{ "type": "genome", "identifier": "GCF_008801535.1", "organism": "Pseudomonas koreensis", "title": "Pseudomonas koreensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Gothenburg - CCUG", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008801535.1", "bioproject": "PRJNA224116", "biosample": "SAMN12697588", "wgs_master": "VZPN00000000.1", "refseq_category": "na", "taxid": "198620", "species_taxid": "198620", "organism_name": "Pseudomonas koreensis", "infraspecific_name": "strain=CCUG 51519", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/10/01", "asm_name": "ASM880153v1", "asm_submitter": "University of Gothenburg - CCUG", "gbrs_paired_asm": "GCA_008801535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/801/535/GCF_008801535.1_ASM880153v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6084671", "genome_size_ungapped": "6084671", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008801535.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "5591", "protein_coding_gene_count": "5457", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-10-01", "dateModified": "2019-10-01", "datePublished": "2019-10-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas koreensis" ], "sample_taxid": [ "198620" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.694 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)": "6084671", "Number of Sequences": "33", "Longest Sequences (bp)": "827161", "N50 (bp)": "483184", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.6", "Number of CDSs": "5508", "Average Protein Length": "322.9", "Coding Ratio (%)": "87.7", "Number of rRNAs": "4", "Number of tRNAs": "74", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas koreensis", "strain": "strain=CCUG 51519", "accession": "GCA_008801535.1", "taxid": 198620, "species_taxid": 198620, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 2015, "total_fragments": 2017, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas koreensis", "strain": "strain=DSM 16610", "accession": "GCA_012986595.1", "taxid": 198620, "species_taxid": 198620, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9972, "matched_fragments": 2011, "total_fragments": 2017, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas koreensis", "strain": "strain=JCM 14769", "accession": "GCA_014646955.1", "taxid": 198620, "species_taxid": 198620, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9925, "matched_fragments": 2006, "total_fragments": 2017, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas monsensis", "strain": "strain=PGSB 8459", "accession": "GCA_014268495.2", "taxid": 2745509, "species_taxid": 2745509, "relation_to_type": "type", "validated": true, "ani": 90.1478, "matched_fragments": 1732, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas baetica", "strain": "strain=LMG 25716", "accession": "GCA_002813455.1", "taxid": 674054, "species_taxid": 674054, "relation_to_type": "type", "validated": true, "ani": 89.0336, "matched_fragments": 1668, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas baetica", "strain": "strain=a390", "accession": "GCA_003031005.1", "taxid": 674054, "species_taxid": 674054, "relation_to_type": "type", "validated": true, "ani": 89.0076, "matched_fragments": 1640, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas germanica", "strain": "strain=FIT28", "accession": "GCA_019614655.1", "taxid": 2815720, "species_taxid": 2815720, "relation_to_type": "type", "validated": true, "ani": 88.9945, "matched_fragments": 1743, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas crudilactis", "strain": "strain=UCMA 17988", "accession": "GCA_013433315.1", "taxid": 2697028, "species_taxid": 2697028, "relation_to_type": "type", "validated": true, "ani": 88.9439, "matched_fragments": 1708, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas kribbensis", "strain": "strain=46-2", "accession": "GCA_003352185.1", "taxid": 1628086, "species_taxid": 1628086, "relation_to_type": "type", "validated": true, "ani": 88.9069, "matched_fragments": 1668, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pharyngis", "strain": "strain=BML-PP036", "accession": "GCA_021602345.1", "taxid": 2892333, "species_taxid": 2892333, "relation_to_type": "type", "validated": true, "ani": 88.8272, "matched_fragments": 1680, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sputi", "strain": "strain=BML-PP014", "accession": "GCA_021603585.1", "taxid": 2892325, "species_taxid": 2892325, "relation_to_type": "type", "validated": true, "ani": 88.7972, "matched_fragments": 1623, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas iranensis", "strain": "strain=SWRI54", "accession": "GCA_014268585.2", "taxid": 2745503, "species_taxid": 2745503, "relation_to_type": "type", "validated": true, "ani": 88.1468, "matched_fragments": 1568, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas triticicola", "strain": "strain=SWRI88", "accession": "GCA_019145375.1", "taxid": 2842345, "species_taxid": 2842345, "relation_to_type": "type", "validated": true, "ani": 88.0022, "matched_fragments": 1538, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hamedanensis", "strain": "strain=SWRI65", "accession": "GCA_014268595.2", "taxid": 2745504, "species_taxid": 2745504, "relation_to_type": "type", "validated": true, "ani": 87.8048, "matched_fragments": 1569, "total_fragments": 2017, "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": 83.4884, "matched_fragments": 1334, "total_fragments": 2017, "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": 83.4773, "matched_fragments": 1271, "total_fragments": 2017, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_012986595.1", "gtdb_species": "s__Pseudomonas_E koreensis", "ani": 99.9972, "matched_fragments": 2011, "total_fragments": 2017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "97.85", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCF_003999415.1", "gtdb_species": "s__Pseudomonas_E koreensis_E", "ani": 92.8845, "matched_fragments": 1737, "total_fragments": 2017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002878485.1", "gtdb_species": "s__Pseudomonas_E sp002878485", "ani": 92.3181, "matched_fragments": 1686, "total_fragments": 2017, "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_004683905.1", "gtdb_species": "s__Pseudomonas_E putida_A", "ani": 92.0944, "matched_fragments": 1784, "total_fragments": 2017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.80", "min_intra_species_ani": "95.08", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_000292795.1", "gtdb_species": "s__Pseudomonas_E fluorescens_H", "ani": 92.082, "matched_fragments": 1773, "total_fragments": 2017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "97.99", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000633255.1", "gtdb_species": "s__Pseudomonas_E sp000633255", "ani": 92.0676, "matched_fragments": 1743, "total_fragments": 2017, "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_000631985.1", "gtdb_species": "s__Pseudomonas_E sp000631985", "ani": 91.9812, "matched_fragments": 1750, "total_fragments": 2017, "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_000282275.2", "gtdb_species": "s__Pseudomonas_E sp000282275", "ani": 91.9607, "matched_fragments": 1741, "total_fragments": 2017, "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_002287825.1", "gtdb_species": "s__Pseudomonas_E koreensis_B", "ani": 91.7105, "matched_fragments": 1750, "total_fragments": 2017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.58", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_003061005.1", "gtdb_species": "s__Pseudomonas_E sp003061005", "ani": 91.5426, "matched_fragments": 1624, "total_fragments": 2017, "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_014268495.2", "gtdb_species": "s__Pseudomonas_E fluorescens_BC", "ani": 90.1401, "matched_fragments": 1733, "total_fragments": 2017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.66", "min_intra_species_ani": "98.66", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018326005.1", "gtdb_species": "s__Pseudomonas_E sp002901475", "ani": 89.4058, "matched_fragments": 1738, "total_fragments": 2017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.45", "min_intra_species_ani": "98.45", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016651305.1", "gtdb_species": "s__Pseudomonas_E sp016651305", "ani": 89.1514, "matched_fragments": 1724, "total_fragments": 2017, "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_002813455.1", "gtdb_species": "s__Pseudomonas_E baetica", "ani": 89.057, "matched_fragments": 1666, "total_fragments": 2017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "95.55", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014472415.1", "gtdb_species": "s__Pseudomonas_E sp014472415", "ani": 89.0033, "matched_fragments": 1599, "total_fragments": 2017, "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": 30.0, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 6351437.625, "gc_content": 59.784, "coding_genes": 5715.0, "rRNA16S_genes": 5.333, "tRNA_genes": 70.75, "gram_stain": 0.0, "sporulation": 0.013, "motility": 0.975, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.926, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.073, "bacillus_cell_shape": 0.988, "coccus_cell_shape": 0.011, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudomonas", "koreensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }