{ "type": "genome", "identifier": "GCF_018336155.1", "organism": "Pseudomonas rustica", "title": "Pseudomonas rustica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Max Rubner-Institut", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018336155.1", "bioproject": "PRJNA224116", "biosample": "SAMN18880036", "wgs_master": "JAGYHF000000000.1", "refseq_category": "reference genome", "taxid": "2827099", "species_taxid": "2827099", "organism_name": "Pseudomonas rustica", "infraspecific_name": "strain=MBT-4", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/10", "asm_name": "ASM1833615v1", "asm_submitter": "Max Rubner-Institut", "gbrs_paired_asm": "GCA_018336155.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/336/155/GCF_018336155.1_ASM1833615v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5861604", "genome_size_ungapped": "5861604", "gc_percent": "59.000000", "replicon_count": "0", "scaffold_count": "46", "contig_count": "46", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018336155.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "5388", "protein_coding_gene_count": "5251", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-10", "dateModified": "2021-05-10", "datePublished": "2021-05-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas rustica" ], "sample_taxid": [ "2827099" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Lower Saxony" ], "sample_host_location_id": [], "data_size": "1.638 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5861604", "Number of Sequences": "46", "Longest Sequences (bp)": "678849", "N50 (bp)": "446374", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.9", "Number of CDSs": "5355", "Average Protein Length": "317.5", "Coding Ratio (%)": "87.0", "Number of rRNAs": "3", "Number of tRNAs": "59", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas crudilactis", "strain": "strain=UCMA 17988", "accession": "GCA_013433315.1", "taxid": 2697028, "species_taxid": 2697028, "relation_to_type": "type", "validated": true, "ani": 90.3838, "matched_fragments": 1583, "total_fragments": 1934, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas tensinigenes", "strain": "strain=ZA 5.3", "accession": "GCA_014268445.2", "taxid": 2745511, "species_taxid": 2745511, "relation_to_type": "type", "validated": true, "ani": 90.3738, "matched_fragments": 1586, "total_fragments": 1934, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas neuropathica", "strain": "strain=P155", "accession": "GCA_015461835.1", "taxid": 2730425, "species_taxid": 2730425, "relation_to_type": "type", "validated": true, "ani": 90.2263, "matched_fragments": 1552, "total_fragments": 1934, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas zeae", "strain": "strain=OE 48.2", "accession": "GCA_014268485.2", "taxid": 2745510, "species_taxid": 2745510, "relation_to_type": "type", "validated": true, "ani": 90.221, "matched_fragments": 1554, "total_fragments": 1934, "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": 90.1568, "matched_fragments": 1561, "total_fragments": 1934, "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": 89.3045, "matched_fragments": 1459, "total_fragments": 1934, "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": 89.2607, "matched_fragments": 1520, "total_fragments": 1934, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas allokribbensis", "strain": "strain=IzPS23", "accession": "GCA_014863605.1", "taxid": 2774460, "species_taxid": 2774460, "relation_to_type": "type", "validated": true, "ani": 88.0603, "matched_fragments": 1515, "total_fragments": 1934, "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": 88.0448, "matched_fragments": 1490, "total_fragments": 1934, "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": 87.9374, "matched_fragments": 1471, "total_fragments": 1934, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas laurylsulfativorans", "strain": "strain=AP3_22", "accession": "GCA_002906155.1", "taxid": 1943631, "species_taxid": 1943631, "relation_to_type": "type", "validated": true, "ani": 85.5532, "matched_fragments": 1327, "total_fragments": 1934, "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": 83.1713, "matched_fragments": 1164, "total_fragments": 1934, "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": 81.4799, "matched_fragments": 771, "total_fragments": 1934, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001269815.1", "gtdb_species": "s__Pseudomonas_E sp001269815", "ani": 97.4181, "matched_fragments": 1705, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.38", "min_intra_species_ani": "97.36", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_000282515.1", "gtdb_species": "s__Pseudomonas_E sp000282515", "ani": 91.8954, "matched_fragments": 1497, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.31", "min_intra_species_ani": "97.31", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004124275.1", "gtdb_species": "s__Pseudomonas_E sp004124275", "ani": 90.7624, "matched_fragments": 1571, "total_fragments": 1934, "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_018138145.1", "gtdb_species": "s__Pseudomonas_E koreensis_A", "ani": 90.657, "matched_fragments": 1572, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.53", "min_intra_species_ani": "97.00", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001297015.1", "gtdb_species": "s__Pseudomonas_E sp001297015", "ani": 90.5992, "matched_fragments": 1579, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.77", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001648775.1", "gtdb_species": "s__Pseudomonas_E fluorescens_M", "ani": 90.5843, "matched_fragments": 1572, "total_fragments": 1934, "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_009764645.1", "gtdb_species": "s__Pseudomonas_E sp009764645", "ani": 90.5354, "matched_fragments": 1464, "total_fragments": 1934, "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_000783395.1", "gtdb_species": "s__Pseudomonas_E helmanticensis", "ani": 90.5293, "matched_fragments": 1538, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.23", "min_intra_species_ani": "95.21", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900580865.1", "gtdb_species": "s__Pseudomonas_E sp900580865", "ani": 90.4681, "matched_fragments": 1577, "total_fragments": 1934, "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_014268445.2", "gtdb_species": "s__Pseudomonas_E sp900187515", "ani": 90.3938, "matched_fragments": 1584, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.92", "min_intra_species_ani": "96.07", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_009834515.1", "gtdb_species": "s__Pseudomonas_E sp009834515", "ani": 90.3843, "matched_fragments": 1535, "total_fragments": 1934, "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_902497745.1", "gtdb_species": "s__Pseudomonas_E fluorescens_BM", "ani": 90.3762, "matched_fragments": 1564, "total_fragments": 1934, "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_013433315.1", "gtdb_species": "s__Pseudomonas_E crudilactis", "ani": 90.3759, "matched_fragments": 1583, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "98.37", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900187605.1", "gtdb_species": "s__Pseudomonas_E sp900187605", "ani": 90.3279, "matched_fragments": 1557, "total_fragments": 1934, "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": "98.53", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_015461835.1", "gtdb_species": "s__Pseudomonas_E neuropathica", "ani": 90.222, "matched_fragments": 1552, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.00", "min_intra_species_ani": "95.48", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_016650635.1", "gtdb_species": "s__Pseudomonas_E sp016650635", "ani": 90.0004, "matched_fragments": 1581, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.85", "min_intra_species_ani": "97.85", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_017980685.1", "gtdb_species": "s__Pseudomonas_E iridis", "ani": 88.806, "matched_fragments": 1452, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.83", "min_intra_species_ani": "96.38", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_016651255.1", "gtdb_species": "s__Pseudomonas_E sp016651255", "ani": 88.3808, "matched_fragments": 991, "total_fragments": 1934, "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_004682045.1", "gtdb_species": "s__Pseudomonas_E nabeulensis", "ani": 83.149, "matched_fragments": 1119, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.61", "min_intra_species_ani": "95.59", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_019139815.1", "gtdb_species": "s__Pseudomonas_E sp900005815", "ani": 83.0303, "matched_fragments": 1110, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.55", "min_intra_species_ani": "99.31", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001439845.1", "gtdb_species": "s__Pseudomonas_E lactis", "ani": 82.8116, "matched_fragments": 1135, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.24", "min_intra_species_ani": "95.50", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.81", "num_clustered_genomes": 30, "status": "-" }, { "accession": "GCF_900105675.1", "gtdb_species": "s__Pseudomonas_E synxantha", "ani": 82.5839, "matched_fragments": 1131, "total_fragments": 1934, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.7053, "mean_intra_species_ani": "98.15", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.84", "num_clustered_genomes": 14, "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", "rustica" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }