{ "type": "genome", "identifier": "GCF_000420025.1", "organism": "Patulibacter americanus DSM 16676", "title": "Patulibacter americanus DSM 16676", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000420025.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440564", "wgs_master": "ATUD00000000.1", "refseq_category": "reference genome", "taxid": "1122939", "species_taxid": "588672", "organism_name": "Patulibacter americanus DSM 16676", "infraspecific_name": "strain=DSM 16676", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/09", "asm_name": "ASM42002v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000420025.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/420/025/GCF_000420025.1_ASM42002v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4470560", "genome_size_ungapped": "4470560", "gc_percent": "74.500000", "replicon_count": "0", "scaffold_count": "32", "contig_count": "32", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000420025.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "4171", "protein_coding_gene_count": "4078", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-09", "dateModified": "2013-07-09", "datePublished": "2013-07-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Patulibacter americanus DSM 16676" ], "sample_taxid": [ "1122939" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.167 MB", "sample_ph_range": { "min": 59.0, "max": 59.0 }, "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)": "4470560", "Number of Sequences": "32", "Longest Sequences (bp)": "888876", "N50 (bp)": "279502", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "74.4", "Number of CDSs": "4111", "Average Protein Length": "329.8", "Coding Ratio (%)": "91.0", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Patulibacter americanus", "strain": "strain=DSM 16676", "accession": "GCA_000420025.1", "taxid": 588672, "species_taxid": 588672, 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"ani": 77.2462, "matched_fragments": 556, "total_fragments": 1474, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Conexibacter arvalis", "strain": "strain=DSM 23288", "accession": "GCA_014199525.1", "taxid": 912552, "species_taxid": 912552, "relation_to_type": "type", "validated": true, "ani": 76.9607, "matched_fragments": 618, "total_fragments": 1474, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Capillimicrobium parvum", "strain": "strain=0166_1", "accession": "GCA_021172045.1", "taxid": 2884022, "species_taxid": 2884022, "relation_to_type": "type", "validated": true, "ani": 76.8312, "matched_fragments": 554, "total_fragments": 1474, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Conexibacter woesei", "strain": "strain=DSM 14684", "accession": "GCA_000025265.1", "taxid": 191495, "species_taxid": 191495, "relation_to_type": "type", "validated": true, "ani": 76.8093, "matched_fragments": 625, "total_fragments": 1474, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium rhizomatis", "strain": "strain=JCM 30598", "accession": "GCA_008710745.1", "taxid": 1631477, "species_taxid": 1631477, "relation_to_type": "type", "validated": true, "ani": 75.1912, "matched_fragments": 147, "total_fragments": 1474, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium helvum", "strain": "strain=NEAU-LLC", "accession": "GCA_014779795.1", "taxid": 2773713, "species_taxid": 2773713, "relation_to_type": "type", "validated": true, "ani": 75.1216, "matched_fragments": 232, "total_fragments": 1474, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter algicola", "strain": "strain=CrO1", "accession": "GCA_016641735.1", "taxid": 2795217, "species_taxid": 2795217, "relation_to_type": "type", "validated": true, "ani": 75.0292, "matched_fragments": 177, "total_fragments": 1474, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000420025.1", "gtdb_species": "s__Patulibacter americanus", "ani": 100.0, "matched_fragments": 1473, "total_fragments": 1474, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter", "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_017916475.1", "gtdb_species": "s__Patulibacter sp017916475", "ani": 82.9218, "matched_fragments": 947, "total_fragments": 1474, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_015478825.1", "gtdb_species": "s__Patulibacter sp015478825", "ani": 80.4327, "matched_fragments": 538, "total_fragments": 1474, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter", "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_000240225.1", "gtdb_species": "s__Patulibacter medicamentivorans", "ani": 80.0906, "matched_fragments": 720, "total_fragments": 1474, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter", "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_017084525.1", "gtdb_species": "s__Baekduia sp017084525", "ani": 77.4087, "matched_fragments": 591, "total_fragments": 1474, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia", "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_016463765.1", "gtdb_species": "s__SYBY01 sp016463765", "ani": 76.839, "matched_fragments": 448, "total_fragments": 1474, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01", "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_000688095.1", "gtdb_species": "s__Baekduia sp000688095", "ani": 76.7932, "matched_fragments": 607, "total_fragments": 1474, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia", "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": -0.359, "cell_length": 0.001, "doubling_h": null, "growth_tmp": 27.0, "optimum_tmp": 29.0, "optimum_ph": 7.0, "genome_size": 4470560.0, "gc_content": 74.1, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 1.0, "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": [ "Patulibacter", "americanus", "DSM", "16676" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }