{ "type": "genome", "identifier": "GCF_016405165.1", "organism": "Pseudomonas alvandae", "title": "Pseudomonas alvandae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Kontanz", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016405165.1", "bioproject": "PRJNA224116", "biosample": "SAMN17126823", "wgs_master": "JAEKIK000000000.1", "refseq_category": "na", "taxid": "2842348", "species_taxid": "2842348", "organism_name": "Pseudomonas alvandae", "infraspecific_name": "na", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/12/26", "asm_name": "ASM1640516v1", "asm_submitter": "University of Kontanz", "gbrs_paired_asm": "GCA_016405165.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/405/165/GCF_016405165.1_ASM1640516v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from synonym type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6189265", "genome_size_ungapped": "6189125", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "55", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016405165.1-RS_2024_07_21", "annotation_date": "2024-07-21", "total_gene_count": "5580", "protein_coding_gene_count": "5470", "non_coding_gene_count": "59", "pubmed_id": "35072599" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-12-26", "dateModified": "2020-12-26", "datePublished": "2020-12-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas alvandae" ], "sample_taxid": [ "2842348" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Insel Reichenau, Lake Constance" ], "sample_host_location_id": [], "data_size": "1.733 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6189265", "Number of Sequences": "55", "Longest Sequences (bp)": "342522", "N50 (bp)": "165970", "Gap Ratio (%)": "0.002262", "GCcontent (%)": "61.0", "Number of CDSs": "5515", "Average Protein Length": "330.4", "Coding Ratio (%)": "88.3", "Number of rRNAs": "1", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas thivervalensis", "strain": "strain=DSM 13194", "accession": "GCA_001269655.1", "taxid": 86265, "species_taxid": 86265, "relation_to_type": "type", "validated": true, "ani": 88.773, "matched_fragments": 1620, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas zanjanensis", "strain": "strain=SWRI12", "accession": "GCA_014268745.2", "taxid": 2745496, "species_taxid": 2745496, "relation_to_type": "type", "validated": true, "ani": 88.6987, "matched_fragments": 1549, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas marvdashtae", "strain": "strain=SWRI102", "accession": "GCA_014268655.2", "taxid": 2745500, "species_taxid": 2745500, "relation_to_type": "type", "validated": true, "ani": 88.6705, "matched_fragments": 1547, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas kilonensis", "strain": "strain=DSM 13647", "accession": "GCA_001269885.1", "taxid": 132476, "species_taxid": 132476, "relation_to_type": "type", "validated": true, "ani": 88.531, "matched_fragments": 1568, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicacearum subsp. brassicacearum", "strain": "strain=CCUG 51508", "accession": "GCA_008801605.1", "taxid": 86264, "species_taxid": 930166, "relation_to_type": "type", "validated": true, "ani": 88.4456, "matched_fragments": 1610, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicacearum", "strain": "strain=JCM 11938", "accession": "GCA_012034345.1", "taxid": 930166, "species_taxid": 930166, "relation_to_type": "suspected-type", "validated": true, "ani": 88.4358, "matched_fragments": 1627, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas bijieensis", "strain": "strain=L22-9", "accession": "GCA_013347965.1", "taxid": 2681983, "species_taxid": 2681983, "relation_to_type": "type", "validated": true, "ani": 88.1375, "matched_fragments": 1609, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas rhizophila", "strain": "strain=S211", "accession": "GCA_003033885.1", "taxid": 2045200, "species_taxid": 2045200, "relation_to_type": "type", "validated": true, "ani": 87.0385, "matched_fragments": 1486, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mediterranea", "strain": "strain=DSM 16733", "accession": "GCA_900106005.1", "taxid": 183795, "species_taxid": 183795, "relation_to_type": "type", "validated": true, "ani": 87.0048, "matched_fragments": 1494, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas corrugata", "strain": "strain=NCPPB2445", "accession": "GCA_001411965.1", "taxid": 47879, "species_taxid": 47879, "relation_to_type": "type", "validated": true, "ani": 86.4653, "matched_fragments": 1421, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas corrugata", "strain": "strain=DSM 7228", "accession": "GCA_001269905.1", "taxid": 47879, "species_taxid": 47879, "relation_to_type": "type", "validated": true, "ani": 86.4016, "matched_fragments": 1457, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas corrugata", "strain": "strain=NCPPB2445", "accession": "GCA_003699065.1", "taxid": 47879, "species_taxid": 47879, "relation_to_type": "type", "validated": true, "ani": 86.3811, "matched_fragments": 1427, "total_fragments": 2035, "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": 84.2991, "matched_fragments": 1217, "total_fragments": 2035, "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": 84.2789, "matched_fragments": 1212, "total_fragments": 2035, "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": 83.4092, "matched_fragments": 1215, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicae", "strain": "strain=MAFF 212427", "accession": "GCA_010671725.1", "taxid": 2708063, "species_taxid": 2708063, "relation_to_type": "type", "validated": true, "ani": 82.0309, "matched_fragments": 785, "total_fragments": 2035, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_019141525.1", "gtdb_species": "s__Pseudomonas_E fluorescens_T", "ani": 98.7981, "matched_fragments": 1857, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_013608025.1", "gtdb_species": "s__Pseudomonas_E neoaurantiaca", "ani": 94.3715, "matched_fragments": 1718, "total_fragments": 2035, "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_000802155.2", "gtdb_species": "s__Pseudomonas_E frederiksbergensis_A", "ani": 90.4763, "matched_fragments": 1633, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001269655.1", "gtdb_species": "s__Pseudomonas_E thivervalensis", "ani": 88.7973, "matched_fragments": 1616, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_014268745.2", "gtdb_species": "s__Pseudomonas_E sp014268745", "ani": 88.7053, "matched_fragments": 1547, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.32", "min_intra_species_ani": "95.56", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014268655.2", "gtdb_species": "s__Pseudomonas_E sp014268655", "ani": 88.6705, "matched_fragments": 1547, "total_fragments": 2035, "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": "96.17", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900581005.1", "gtdb_species": "s__Pseudomonas_E sp900581005", "ani": 88.6235, "matched_fragments": 1548, "total_fragments": 2035, "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_001307275.1", "gtdb_species": "s__Pseudomonas_E fluorescens_AA", "ani": 88.5301, "matched_fragments": 1607, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.99", "min_intra_species_ani": "95.90", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_008801605.1", "gtdb_species": "s__Pseudomonas_E brassicacearum", "ani": 88.4372, "matched_fragments": 1611, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "96.48", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.86", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_001623525.1", "gtdb_species": "s__Pseudomonas_E fluorescens_Q", "ani": 88.1857, "matched_fragments": 1607, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "97.11", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_013347965.1", "gtdb_species": "s__Pseudomonas_E bijieensis", "ani": 88.1692, "matched_fragments": 1604, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.40", "min_intra_species_ani": "95.64", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_018325905.1", "gtdb_species": "s__Pseudomonas_E sp018325905", "ani": 88.0572, "matched_fragments": 1600, "total_fragments": 2035, "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_000585995.1", "gtdb_species": "s__Pseudomonas_E brassicacearum_A", "ani": 87.8582, "matched_fragments": 1554, "total_fragments": 2035, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.55", "min_intra_species_ani": "95.52", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "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", "alvandae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }