{ "type": "genome", "identifier": "GCF_000689415.1", "organism": "Pseudomonas knackmussii B13", "title": "Pseudomonas knackmussii B13", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CHUV-UNIL", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000689415.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3139009", "wgs_master": "na", "refseq_category": "na", "taxid": "1301098", "species_taxid": "65741", "organism_name": "Pseudomonas knackmussii B13", "infraspecific_name": "strain=B13", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/05/07", "asm_name": "PKB13", "asm_submitter": "CHUV-UNIL", "gbrs_paired_asm": "GCA_000689415.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/689/415/GCF_000689415.1_PKB13", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6162905", "genome_size_ungapped": "6162905", "gc_percent": "65.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000689415.1-RS_2024_04_06", "annotation_date": "2024-04-06", "total_gene_count": "5832", "protein_coding_gene_count": "5639", "non_coding_gene_count": "79", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-05-07", "dateModified": "2014-05-07", "datePublished": "2014-05-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas knackmussii B13" ], "sample_taxid": [ "1301098" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.686 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)": "6162905", "Number of Sequences": "1", "Longest Sequences (bp)": "6162905", "N50 (bp)": "6162905", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.6", "Number of CDSs": "5835", "Average Protein Length": "313.7", "Coding Ratio (%)": "89.1", "Number of rRNAs": "13", "Number of tRNAs": "63", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas knackmussii", "strain": "strain=B13", "accession": "GCA_000689415.1", "taxid": 65741, "species_taxid": 65741, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2036, "total_fragments": 2054, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas delhiensis", "strain": "strain=CCM 7361", "accession": "GCA_900099945.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 88.9228, "matched_fragments": 1460, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas delhiensis", "strain": "strain=RLD-1", "accession": "GCA_900187975.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 88.8984, "matched_fragments": 1475, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas citronellolis", "strain": "strain=DSM 50332", "accession": "GCA_004745455.1", "taxid": 53408, "species_taxid": 53408, "relation_to_type": "type", "validated": true, "ani": 88.844, "matched_fragments": 1543, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas citronellolis", "strain": "strain=LMG 18378", "accession": "GCA_900112375.1", "taxid": 53408, "species_taxid": 53408, "relation_to_type": "type", "validated": true, "ani": 88.8334, "matched_fragments": 1532, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas citronellolis", "strain": "strain=NBRC 103043", "accession": "GCA_002091555.1", "taxid": 53408, "species_taxid": 53408, "relation_to_type": "type", "validated": true, "ani": 88.8301, "matched_fragments": 1524, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas jinjuensis", "strain": "strain=JCM 21621", "accession": "GCA_900103845.1", "taxid": 198616, "species_taxid": 198616, "relation_to_type": "type", "validated": true, "ani": 86.0298, "matched_fragments": 1248, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas nitroreducens", "strain": "strain=NBRC 12694", "accession": "GCA_002091755.1", "taxid": 46680, "species_taxid": 46680, "relation_to_type": "suspected-type", "validated": true, "ani": 85.9307, "matched_fragments": 1396, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas insulae", "strain": "strain=UL073", "accession": "GCA_016901015.1", "taxid": 2809017, "species_taxid": 2809017, "relation_to_type": "type", "validated": true, "ani": 82.8274, "matched_fragments": 1048, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 82.8131, "matched_fragments": 931, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=FDAARGOS_876", "accession": "GCA_016028635.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "suspected-type", "validated": true, "ani": 81.2921, "matched_fragments": 748, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=DSM 50238", "accession": "GCA_002891015.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "type", "validated": true, "ani": 81.2033, "matched_fragments": 745, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=DSM 50238", "accession": "GCA_024448505.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "type", "validated": true, "ani": 81.1113, "matched_fragments": 737, "total_fragments": 2054, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000689415.1", "gtdb_species": "s__Pseudomonas knackmussii", "ani": 100.0, "matched_fragments": 2038, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_900187975.1", "gtdb_species": "s__Pseudomonas delhiensis", "ani": 88.8887, "matched_fragments": 1476, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.078, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "97.59", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900112375.1", "gtdb_species": "s__Pseudomonas citronellolis", "ani": 88.8723, "matched_fragments": 1529, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.078, "mean_intra_species_ani": "97.44", "min_intra_species_ani": "97.08", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 26, "status": "-" }, { "accession": "GCF_900099785.1", "gtdb_species": "s__Pseudomonas panipatensis", "ani": 86.9621, "matched_fragments": 1455, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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_017491605.1", "gtdb_species": "s__Pseudomonas sp017491605", "ani": 86.5881, "matched_fragments": 1398, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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_000349845.1", "gtdb_species": "s__Pseudomonas sp000349845", "ani": 86.4422, "matched_fragments": 1302, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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_002452115.1", "gtdb_species": "s__Pseudomonas nitroreducens_B", "ani": 86.3148, "matched_fragments": 1258, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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_014204515.1", "gtdb_species": "s__Pseudomonas nitritireducens_A", "ani": 86.2484, "matched_fragments": 1420, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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_008807415.1", "gtdb_species": "s__Pseudomonas sp002079985", "ani": 86.2194, "matched_fragments": 1474, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "95.53", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000955805.1", "gtdb_species": "s__Pseudomonas sp000955805", "ani": 86.1951, "matched_fragments": 1455, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009189165.1", "gtdb_species": "s__Pseudomonas sp009189165", "ani": 86.1403, "matched_fragments": 1433, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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_900103845.1", "gtdb_species": "s__Pseudomonas jinjuensis", "ani": 86.0415, "matched_fragments": 1247, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016919445.1", "gtdb_species": "s__Pseudomonas sp016919445", "ani": 85.8844, "matched_fragments": 1430, "total_fragments": 2054, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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": 30.0, "optimum_tmp": 30.5, "optimum_ph": 7.2, "genome_size": 6162906.25, "gc_content": 65.6, "coding_genes": 5620.0, "rRNA16S_genes": 4.0, "tRNA_genes": 61.0, "gram_stain": 0.0, "sporulation": 0.013, "motility": 1.0, "range_salinity": 0.666, "facultative_respiration": 0.021, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.978, "mesophilic_range_tmp": 0.926, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.073, "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", "knackmussii", "B13" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }