{ "type": "genome", "identifier": "GCF_002632585.1", "organism": "Xenorhabdus szentirmaii DSM 16338", "title": "Xenorhabdus szentirmaii DSM 16338", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Goethe University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002632585.1", "bioproject": "PRJNA224116", "biosample": "SAMN05375093", "wgs_master": "NIBV00000000.1", "refseq_category": "na", "taxid": "1427518", "species_taxid": "290112", "organism_name": "Xenorhabdus szentirmaii DSM 16338", "infraspecific_name": "strain=DSM 16338", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/23", "asm_name": "ASM263258v1", "asm_submitter": "Goethe University", "gbrs_paired_asm": "GCA_002632585.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/632/585/GCF_002632585.1_ASM263258v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4968473", "genome_size_ungapped": "4962619", "gc_percent": "44.000000", "replicon_count": "0", "scaffold_count": "76", "contig_count": "76", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002632585.1-RS_2024_04_25", "annotation_date": "2024-04-25", "total_gene_count": "4345", "protein_coding_gene_count": "4047", "non_coding_gene_count": "112", "pubmed_id": "28993611" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-23", "dateModified": "2017-10-23", "datePublished": "2017-10-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Xenorhabdus szentirmaii DSM 16338" ], "sample_taxid": [ "1427518" ], "sample_host_organism": [ "Steinernema rarum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Argentina" ], "sample_host_location_id": [], "data_size": "1.405 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)": "4968473", "Number of Sequences": "76", "Longest Sequences (bp)": "2265088", "N50 (bp)": "2145942", "Gap Ratio (%)": "0.117823", "GCcontent (%)": "44.2", "Number of CDSs": "4186", "Average Protein Length": "325.8", "Coding Ratio (%)": "82.3", "Number of rRNAs": "21", "Number of tRNAs": "83", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xenorhabdus szentirmaii", "strain": "strain=DSM 16338", "accession": "GCA_002632585.1", "taxid": 290112, "species_taxid": 290112, "relation_to_type": "type", "validated": true, "ani": 99.9991, "matched_fragments": 1633, "total_fragments": 1636, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xenorhabdus szentirmaii", "strain": "strain=DSM 16338", "accession": "GCA_000531455.1", "taxid": 290112, "species_taxid": 290112, "relation_to_type": "type", "validated": true, "ani": 99.9365, "matched_fragments": 1517, "total_fragments": 1636, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xenorhabdus nematophila", "strain": "strain=ATCC 19061", "accession": "GCA_000252955.1", "taxid": 628, "species_taxid": 628, "relation_to_type": "type", "validated": true, "ani": 83.3662, "matched_fragments": 895, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus mauleonii", "strain": "strain=DSM 17908", "accession": "GCA_900113945.1", "taxid": 351675, "species_taxid": 351675, "relation_to_type": "type", "validated": true, "ani": 83.3276, "matched_fragments": 973, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus mauleonii", "strain": "strain=DSM 17908", "accession": "GCA_002632685.1", "taxid": 351675, "species_taxid": 351675, "relation_to_type": "type", "validated": true, "ani": 83.3224, "matched_fragments": 983, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus lircayensis", "strain": "strain=VLS", "accession": "GCA_016306625.1", "taxid": 2763499, "species_taxid": 2763499, "relation_to_type": "type", "validated": true, "ani": 83.0599, "matched_fragments": 911, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus japonica", "strain": "strain=DSM 16522", "accession": "GCA_900115195.1", "taxid": 53341, "species_taxid": 53341, "relation_to_type": "type", "validated": true, "ani": 82.2672, "matched_fragments": 775, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus miraniensis", "strain": "strain=DSM 17902", "accession": "GCA_002632615.1", "taxid": 351674, "species_taxid": 351674, "relation_to_type": "type", "validated": true, "ani": 82.138, "matched_fragments": 912, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus beddingii", "strain": "strain=DSM 4764", "accession": "GCA_002127545.1", "taxid": 40578, "species_taxid": 40578, "relation_to_type": "type", "validated": true, "ani": 82.123, "matched_fragments": 812, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus ishibashii", "strain": "strain=DSM 22670", "accession": "GCA_002632755.1", "taxid": 1034471, "species_taxid": 1034471, "relation_to_type": "type", "validated": true, "ani": 82.0051, "matched_fragments": 770, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus eapokensis", "strain": "strain=DL20", "accession": "GCA_001908105.1", "taxid": 1873482, "species_taxid": 1873482, "relation_to_type": "type", "validated": true, "ani": 81.9479, "matched_fragments": 782, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus thuongxuanensis", "strain": "strain=30TX1", "accession": "GCA_001908095.1", "taxid": 1873484, "species_taxid": 1873484, "relation_to_type": "type", "validated": true, "ani": 81.7451, "matched_fragments": 769, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus bovienii", "strain": "strain=T228", "accession": "GCA_024721015.1", "taxid": 40576, "species_taxid": 40576, "relation_to_type": "type", "validated": true, "ani": 81.1991, "matched_fragments": 737, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hafnia paralvei", "strain": "strain=ATCC 29927", "accession": "GCA_023698525.1", "taxid": 546367, "species_taxid": 546367, "relation_to_type": "type", "validated": true, "ani": 79.217, "matched_fragments": 148, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photorhabdus hindustanensis", "strain": "strain=H1", "accession": "GCA_002968995.1", "taxid": 2918802, "species_taxid": 2918802, "relation_to_type": "type", "validated": true, "ani": 78.662, "matched_fragments": 355, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photorhabdus temperata", "strain": "strain=DSM 14550", "accession": "GCA_025384845.1", "taxid": 574560, "species_taxid": 574560, "relation_to_type": "type", "validated": true, "ani": 78.6512, "matched_fragments": 376, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002632585.1", "gtdb_species": "s__Xenorhabdus szentirmaii", "ani": 99.9991, "matched_fragments": 1634, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.85", "min_intra_species_ani": "99.72", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000252955.1", "gtdb_species": "s__Xenorhabdus nematophila", "ani": 83.3779, "matched_fragments": 897, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "98.94", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_900113945.1", "gtdb_species": "s__Xenorhabdus mauleonii", "ani": 83.3362, "matched_fragments": 970, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016306625.1", "gtdb_species": "s__Xenorhabdus sp016306625", "ani": 83.065, "matched_fragments": 910, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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_900115195.1", "gtdb_species": "s__Xenorhabdus japonica", "ani": 82.278, "matched_fragments": 775, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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_002632615.1", "gtdb_species": "s__Xenorhabdus miraniensis", "ani": 82.1662, "matched_fragments": 909, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.51", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003610465.1", "gtdb_species": "s__Xenorhabdus ehlersii", "ani": 82.118, "matched_fragments": 811, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.74", "min_intra_species_ani": "99.51", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002127545.1", "gtdb_species": "s__Xenorhabdus beddingii", "ani": 82.1022, "matched_fragments": 813, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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_001037465.1", "gtdb_species": "s__Xenorhabdus khoisanae", "ani": 82.0552, "matched_fragments": 889, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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_002632755.1", "gtdb_species": "s__Xenorhabdus ishibashii", "ani": 82.0162, "matched_fragments": 770, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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_001908105.1", "gtdb_species": "s__Xenorhabdus eapokensis", "ani": 81.8963, "matched_fragments": 789, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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_002632725.1", "gtdb_species": "s__Xenorhabdus hominickii", "ani": 81.7617, "matched_fragments": 881, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001908095.1", "gtdb_species": "s__Xenorhabdus thuongxuanensis", "ani": 81.7408, "matched_fragments": 766, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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_015163665.1", "gtdb_species": "s__Xenorhabdus sp015163665", "ani": 81.7381, "matched_fragments": 779, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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_002127535.1", "gtdb_species": "s__Xenorhabdus vietnamensis", "ani": 81.7287, "matched_fragments": 886, "total_fragments": 1636, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "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": -0.236, "cell_length": 0.444, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 30.0, "optimum_ph": 7.2, "genome_size": 4824775.0, "gc_content": 44.612, "coding_genes": 3821.286, "rRNA16S_genes": 7.0, "tRNA_genes": 79.6, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.666, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Xenorhabdus", "szentirmaii", "DSM", "16338" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }