{ "type": "genome", "identifier": "GCF_000730585.1", "organism": "Pseudomonas japonica NBRC 103040 = DSM 22348", "title": "Pseudomonas japonica NBRC 103040 = DSM 22348", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000730585.1", "bioproject": "PRJNA224116", "biosample": "SAMD00018431", "wgs_master": "BBIR00000000.1", "refseq_category": "reference genome", "taxid": "1215104", "species_taxid": "256466", "organism_name": "Pseudomonas japonica NBRC 103040 = DSM 22348", "infraspecific_name": "strain=NBRC 103040", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/07/10", "asm_name": "ASM73058v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_000730585.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/730/585/GCF_000730585.1_ASM73058v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6663130", "genome_size_ungapped": "6663130", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "162", "contig_count": "162", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000730585.1-RS_2024_08_08", "annotation_date": "2024-08-08", "total_gene_count": "5902", "protein_coding_gene_count": "5772", "non_coding_gene_count": "69", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-07-10", "dateModified": "2014-07-10", "datePublished": "2014-07-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas japonica NBRC 103040 = DSM 22348" ], "sample_taxid": [ "1215104" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Tokyo" ], "sample_host_location_id": [], "data_size": "1.844 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)": "6663130", "Number of Sequences": "162", "Longest Sequences (bp)": "311301", "N50 (bp)": "88070", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.2", "Number of CDSs": "5814", "Average Protein Length": "338.8", "Coding Ratio (%)": "88.7", "Number of rRNAs": "4", "Number of tRNAs": "66", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas japonica", "strain": "strain=NBRC 103040", "accession": "GCA_000730585.1", "taxid": 256466, "species_taxid": 256466, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2131, "total_fragments": 2140, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas japonica", "strain": "strain=DSM 22348", "accession": "GCA_900188455.1", "taxid": 256466, "species_taxid": 256466, "relation_to_type": "type", "validated": true, "ani": 99.9859, "matched_fragments": 2125, "total_fragments": 2140, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas bharatica", "strain": "strain=CSV86", "accession": "GCA_000319305.2", "taxid": 2692112, "species_taxid": 2692112, "relation_to_type": "type", "validated": true, "ani": 88.2682, "matched_fragments": 1496, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_013373935.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 85.102, "matched_fragments": 1139, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_021602585.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 85.066, "matched_fragments": 1191, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicae", "strain": "strain=MAFF 212427", "accession": "GCA_010671725.1", "taxid": 2708063, "species_taxid": 2708063, "relation_to_type": "type", "validated": true, "ani": 84.7792, "matched_fragments": 1029, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alkylphenolica", "strain": "strain=KL28", "accession": "GCA_000746525.1", "taxid": 237609, "species_taxid": 237609, "relation_to_type": "type", "validated": true, "ani": 84.5696, "matched_fragments": 1149, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas vranovensis", "strain": "strain=DSM 16006", "accession": "GCA_000425805.1", "taxid": 321661, "species_taxid": 321661, "relation_to_type": "type", "validated": true, "ani": 84.2146, "matched_fragments": 1192, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas urethralis", "strain": "strain=BML-PP042", "accession": "GCA_021602465.1", "taxid": 2740517, "species_taxid": 2740517, "relation_to_type": "suspected-type", "validated": true, "ani": 84.0177, "matched_fragments": 1173, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas capeferrum", "strain": "strain=WCS358", "accession": "GCA_022548835.1", "taxid": 1495066, "species_taxid": 1495066, "relation_to_type": "type", "validated": true, "ani": 83.923, "matched_fragments": 1096, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aurantiaca", "strain": "strain=DSM 19603", "accession": "GCA_003851835.1", "taxid": 86192, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 83.4206, "matched_fragments": 1213, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas defluvii", "strain": "strain=WCHP16", "accession": "GCA_001695625.1", "taxid": 1876757, "species_taxid": 1876757, "relation_to_type": "type", "validated": true, "ani": 83.0505, "matched_fragments": 948, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas laurentiana", "strain": "strain=JCM 32154", "accession": "GCA_014648275.1", "taxid": 2364649, "species_taxid": 2364649, "relation_to_type": "type", "validated": true, "ani": 82.8114, "matched_fragments": 1025, "total_fragments": 2140, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900188455.1", "gtdb_species": "s__Pseudomonas_E japonica", "ani": 99.9859, "matched_fragments": 2125, "total_fragments": 2140, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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": "conclusive" }, { "accession": "GCF_001941965.1", "gtdb_species": "s__Pseudomonas_E putida_L", "ani": 89.2681, "matched_fragments": 1561, "total_fragments": 2140, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_003523465.1", "gtdb_species": "s__Pseudomonas_E sp003523465", "ani": 88.9416, "matched_fragments": 682, "total_fragments": 2140, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_000319305.2", "gtdb_species": "s__Pseudomonas_E putida_C", "ani": 88.3162, "matched_fragments": 1491, "total_fragments": 2140, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.35", "min_intra_species_ani": "97.35", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900187455.1", "gtdb_species": "s__Pseudomonas_E sp900187455", "ani": 87.6868, "matched_fragments": 1556, "total_fragments": 2140, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_003231275.1", "gtdb_species": "s__Pseudomonas_E huaxiensis", "ani": 87.4145, "matched_fragments": 1537, "total_fragments": 2140, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.93", "min_intra_species_ani": "95.93", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003105155.1", "gtdb_species": "s__Pseudomonas_E sp003105155", "ani": 85.3274, "matched_fragments": 1172, "total_fragments": 2140, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_004214895.1", "gtdb_species": "s__Pseudomonas_E sp004214895", "ani": 84.7562, "matched_fragments": 1229, "total_fragments": 2140, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.0, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 6681622.667, "gc_content": 64.099, "coding_genes": 5204.79, "rRNA16S_genes": 5.319, "tRNA_genes": 67.35, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.666, "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": [ "Pseudomonas", "japonica", "NBRC", "103040", "=", "DSM", "22348" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }