{ "type": "genome", "identifier": "GCF_019139535.1", "organism": "Pseudomonas muyukensis", "title": "Pseudomonas muyukensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "KU Leuven", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019139535.1", "bioproject": "PRJNA224116", "biosample": "SAMN19473673", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2842357", "species_taxid": "2842357", "organism_name": "Pseudomonas muyukensis", "infraspecific_name": "strain=COW39", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/06", "asm_name": "ASM1913953v1", "asm_submitter": "KU Leuven", "gbrs_paired_asm": "GCA_019139535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/139/535/GCF_019139535.1_ASM1913953v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5527654", "genome_size_ungapped": "5527654", "gc_percent": "65.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019139535.1-RS_2024_07_22", "annotation_date": "2024-07-22", "total_gene_count": "4920", "protein_coding_gene_count": "4788", "non_coding_gene_count": "99", "pubmed_id": "34442845" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-06", "dateModified": "2021-07-06", "datePublished": "2021-07-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas muyukensis" ], "sample_taxid": [ "2842357" ], "sample_host_organism": [ "Xanthosoma sagittifolium" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Cameroon: Ekona" ], "sample_host_location_id": [], "data_size": "1.507 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)": "5527654", "Number of Sequences": "1", "Longest Sequences (bp)": "5527654", "N50 (bp)": "5527654", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.1", "Number of CDSs": "4865", "Average Protein Length": "336.2", "Coding Ratio (%)": "88.8", "Number of rRNAs": "19", "Number of tRNAs": "81", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas muyukensis", "strain": "strain=COW39", "accession": "GCA_019139535.1", "taxid": 2842357, "species_taxid": 2842357, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1841, "total_fragments": 1842, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas xantholysinigenes", "strain": "strain=RW9S1A", "accession": "GCA_014268885.2", "taxid": 2745490, "species_taxid": 2745490, "relation_to_type": "type", "validated": true, "ani": 91.6892, "matched_fragments": 1597, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mosselii", "strain": "strain=DSM 17497", "accession": "GCA_019823065.1", "taxid": 78327, "species_taxid": 78327, "relation_to_type": "type", "validated": true, "ani": 90.1615, "matched_fragments": 1489, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mosselii", "strain": "strain=DSM 17497", "accession": "GCA_000621225.1", "taxid": 78327, "species_taxid": 78327, "relation_to_type": "type", "validated": true, "ani": 90.0607, "matched_fragments": 1503, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas maumuensis", "strain": "strain=COW77", "accession": "GCA_019139675.1", "taxid": 2842354, "species_taxid": 2842354, "relation_to_type": "type", "validated": true, "ani": 89.854, "matched_fragments": 1497, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas soli", "strain": "strain=LMG 27941", "accession": "GCA_900110655.1", "taxid": 1306993, "species_taxid": 1306993, "relation_to_type": "type", "validated": true, "ani": 89.6005, "matched_fragments": 1486, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas entomophila", "strain": "strain=L48", "accession": "GCA_000026105.1", "taxid": 312306, "species_taxid": 312306, "relation_to_type": "suspected-type", "validated": true, "ani": 89.3091, "matched_fragments": 1481, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sichuanensis", "strain": "strain=WCHPs060039", "accession": "GCA_003231305.1", "taxid": 2213015, "species_taxid": 2213015, "relation_to_type": "type", "validated": true, "ani": 89.0439, "matched_fragments": 1387, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas xanthosomae", "strain": "strain=COR54", "accession": "GCA_019139835.1", "taxid": 2842356, "species_taxid": 2842356, "relation_to_type": "type", "validated": true, "ani": 88.5863, "matched_fragments": 1429, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fakonensis", "strain": "strain=COW40", "accession": "GCA_019139895.1", "taxid": 2842355, "species_taxid": 2842355, "relation_to_type": "type", "validated": true, "ani": 88.5428, "matched_fragments": 1465, "total_fragments": 1842, "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": 86.8531, "matched_fragments": 1308, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas urethralis", "strain": "strain=BML-PP042", "accession": "GCA_013373915.1", "taxid": 2740517, "species_taxid": 2740517, "relation_to_type": "suspected-type", "validated": true, "ani": 86.7704, "matched_fragments": 1297, "total_fragments": 1842, "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": 82.448, "matched_fragments": 849, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aromaticivorans", "strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 81.4399, "matched_fragments": 681, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mangiferae", "strain": "strain=DMKU BBB3-04", "accession": "GCA_007109405.1", "taxid": 2593654, "species_taxid": 2593654, "relation_to_type": "type", "validated": true, "ani": 81.3069, "matched_fragments": 839, "total_fragments": 1842, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_019139535.1", "gtdb_species": "s__Pseudomonas_E sp019139535", "ani": 100.0, "matched_fragments": 1841, "total_fragments": 1842, "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": "conclusive" }, { "accession": "GCF_004519305.1", "gtdb_species": "s__Pseudomonas_E sp004519305", "ani": 94.2628, "matched_fragments": 1581, "total_fragments": 1842, "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_014268885.2", "gtdb_species": "s__Pseudomonas_E sp014268885", "ani": 91.7096, "matched_fragments": 1595, "total_fragments": 1842, "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_016861355.1", "gtdb_species": "s__Pseudomonas_E sp001259595", "ani": 90.3734, "matched_fragments": 1544, "total_fragments": 1842, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.3017, "mean_intra_species_ani": "95.65", "min_intra_species_ani": "95.59", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003205295.1", "gtdb_species": "s__Pseudomonas_E mosselii_B", "ani": 90.3603, "matched_fragments": 1516, "total_fragments": 1842, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.3017, "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_000621225.1", "gtdb_species": "s__Pseudomonas_E mosselii", "ani": 90.047, "matched_fragments": 1504, "total_fragments": 1842, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "97.48", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_019139675.1", "gtdb_species": "s__Pseudomonas_E sp019139675", "ani": 89.8809, "matched_fragments": 1495, "total_fragments": 1842, "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_900110655.1", "gtdb_species": "s__Pseudomonas_E soli", "ani": 89.5798, "matched_fragments": 1488, "total_fragments": 1842, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "95.09", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_011752525.1", "gtdb_species": "s__Pseudomonas_E sp011752525", "ani": 89.3727, "matched_fragments": 1426, "total_fragments": 1842, "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_015354575.1", "gtdb_species": "s__Pseudomonas_E sp015354575", "ani": 89.0534, "matched_fragments": 1436, "total_fragments": 1842, "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_019139835.1", "gtdb_species": "s__Pseudomonas_E sp019139835", "ani": 88.5361, "matched_fragments": 1435, "total_fragments": 1842, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.50", "min_intra_species_ani": "95.50", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.767, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 5663774.24, "gc_content": 60.938, "coding_genes": 5204.79, "rRNA16S_genes": 5.319, "tRNA_genes": 67.35, "gram_stain": 0.0, "sporulation": 0.013, "motility": 0.975, "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": 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", "muyukensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }