{ "type": "genome", "identifier": "GCF_000341225.1", "organism": "Nocardiopsis alba DSM 43377", "title": "Nocardiopsis alba DSM 43377", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Yunnan Institute of Microbiology, Yunnan University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000341225.1", "bioproject": "PRJNA224116", "biosample": "SAMN02472146", "wgs_master": "ANAC00000000.1", "refseq_category": "na", "taxid": "1245473", "species_taxid": "53437", "organism_name": "Nocardiopsis alba DSM 43377", "infraspecific_name": "strain=DSM 43377", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/02/19", "asm_name": "SOAPdenovo1.06", "asm_submitter": "Yunnan Institute of Microbiology, Yunnan University", "gbrs_paired_asm": "GCA_000341225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/341/225/GCF_000341225.1_SOAPdenovo1.06", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5820411", "genome_size_ungapped": "5820411", "gc_percent": "70.000000", "replicon_count": "0", "scaffold_count": "55", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000341225.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "5178", "protein_coding_gene_count": "5073", "non_coding_gene_count": "65", "pubmed_id": "23626695" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-02-19", "dateModified": "2013-02-19", "datePublished": "2013-02-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardiopsis alba DSM 43377" ], "sample_taxid": [ "1245473" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.574 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5820411", "Number of Sequences": "55", "Longest Sequences (bp)": "614671", "N50 (bp)": "242463", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.8", "Number of CDSs": "5176", "Average Protein Length": "324.2", "Coding Ratio (%)": "86.5", "Number of rRNAs": "2", "Number of tRNAs": "75", "Number of CRISPRs": "26" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardiopsis alba", "strain": "strain=DSM 43377", "accession": "GCA_000341225.1", "taxid": 53437, "species_taxid": 53437, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1909, "total_fragments": 1913, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardiopsis terrae", "strain": "strain=DSM 45157", "accession": "GCA_014874035.1", "taxid": 372655, "species_taxid": 372655, "relation_to_type": "type", "validated": true, "ani": 84.58, "matched_fragments": 1259, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis exhalans", "strain": "strain=JCM11759T", "accession": "GCA_024134545.1", "taxid": 163604, "species_taxid": 163604, "relation_to_type": "type", "validated": true, "ani": 84.5467, "matched_fragments": 1320, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis prasina", "strain": "strain=DSM 43845", "accession": "GCA_000341265.1", "taxid": 2015, "species_taxid": 2015, "relation_to_type": "type", "validated": true, "ani": 84.5402, "matched_fragments": 1269, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis terrae", "strain": "strain=KCTC 19431", "accession": "GCA_014651695.1", "taxid": 372655, "species_taxid": 372655, "relation_to_type": "type", "validated": true, "ani": 84.5369, "matched_fragments": 1276, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis ganjiahuensis", "strain": "strain=DSM 45031", "accession": "GCA_000341085.1", "taxid": 239984, "species_taxid": 239984, "relation_to_type": "type", "validated": true, "ani": 84.5281, "matched_fragments": 1378, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis metallicus", "strain": "strain=DSM 44598", "accession": "GCA_014201115.1", "taxid": 179819, "species_taxid": 179819, "relation_to_type": "type", "validated": true, "ani": 84.5211, "matched_fragments": 1331, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis listeri", "strain": "strain=NBRC 13360", "accession": "GCA_001570765.1", "taxid": 53440, "species_taxid": 53440, "relation_to_type": "type", "validated": true, "ani": 84.514, "matched_fragments": 1266, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis alkaliphila", "strain": "strain=YIM 80379", "accession": "GCA_000341005.1", "taxid": 225762, "species_taxid": 225762, "relation_to_type": "type", "validated": true, "ani": 83.9057, "matched_fragments": 1112, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis dassonvillei subsp. dassonvillei", "strain": "strain=DSM 43111", "accession": "GCA_000092985.1", "taxid": 568208, "species_taxid": 2014, "relation_to_type": "type", "validated": true, "ani": 82.9362, "matched_fragments": 1205, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis halotolerans", "strain": "strain=DSM 44410", "accession": "GCA_000341065.1", "taxid": 124252, "species_taxid": 124252, "relation_to_type": "type", "validated": true, "ani": 82.7583, "matched_fragments": 1066, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis sinuspersici", "strain": "strain=UTMC 00102", "accession": "GCA_001998325.1", "taxid": 501010, "species_taxid": 501010, "relation_to_type": "type", "validated": true, "ani": 82.7103, "matched_fragments": 1164, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis kunsanensis", "strain": "strain=DSM 44524", "accession": "GCA_000340965.1", "taxid": 141693, "species_taxid": 141693, "relation_to_type": "type", "validated": true, "ani": 81.2799, "matched_fragments": 958, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermobifida alba", "strain": "strain=DSM 43795", "accession": "GCA_023208015.1", "taxid": 53522, "species_taxid": 53522, "relation_to_type": "type", "validated": true, "ani": 79.2888, "matched_fragments": 649, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomonospora litoralis", "strain": "strain=M2", "accession": "GCA_004323735.1", "taxid": 2498135, "species_taxid": 2498135, "relation_to_type": "type", "validated": true, "ani": 79.0355, "matched_fragments": 659, "total_fragments": 1913, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000341225.1", "gtdb_species": "s__Nocardiopsis alba", "ani": 100.0, "matched_fragments": 1909, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.56", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_018207095.1", "gtdb_species": "s__Nocardiopsis sp018207095", "ani": 84.9261, "matched_fragments": 1262, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_900143625.1", "gtdb_species": "s__Nocardiopsis sp900143625", "ani": 84.7436, "matched_fragments": 1300, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_014651695.1", "gtdb_species": "s__Nocardiopsis terrae", "ani": 84.5388, "matched_fragments": 1276, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000341085.1", "gtdb_species": "s__Nocardiopsis ganjiahuensis", "ani": 84.5355, "matched_fragments": 1377, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_000341265.1", "gtdb_species": "s__Nocardiopsis prasina", "ani": 84.5342, "matched_fragments": 1270, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.74", "min_intra_species_ani": "95.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001570765.1", "gtdb_species": "s__Nocardiopsis listeri", "ani": 84.5222, "matched_fragments": 1265, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_014201115.1", "gtdb_species": "s__Nocardiopsis metallicus", "ani": 84.5105, "matched_fragments": 1333, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_018388625.1", "gtdb_species": "s__Nocardiopsis sp018388625", "ani": 84.3572, "matched_fragments": 1333, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_000340985.1", "gtdb_species": "s__Nocardiopsis valliformis", "ani": 84.2404, "matched_fragments": 1319, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_000341005.1", "gtdb_species": "s__Nocardiopsis alkaliphila", "ani": 83.9287, "matched_fragments": 1109, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_000092985.1", "gtdb_species": "s__Nocardiopsis dassonvillei", "ani": 82.9429, "matched_fragments": 1204, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.80", "min_intra_species_ani": "95.11", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_009830945.1", "gtdb_species": "s__Nocardiopsis sp009830945", "ani": 82.8553, "matched_fragments": 1109, "total_fragments": 1913, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.72", "min_intra_species_ani": "99.66", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.359, "cell_length": 0.06, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.0, "optimum_ph": 8.126, "genome_size": 5838944.167, "gc_content": 69.7, "coding_genes": 5045.667, "rRNA16S_genes": 5.0, "tRNA_genes": 55.0, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Nocardiopsis", "alba", "DSM", "43377" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }