{ "type": "genome", "identifier": "GCF_002091595.1", "organism": "Pseudomonas fluorescens NBRC 14160", "title": "Pseudomonas fluorescens NBRC 14160", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002091595.1", "bioproject": "PRJNA224116", "biosample": "SAMD00018759", "wgs_master": "BDAA00000000.1", "refseq_category": "na", "taxid": "1215100", "species_taxid": "294", "organism_name": "Pseudomonas fluorescens NBRC 14160", "infraspecific_name": "strain=NBRC 14160", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/03", "asm_name": "ASM209159v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_002091595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/091/595/GCF_002091595.1_ASM209159v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6364335", "genome_size_ungapped": "6364335", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "67", "contig_count": "67", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002091595.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "5917", "protein_coding_gene_count": "5753", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-03", "dateModified": "2017-04-03", "datePublished": "2017-04-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas fluorescens NBRC 14160" ], "sample_taxid": [ "1215100" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "1.788 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)": "6364335", "Number of Sequences": "67", "Longest Sequences (bp)": "1089011", "N50 (bp)": "301180", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.1", "Number of CDSs": "5795", "Average Protein Length": "322.1", "Coding Ratio (%)": "88.0", "Number of rRNAs": "5", "Number of tRNAs": "59", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas fluorescens", "strain": "strain=NBRC 14160", "accession": "GCA_002091595.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 2080, "total_fragments": 2086, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=ATCC 13525", "accession": "GCA_900215245.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9966, "matched_fragments": 2086, "total_fragments": 2086, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=DSM 50090", "accession": "GCA_001269845.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9962, "matched_fragments": 2062, "total_fragments": 2086, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=DSM 50090", "accession": "GCA_007858165.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9953, "matched_fragments": 2060, "total_fragments": 2086, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=NCTC10038", "accession": "GCA_900475215.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9929, "matched_fragments": 2086, "total_fragments": 2086, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=ATCC 13525", "accession": "GCA_002943685.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9724, "matched_fragments": 2046, "total_fragments": 2086, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas marginalis", "strain": "strain=DSM 13124", "accession": "GCA_007858155.1", "taxid": 298, "species_taxid": 298, "relation_to_type": "suspected-type", "validated": true, "ani": 88.2223, "matched_fragments": 1576, "total_fragments": 2086, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pergaminensis", "strain": "strain=1008", "accession": "GCA_024112395.1", "taxid": 2853159, "species_taxid": 2853159, "relation_to_type": "type", "validated": true, "ani": 88.0076, "matched_fragments": 1611, "total_fragments": 2086, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lurida", "strain": "strain=LMG 21995", "accession": "GCA_002563895.1", "taxid": 244566, "species_taxid": 244566, "relation_to_type": "type", "validated": true, "ani": 87.9454, "matched_fragments": 1603, "total_fragments": 2086, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas spelaei", "strain": "strain=CCM 7893", "accession": "GCA_009724245.1", "taxid": 1055469, "species_taxid": 1055469, "relation_to_type": "type", "validated": true, "ani": 85.9291, "matched_fragments": 1486, "total_fragments": 2086, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas karstica", "strain": "strain=CCM 7891", "accession": "GCA_009707515.1", "taxid": 1055468, "species_taxid": 1055468, "relation_to_type": "type", "validated": true, "ani": 85.1426, "matched_fragments": 1310, "total_fragments": 2086, "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": 81.2918, "matched_fragments": 912, "total_fragments": 2086, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas azotifigens", "strain": "strain=DSM 17556", "accession": "GCA_000425625.1", "taxid": 291995, "species_taxid": 291995, "relation_to_type": "type", "validated": true, "ani": 78.6094, "matched_fragments": 573, "total_fragments": 2086, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas rhizoryzae", "strain": "strain=RY24", "accession": "GCA_005250615.1", "taxid": 2571129, "species_taxid": 2571129, "relation_to_type": "type", "validated": true, "ani": 78.2069, "matched_fragments": 497, "total_fragments": 2086, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900215245.1", "gtdb_species": "s__Pseudomonas_E fluorescens", "ani": 99.9966, "matched_fragments": 2086, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.68", "min_intra_species_ani": "99.25", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.92", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCF_001647715.1", "gtdb_species": "s__Pseudomonas_E antarctica_A", "ani": 94.7103, "matched_fragments": 1835, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.45", "min_intra_species_ani": "97.45", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009707325.1", "gtdb_species": "s__Pseudomonas_E sp002263605", "ani": 90.0612, "matched_fragments": 1644, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009834565.1", "gtdb_species": "s__Pseudomonas_E sp009834565", "ani": 89.7347, "matched_fragments": 1762, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.71", "min_intra_species_ani": "97.35", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900624995.1", "gtdb_species": "s__Pseudomonas_E antarctica", "ani": 89.57, "matched_fragments": 1589, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_005938045.2", "gtdb_species": "s__Pseudomonas_E sp005938045", "ani": 89.5104, "matched_fragments": 1721, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.18", "min_intra_species_ani": "95.16", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013385965.1", "gtdb_species": "s__Pseudomonas_E edaphica", "ani": 89.5085, "matched_fragments": 1741, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_900107155.1", "gtdb_species": "s__Pseudomonas_E salomonii", "ani": 89.4884, "matched_fragments": 1731, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "96.43", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_003852315.1", "gtdb_species": "s__Pseudomonas_E sp003014915", "ani": 89.4609, "matched_fragments": 1709, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "96.20", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_002251635.1", "gtdb_species": "s__Pseudomonas_E mandelii_B", "ani": 88.8809, "matched_fragments": 1259, "total_fragments": 2086, "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_900580675.1", "gtdb_species": "s__Pseudomonas_E sp900580675", "ani": 88.6002, "matched_fragments": 1487, "total_fragments": 2086, "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_900591205.1", "gtdb_species": "s__Pseudomonas_E sp900591205", "ani": 88.4294, "matched_fragments": 1619, "total_fragments": 2086, "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_002843605.1", "gtdb_species": "s__Pseudomonas_E sp002843605", "ani": 88.2885, "matched_fragments": 1606, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.70", "min_intra_species_ani": "97.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_900105325.1", "gtdb_species": "s__Pseudomonas_E marginalis", "ani": 88.219, "matched_fragments": 1610, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.53", "min_intra_species_ani": "96.47", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_001439695.1", "gtdb_species": "s__Pseudomonas_E veronii", "ani": 88.0394, "matched_fragments": 1542, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.82", "num_clustered_genomes": 43, "status": "-" }, { "accession": "GCF_009296165.1", "gtdb_species": "s__Pseudomonas_E kitaguniensis", "ani": 87.8931, "matched_fragments": 1401, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.01", "min_intra_species_ani": "96.76", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001439845.1", "gtdb_species": "s__Pseudomonas_E lactis", "ani": 87.4656, "matched_fragments": 1555, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.24", "min_intra_species_ani": "95.50", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.81", "num_clustered_genomes": 30, "status": "-" }, { "accession": "GCF_900105675.1", "gtdb_species": "s__Pseudomonas_E synxantha", "ani": 87.3963, "matched_fragments": 1568, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.7053, "mean_intra_species_ani": "98.15", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.84", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_001439815.1", "gtdb_species": "s__Pseudomonas_E orientalis", "ani": 87.2437, "matched_fragments": 1524, "total_fragments": 2086, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.01", "min_intra_species_ani": "96.05", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.275, "growth_tmp": 29.2, "optimum_tmp": 30.448, "optimum_ph": 7.5, "genome_size": 6259568.844, "gc_content": 60.064, "coding_genes": 5671.69, "rRNA16S_genes": 5.083, "tRNA_genes": 66.85, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": 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", "fluorescens", "NBRC", "14160" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }