{ "type": "genome", "identifier": "GCA_947464665.1", "organism": "Comamonadaceae bacterium", "title": "Comamonadaceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "BIOLOGY CENTRE ASCR, V.V.I., INSTITUTE OF HYDROBIO", "publication": [ {} ], "properties": { "assembly_accession": "GCA_947464665.1", "bioproject": "PRJEB35770", "biosample": "SAMEA112174220", "wgs_master": "CANHXV000000000.1", "refseq_category": "na", "taxid": "1871071", "species_taxid": "1871071", "organism_name": "Comamonadaceae bacterium", "infraspecific_name": "", "isolate": "RE-4nov15-194", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/12/02", "asm_name": "RE-4nov15-194", "submitter": "BIOLOGY CENTRE ASCR, V.V.I., INSTITUTE OF HYDROBIO", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/947/464/665/GCA_947464665.1_RE-4nov15-194", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-12-02", "dateModified": "2022-12-02", "datePublished": "2022-12-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Comamonadaceae bacterium" ], "sample_taxid": [ "1871071" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Czech Republic" ], "sample_host_location_id": [], "data_size": "0.547 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 50.76, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1916284", "Number of Sequences": "209", "Longest Sequences (bp)": "53491", "N50 (bp)": "11616", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "51.6", "Number of CDSs": "1674", "Average Protein Length": "317.6", "Coding Ratio (%)": "83.2", "Number of rRNAs": "0", "Number of tRNAs": "21", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Limnohabitans planktonicus", "strain": "strain=II-D5", "accession": "GCA_001270065.2", "taxid": 540060, "species_taxid": 540060, "relation_to_type": "type", "validated": true, "ani": 76.9934, "matched_fragments": 115, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limnohabitans curvus", "strain": "strain=MWH-C5", "accession": "GCA_003063475.1", "taxid": 323423, "species_taxid": 323423, "relation_to_type": "type", "validated": true, "ani": 76.871, "matched_fragments": 118, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limnohabitans radicicola", "strain": "strain=JUR4", "accession": "GCA_014837235.1", "taxid": 2771427, "species_taxid": 2771427, "relation_to_type": "type", "validated": true, "ani": 76.6669, "matched_fragments": 111, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax temperans", "strain": "strain=DSM 7270", "accession": "GCA_006716905.1", "taxid": 80878, "species_taxid": 80878, "relation_to_type": "type", "validated": true, "ani": 76.2853, "matched_fragments": 60, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax saidenbachensis", "strain": "strain=DSM 22694", "accession": "GCA_001955715.1", "taxid": 1484693, "species_taxid": 1484693, "relation_to_type": "type", "validated": true, "ani": 76.0858, "matched_fragments": 55, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax saidenbachensis", "strain": "strain=ED16", "accession": "GCA_000498435.1", "taxid": 1484693, "species_taxid": 1484693, "relation_to_type": "type", "validated": true, "ani": 76.0858, "matched_fragments": 55, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax soli", "strain": "strain=DSM 25157", "accession": "GCA_900107605.1", "taxid": 592050, "species_taxid": 592050, "relation_to_type": "type", "validated": true, "ani": 75.956, "matched_fragments": 52, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 50.76, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_009693505.1", "gtdb_species": "s__Limnohabitans_A sp009693505", "ani": 87.3858, "matched_fragments": 421, "total_fragments": 541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A", "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": "GCA_005789685.1", "gtdb_species": "s__Limnohabitans_A sp005789685", "ani": 86.7845, "matched_fragments": 292, "total_fragments": 541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A", "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": "GCA_903856875.1", "gtdb_species": "s__Limnohabitans_A sp903856875", "ani": 85.1675, "matched_fragments": 301, "total_fragments": 541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A", "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": "GCA_903844775.1", "gtdb_species": "s__Limnohabitans_A sp903844775", "ani": 82.0596, "matched_fragments": 291, "total_fragments": 541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A", "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": "GCA_903961095.1", "gtdb_species": "s__Limnohabitans_A sp903961095", "ani": 81.7728, "matched_fragments": 347, "total_fragments": 541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.25", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003063375.1", "gtdb_species": "s__Limnohabitans_A sp003063375", "ani": 81.623, "matched_fragments": 376, "total_fragments": 541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A", "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_001269365.1", "gtdb_species": "s__Limnohabitans_A sp001269365", "ani": 80.8721, "matched_fragments": 323, "total_fragments": 541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A", "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_001412575.1", "gtdb_species": "s__Limnohabitans_A sp001412575", "ani": 80.6874, "matched_fragments": 315, "total_fragments": 541, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "97.72", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.247, "cell_length": 0.176, "doubling_h": 1.035, "growth_tmp": 28.094, "optimum_tmp": 29.554, "optimum_ph": 7.082, "genome_size": 4640040.381, "gc_content": 65.016, "coding_genes": 4414.595, "rRNA16S_genes": 3.003, "tRNA_genes": 56.995, "gram_stain": 0.0, "sporulation": 0.018, "motility": 0.797, "range_salinity": 0.2, "facultative_respiration": 0.138, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.861, "mesophilic_range_tmp": 0.96, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.04, "bacillus_cell_shape": 0.855, "coccus_cell_shape": 0.052, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.013, "vibrio_cell_shape": 0.052, "spiral_cell_shape": 0.026 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Limnohabitans_A", "s__Limnohabitans_A sp947464665" ], "_genome_taxon": [ "Comamonadaceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Limnohabitans_A", "s__Limnohabitans_A sp947464665", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Burkholderiales", "Burkholderiaceae", "Limnohabitans", "A", "Limnohabitans", "A", "sp947464665" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }