 28893, "relation_to_type": "type", "validated": true, "ani": 84.9626, "matched_fragments": 1621, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces ardesiacus", "strain": "strain=NBRC 15402", "accession": "GCA_003112575.1", "taxid": 285564, "species_taxid": 285564, "relation_to_type": "type", "validated": true, "ani": 84.8401, "matched_fragments": 1613, "total_fragments": 2547, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 5.21, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003074055.1", "gtdb_species": "s__Streptomyces nigra", "ani": 100.0, "matched_fragments": 2547, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.21", "min_intra_species_ani": "97.15", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_001509795.1", "gtdb_species": "s__Streptomyces sp001509795", "ani": 93.0816, "matched_fragments": 2189, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_008973465.1", "gtdb_species": "s__Streptomyces sp008973465", "ani": 93.0782, "matched_fragments": 2221, "total_fragments": 2547, "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_008704715.1", "gtdb_species": "s__Streptomyces chartreusis", "ani": 87.661, "matched_fragments": 2037, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.83", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_008042075.1", "gtdb_species": "s__Streptomyces sp008042075", "ani": 87.3914, "matched_fragments": 1965, "total_fragments": 2547, "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_015160855.1", "gtdb_species": "s__Streptomyces ferrugineus", "ani": 87.3856, "matched_fragments": 1934, "total_fragments": 2547, "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_001513975.1", "gtdb_species": "s__Streptomyces curacoi", "ani": 87.2645, "matched_fragments": 1817, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "97.22", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000719285.1", "gtdb_species": "s__Streptomyces bicolor", "ani": 87.2229, "matched_fragments": 1860, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001514235.1", "gtdb_species": "s__Streptomyces caeruleatus", "ani": 87.1534, "matched_fragments": 1927, "total_fragments": 2547, "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_014655715.1", "gtdb_species": "s__Streptomyces lanatus", "ani": 87.1102, "matched_fragments": 1967, "total_fragments": 2547, "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_019049285.1", "gtdb_species": "s__Streptomyces sp019049285", "ani": 87.095, "matched_fragments": 1868, "total_fragments": 2547, "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_018604545.1", "gtdb_species": "s__Streptomyces sp018604545", "ani": 85.4773, "matched_fragments": 1760, "total_fragments": 2547, "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_001905725.1", "gtdb_species": "s__Streptomyces sp001905725", "ani": 85.2146, "matched_fragments": 1710, "total_fragments": 2547, "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_003665435.1", "gtdb_species": "s__Streptomyces fungicidicus_A", "ani": 85.2013, "matched_fragments": 1679, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_014656175.1", "gtdb_species": "s__Streptomyces werraensis", "ani": 85.0052, "matched_fragments": 1660, "total_fragments": 2547, "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_014649575.1", "gtdb_species": "s__Streptomyces griseoincarnatus", "ani": 84.9646, "matched_fragments": 1670, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.374, "mean_intra_species_ani": "98.24", "min_intra_species_ani": "97.52", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_014649835.1", "gtdb_species": "s__Streptomyces pilosus", "ani": 84.9522, "matched_fragments": 1622, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "99.43", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_000715605.1", "gtdb_species": "s__Streptomyces speibonae", "ani": 84.7446, "matched_fragments": 1669, "total_fragments": 2547, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.201, "cell_length": -0.05, "doubling_h": 0.103, "growth_tmp": 27.757, "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": 0.998, "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", "nigra" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }