{ "type": "genome", "identifier": "GCF_000620785.1", "organism": "Pseudonocardia acaciae DSM 45401", "title": "Pseudonocardia acaciae DSM 45401", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000620785.1", "bioproject": "PRJNA224116", "biosample": "SAMN02743958", "wgs_master": "JIAI00000000.1", "refseq_category": "reference genome", "taxid": "1123023", "species_taxid": "551276", "organism_name": "Pseudonocardia acaciae DSM 45401", "infraspecific_name": "strain=DSM 45401", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/04/08", "asm_name": "ASM62078v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000620785.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/620/785/GCF_000620785.1_ASM62078v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9931328", "genome_size_ungapped": "9931013", "gc_percent": "72.500000", "replicon_count": "0", "scaffold_count": "94", "contig_count": "95", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000620785.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "9616", "protein_coding_gene_count": "9445", "non_coding_gene_count": "78", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-04-08", "dateModified": "2014-04-08", "datePublished": "2014-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudonocardia acaciae DSM 45401" ], "sample_taxid": [ "1123023" ], "sample_host_organism": [ "Acacia auriculiformis" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand" ], "sample_host_location_id": [], "data_size": "2.636 MB", "sample_ph_range": { "min": 58.0, "max": 58.0 }, "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)": "9931328", "Number of Sequences": "94", "Longest Sequences (bp)": "1971216", "N50 (bp)": "506097", "Gap Ratio (%)": "0.003172", "GCcontent (%)": "72.3", "Number of CDSs": "9554", "Average Protein Length": "312.6", "Coding Ratio (%)": "90.2", "Number of rRNAs": "3", "Number of tRNAs": "96", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudonocardia acaciae", "strain": "strain=DSM 45401", "accession": "GCA_000620785.1", "taxid": 551276, "species_taxid": 551276, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3260, "total_fragments": 3262, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudonocardia spinosispora", "strain": "strain=DSM 44797", "accession": "GCA_000429025.1", "taxid": 103441, "species_taxid": 103441, "relation_to_type": "type", "validated": true, "ani": 79.6636, "matched_fragments": 1361, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia bannensis", "strain": "strain=DSM 45300", "accession": "GCA_012911875.1", "taxid": 630973, "species_taxid": 630973, "relation_to_type": "type", "validated": true, "ani": 78.7711, "matched_fragments": 879, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia acidicola", "strain": "strain=K10HN5", "accession": "GCA_012911935.1", "taxid": 2724939, "species_taxid": 2724939, "relation_to_type": "type", "validated": true, "ani": 78.5461, "matched_fragments": 1043, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia hydrocarbonoxydans", "strain": "strain=NBRC 14498", "accession": "GCA_006539565.1", "taxid": 76726, "species_taxid": 76726, "relation_to_type": "type", "validated": true, "ani": 78.1643, "matched_fragments": 931, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia kunmingensis", "strain": "strain=DSM 45301", "accession": "GCA_006716445.1", "taxid": 630975, "species_taxid": 630975, "relation_to_type": "type", "validated": true, "ani": 77.9008, "matched_fragments": 1245, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia oroxyli", "strain": "strain=CGMCC 4.3143", "accession": "GCA_900102195.1", "taxid": 366584, "species_taxid": 366584, "relation_to_type": "type", "validated": true, "ani": 77.9001, "matched_fragments": 869, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia petroleophila", "strain": "strain=CGMCC 4.1532", "accession": "GCA_014235185.1", "taxid": 37331, "species_taxid": 37331, "relation_to_type": "type", "validated": true, "ani": 77.8334, "matched_fragments": 1038, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia terrae", "strain": "strain=RS11V-5", "accession": "GCA_021343995.1", "taxid": 2905831, "species_taxid": 2905831, "relation_to_type": "type", "validated": true, "ani": 77.7677, "matched_fragments": 1043, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia pini", "strain": "strain=CAP47R", "accession": "GCA_013870575.1", "taxid": 2758030, "species_taxid": 2758030, "relation_to_type": "type", "validated": true, "ani": 77.7065, "matched_fragments": 607, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharopolyspora subtropica", "strain": "strain=CGMCC 4.7206", "accession": "GCA_014646075.1", "taxid": 1530170, "species_taxid": 1530170, "relation_to_type": "type", "validated": true, "ani": 77.5864, "matched_fragments": 752, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia autotrophica", "strain": "strain=NBRC 12743", "accession": "GCA_003945385.1", "taxid": 2074, "species_taxid": 2074, "relation_to_type": "suspected-type", "validated": true, "ani": 77.3776, "matched_fragments": 1032, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix tamanrassetensis", "strain": "strain=CECT 8640", "accession": "GCA_014203665.1", "taxid": 1051531, "species_taxid": 1051531, "relation_to_type": "type", "validated": true, "ani": 77.293, "matched_fragments": 986, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora enzanensis", "strain": "strain=DSM 44649", "accession": "GCA_000374445.1", "taxid": 155975, "species_taxid": 155975, "relation_to_type": "type", "validated": true, "ani": 77.1719, "matched_fragments": 879, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora cianjurensis", "strain": "strain=DSM 45657", "accession": "GCA_003663795.1", "taxid": 585224, "species_taxid": 585224, "relation_to_type": "type", "validated": true, "ani": 77.126, "matched_fragments": 830, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora terrae", "strain": "strain=DSM 44260", "accession": "GCA_900111175.1", "taxid": 155974, "species_taxid": 155974, "relation_to_type": "type", "validated": true, "ani": 77.0802, "matched_fragments": 843, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora auranticolor", "strain": "strain=YU 961-1", "accession": "GCA_002934265.1", "taxid": 155976, "species_taxid": 155976, "relation_to_type": "type", "validated": true, "ani": 76.9513, "matched_fragments": 967, "total_fragments": 3262, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000620785.1", "gtdb_species": "s__Pseudonocardia acaciae", "ani": 100.0, "matched_fragments": 3260, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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": "conclusive" }, { "accession": "GCF_014208095.1", "gtdb_species": "s__Pseudonocardia eucalypti", "ani": 81.4737, "matched_fragments": 1629, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_000429025.1", "gtdb_species": "s__Pseudonocardia spinosispora", "ani": 79.6837, "matched_fragments": 1357, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_013695005.1", "gtdb_species": "s__Pseudonocardia sp013695005", "ani": 79.1469, "matched_fragments": 393, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_012911875.1", "gtdb_species": "s__Pseudonocardia bannensis", "ani": 78.7394, "matched_fragments": 885, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_012911935.1", "gtdb_species": "s__Pseudonocardia sp012911935", "ani": 78.4778, "matched_fragments": 1062, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_006539565.1", "gtdb_species": "s__Pseudonocardia hydrocarbonoxydans", "ani": 78.1804, "matched_fragments": 926, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_019263595.1", "gtdb_species": "s__Pseudonocardia sp019263595", "ani": 78.0465, "matched_fragments": 890, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_005405885.1", "gtdb_species": "s__Gandjariella thermophila", "ani": 77.9949, "matched_fragments": 930, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella", "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_006716445.1", "gtdb_species": "s__Pseudonocardia kunmingensis", "ani": 77.9262, "matched_fragments": 1237, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_900102195.1", "gtdb_species": "s__Pseudonocardia oroxyli", "ani": 77.8972, "matched_fragments": 871, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_014235185.1", "gtdb_species": "s__Pseudonocardia sp014235185", "ani": 77.8405, "matched_fragments": 1035, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_001698125.1", "gtdb_species": "s__Pseudonocardia sp001698125", "ani": 77.4219, "matched_fragments": 981, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_003945385.1", "gtdb_species": "s__Pseudonocardia autotrophica", "ani": 77.3709, "matched_fragments": 1034, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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": 4, "status": "-" }, { "accession": "GCF_000374445.1", "gtdb_species": "s__Actinokineospora enzanensis", "ani": 77.1411, "matched_fragments": 890, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora", "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_002934265.1", "gtdb_species": "s__Actinokineospora auranticolor", "ani": 76.9526, "matched_fragments": 966, "total_fragments": 3262, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora", "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": -0.019, "cell_length": 0.157, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 6.5, "genome_size": 9931328.0, "gc_content": 71.383, "coding_genes": 6678.667, "rRNA16S_genes": 3.0, "tRNA_genes": 46.0, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.0, "range_salinity": null, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudonocardia", "acaciae", "DSM", "45401" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }