{ "type": "genome", "identifier": "GCF_900475285.1", "organism": "Pseudomonas taetrolens", "title": "Pseudomonas taetrolens", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900475285.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3711430", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "47884", "species_taxid": "47884", "organism_name": "Pseudomonas taetrolens", "infraspecific_name": "strain=NCTC10697", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/17", "asm_name": "43222_B01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900475285.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/475/285/GCF_900475285.1_43222_B01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4843871", "genome_size_ungapped": "4843871", "gc_percent": "58.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900475285.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "4423", "protein_coding_gene_count": "4253", "non_coding_gene_count": "90", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-17", "dateModified": "2018-06-17", "datePublished": "2018-06-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas taetrolens" ], "sample_taxid": [ "47884" ], "sample_host_organism": [ "not available" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.364 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)": "4843871", "Number of Sequences": "1", "Longest Sequences (bp)": "4843871", "N50 (bp)": "4843871", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.3", "Number of CDSs": "4378", "Average Protein Length": "326.6", "Coding Ratio (%)": "88.6", "Number of rRNAs": "19", "Number of tRNAs": "68", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas taetrolens", "strain": "strain=NCTC10697", "accession": "GCA_900475285.1", "taxid": 47884, "species_taxid": 47884, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1611, "total_fragments": 1614, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas taetrolens", "strain": "strain=DSM 21104", "accession": "GCA_001042915.1", "taxid": 47884, "species_taxid": 47884, "relation_to_type": "type", "validated": true, "ani": 99.9832, "matched_fragments": 1592, "total_fragments": 1614, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas deceptionensis", "strain": "strain=LMG 25555", "accession": "GCA_900106095.1", "taxid": 882211, "species_taxid": 882211, "relation_to_type": "type", "validated": true, "ani": 85.492, "matched_fragments": 1164, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas deceptionensis", "strain": "strain=DSM 26521", "accession": "GCA_001042895.1", "taxid": 882211, "species_taxid": 882211, "relation_to_type": "type", "validated": true, "ani": 85.3859, "matched_fragments": 1164, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fragi", "strain": "strain=NRRL B-727", "accession": "GCA_900105835.1", "taxid": 296, "species_taxid": 296, "relation_to_type": "type", "validated": true, "ani": 85.0758, "matched_fragments": 1134, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fragi", "strain": "strain=NBRC 3458", "accession": "GCA_002091615.1", "taxid": 296, "species_taxid": 296, "relation_to_type": "type", "validated": true, "ani": 85.0204, "matched_fragments": 1117, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas helleri", "strain": "strain=DSM 29165", "accession": "GCA_001043025.1", "taxid": 1608996, "species_taxid": 1608996, "relation_to_type": "type", "validated": true, "ani": 84.023, "matched_fragments": 1074, "total_fragments": 1614, "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": 81.4804, "matched_fragments": 886, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas jessenii", "strain": "strain=DSM 17150", "accession": "GCA_002236115.1", "taxid": 77298, "species_taxid": 77298, "relation_to_type": "suspected-type", "validated": true, "ani": 81.4705, "matched_fragments": 899, "total_fragments": 1614, "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": 81.4525, "matched_fragments": 873, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas reinekei", "strain": "strain=MT1", "accession": "GCA_001945365.1", "taxid": 395598, "species_taxid": 395598, "relation_to_type": "type", "validated": true, "ani": 81.4106, "matched_fragments": 867, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas reinekei", "strain": "strain=CCUG 53116", "accession": "GCA_008801455.1", "taxid": 395598, "species_taxid": 395598, "relation_to_type": "type", "validated": true, "ani": 81.4033, "matched_fragments": 873, "total_fragments": 1614, "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": 81.3858, "matched_fragments": 865, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "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": 81.3782, "matched_fragments": 898, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas amygdali", "strain": "strain=DSM 105780", "accession": "GCA_022828345.1", "taxid": 47877, "species_taxid": 47877, "relation_to_type": "pathovar", "validated": true, "ani": 80.1293, "matched_fragments": 631, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900475285.1", "gtdb_species": "s__Pseudomonas_E taetrolens", "ani": 100.0, "matched_fragments": 1612, "total_fragments": 1614, "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": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_900106095.1", "gtdb_species": "s__Pseudomonas_E deceptionensis", "ani": 85.5098, "matched_fragments": 1166, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900105835.1", "gtdb_species": "s__Pseudomonas_E fragi", "ani": 85.0875, "matched_fragments": 1133, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "96.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 28, "status": "-" }, { "accession": "GCF_904063065.1", "gtdb_species": "s__Pseudomonas_E paraversuta", "ani": 84.8881, "matched_fragments": 1154, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "99.22", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_002269505.1", "gtdb_species": "s__Pseudomonas_E fragi_D", "ani": 84.8768, "matched_fragments": 1102, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.09", "min_intra_species_ani": "96.09", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900618535.1", "gtdb_species": "s__Pseudomonas_E bubulae", "ani": 84.7652, "matched_fragments": 1121, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.12", "min_intra_species_ani": "98.96", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_000282975.1", "gtdb_species": "s__Pseudomonas_E psychrophila_A", "ani": 83.7287, "matched_fragments": 1028, "total_fragments": 1614, "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_001043055.1", "gtdb_species": "s__Pseudomonas_E weihenstephanensis", "ani": 83.7162, "matched_fragments": 1035, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.02", "min_intra_species_ani": "97.13", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_009600315.1", "gtdb_species": "s__Pseudomonas_E helleri_A", "ani": 83.4948, "matched_fragments": 1034, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.82", "min_intra_species_ani": "99.80", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_007858365.1", "gtdb_species": "s__Pseudomonas_E saxonica", "ani": 83.3705, "matched_fragments": 1049, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "98.82", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000282415.1", "gtdb_species": "s__Pseudomonas_E sp000282415", "ani": 81.7034, "matched_fragments": 849, "total_fragments": 1614, "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": "97.21", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_018502625.1", "gtdb_species": "s__Pseudomonas_E fluorescens_BW", "ani": 81.6558, "matched_fragments": 883, "total_fragments": 1614, "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_016650695.1", "gtdb_species": "s__Pseudomonas_E sp016650695", "ani": 81.6016, "matched_fragments": 863, "total_fragments": 1614, "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_002303925.1", "gtdb_species": "s__Pseudomonas_E sp002303925", "ani": 81.5746, "matched_fragments": 864, "total_fragments": 1614, "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": "99.04", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000802965.1", "gtdb_species": "s__Pseudomonas_E fluorescens_A", "ani": 81.5275, "matched_fragments": 857, "total_fragments": 1614, "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_002091715.1", "gtdb_species": "s__Pseudomonas_E migulae", "ani": 81.5235, "matched_fragments": 865, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.54", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002236115.1", "gtdb_species": "s__Pseudomonas_E jessenii", "ani": 81.4569, "matched_fragments": 899, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.88", "min_intra_species_ani": "96.89", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_016909445.1", "gtdb_species": "s__Pseudomonas_E stutzeri_A", "ani": 81.3193, "matched_fragments": 873, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.88", "min_intra_species_ani": "96.88", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "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": 4905539.5, "gc_content": 58.28, "coding_genes": 4255.0, "rRNA16S_genes": 5.319, "tRNA_genes": 68.0, "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", "taetrolens" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }