{ "type": "genome", "identifier": "GCA_004796375.1", "organism": "Desulfobacteraceae bacterium", "title": "Desulfobacteraceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Texas A&M - Corpus Christi", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004796375.1", "bioproject": "PRJNA490746", "biosample": "SAMN10091129", "wgs_master": "QZLA00000000.1", "refseq_category": "na", "taxid": "2049433", "species_taxid": "2049433", "organism_name": "Desulfobacteraceae bacterium", "infraspecific_name": "", "isolate": "Madre2", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/16", "asm_name": "ASM479637v1", "submitter": "Texas A&M - Corpus Christi", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/796/375/GCA_004796375.1_ASM479637v1", "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": "2019-04-16", "dateModified": "2019-04-16", "datePublished": "2019-04-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfobacteraceae bacterium" ], "sample_taxid": [ "2049433" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Texas, Kleberg County, Upper Laguna Madre" ], "sample_host_location_id": [], "data_size": "1.602 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.45, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "5613049", "Number of Sequences": "410", "Longest Sequences (bp)": "107130", "N50 (bp)": "21258", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.5", "Number of CDSs": "4566", "Average Protein Length": "341.0", "Coding Ratio (%)": "83.2", "Number of rRNAs": "1", "Number of tRNAs": "32", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfospira joergensenii", "strain": "strain=DSM 10085", "accession": "GCA_000420085.1", "taxid": 53329, "species_taxid": 53329, "relation_to_type": "type", "validated": true, "ani": 76.76, "matched_fragments": 221, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfotignum balticum", "strain": "strain=DSM 7044", "accession": "GCA_000421285.1", "taxid": 115781, "species_taxid": 115781, "relation_to_type": "type", "validated": true, "ani": 76.5767, "matched_fragments": 166, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobacter vibrioformis", "strain": "strain=DSM 8776", "accession": "GCA_000745975.1", "taxid": 34031, "species_taxid": 34031, "relation_to_type": "type", "validated": true, "ani": 76.3942, "matched_fragments": 92, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfotignum phosphitoxidans", "strain": "strain=DSM 13687", "accession": "GCA_000350545.1", "taxid": 190898, "species_taxid": 190898, "relation_to_type": "type", "validated": true, "ani": 76.367, "matched_fragments": 169, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobacula phenolica", "strain": "strain=DSM 3384", "accession": "GCA_900105645.1", "taxid": 90732, "species_taxid": 90732, "relation_to_type": "type", "validated": true, "ani": 76.2697, "matched_fragments": 89, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobacter hydrogenophilus", "strain": "strain=DSM 3380", "accession": "GCA_003261095.1", "taxid": 2291, "species_taxid": 2291, "relation_to_type": "type", "validated": true, "ani": 76.2665, "matched_fragments": 81, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobacter hydrogenophilus", "strain": "strain=AcRS1", "accession": "GCA_004319545.1", "taxid": 2291, "species_taxid": 2291, "relation_to_type": "type", "validated": true, "ani": 76.2465, "matched_fragments": 82, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobacter hydrogenophilus", "strain": "strain=DSM 3380", "accession": "GCA_010499545.1", "taxid": 2291, "species_taxid": 2291, "relation_to_type": "type", "validated": true, "ani": 76.2461, "matched_fragments": 82, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobacter latus", "strain": "strain=AcRS2", "accession": "GCA_013389365.1", "taxid": 2292, "species_taxid": 2292, "relation_to_type": "type", "validated": true, "ani": 76.2451, "matched_fragments": 80, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobacula toluolica", "strain": "strain=Tol2", "accession": "GCA_000307105.1", "taxid": 28223, "species_taxid": 28223, "relation_to_type": "type", "validated": true, "ani": 76.1802, "matched_fragments": 96, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfobacter curvatus", "strain": "strain=DSM 3379", "accession": "GCA_000373985.1", "taxid": 2290, "species_taxid": 2290, "relation_to_type": "type", "validated": true, "ani": 76.1502, "matched_fragments": 89, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulforapulum autotrophicum", "strain": "strain=HRM2", "accession": "GCA_000020365.1", "taxid": 2296, "species_taxid": 2296, "relation_to_type": "type", "validated": true, "ani": 75.538, "matched_fragments": 92, "total_fragments": 1648, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.45, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004796375.1", "gtdb_species": "s__MADRE2 sp004796375", "ani": 100.0, "matched_fragments": 1627, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__MADRE2", "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": "conclusive" }, { "accession": "GCF_000420085.1", "gtdb_species": "s__Desulfospira joergensenii", "ani": 76.7706, "matched_fragments": 220, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfospira", "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_011390335.1", "gtdb_species": "s__Desulfotignum sp011390335", "ani": 76.7421, "matched_fragments": 184, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum", "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_003538835.1", "gtdb_species": "s__Desulfobacter sp003538835", "ani": 76.6201, "matched_fragments": 149, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter", "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_002085465.1", "gtdb_species": "s__NBML01 sp002085465", "ani": 76.4474, "matched_fragments": 55, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01", "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_000350545.1", "gtdb_species": "s__Desulfotignum phosphitoxidans", "ani": 76.4209, "matched_fragments": 164, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum", "ani_circumscription_radius": 96.875, "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_011389555.1", "gtdb_species": "s__Desulfotignum sp011389555", "ani": 76.4116, "matched_fragments": 144, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum", "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_016743945.1", "gtdb_species": "s__NBML01 sp016743945", "ani": 76.3829, "matched_fragments": 152, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01", "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_012031875.1", "gtdb_species": "s__Desulfobacula sp012031875", "ani": 76.3451, "matched_fragments": 168, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula", "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_016744295.1", "gtdb_species": "s__NBML01 sp016744295", "ani": 76.2775, "matched_fragments": 150, "total_fragments": 1648, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": 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"N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.042, "cell_length": 0.364, "doubling_h": 1.305, "growth_tmp": 28.037, "optimum_tmp": 30.588, "optimum_ph": 7.267, "genome_size": 5675869.625, "gc_content": 51.573, "coding_genes": 4621.583, "rRNA16S_genes": 3.75, "tRNA_genes": 52.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.619, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.695, "coccus_cell_shape": 0.043, "filament_cell_shape": 0.043, "coccobacillus_cell_shape": 0.086, "vibrio_cell_shape": 0.13, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Desulfobacteria", "o__Desulfobacterales", "f__Desulfobacteraceae", "g__MADRE2", "s__MADRE2 sp004796375" ], 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