{ "type": "genome", "identifier": "GCF_000167355.1", "organism": "Desulfuromonas acetoxidans DSM 684", "title": "Desulfuromonas acetoxidans DSM 684", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000167355.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441806", "wgs_master": "AAEW00000000.2", "refseq_category": "reference genome", "taxid": "281689", "species_taxid": "891", "organism_name": "Desulfuromonas acetoxidans DSM 684", "infraspecific_name": "strain=DSM 684", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2006/05/12", "asm_name": "ASM16735v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000167355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/167/355/GCF_000167355.1_ASM16735v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3828328", "genome_size_ungapped": "3828312", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "51", "contig_count": "51", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000167355.1-RS_2024_03_20", "annotation_date": "2024-03-20", "total_gene_count": "3385", "protein_coding_gene_count": "3310", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2006-05-12", "dateModified": "2006-05-12", "datePublished": "2006-05-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfuromonas acetoxidans DSM 684" ], "sample_taxid": [ "281689" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.089 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 92.19, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3828328", "Number of Sequences": "51", "Longest Sequences (bp)": "313951", "N50 (bp)": "195317", "Gap Ratio (%)": "0.000627", "GCcontent (%)": "51.8", "Number of CDSs": "3337", "Average Protein Length": "333.0", "Coding Ratio (%)": "87.1", "Number of rRNAs": "4", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfuromonas acetoxidans", "strain": "strain=DSM 684", "accession": "GCA_000167355.1", "taxid": 891, "species_taxid": 891, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1244, "total_fragments": 1247, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulfuromonas thiophila", "strain": "strain=DSM 8987", "accession": "GCA_900101955.1", "taxid": 57664, "species_taxid": 57664, "relation_to_type": "type", "validated": true, "ani": 77.6288, "matched_fragments": 147, "total_fragments": 1247, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Syntrophotalea carbinolica", "strain": "strain=DSM 2380", "accession": "GCA_000012885.1", "taxid": 19, "species_taxid": 19, "relation_to_type": "type", "validated": true, "ani": 77.0667, "matched_fragments": 60, "total_fragments": 1247, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geoalkalibacter halelectricus", "strain": "strain=SAP-1", "accession": "GCA_025263685.1", "taxid": 2847045, "species_taxid": 2847045, "relation_to_type": "type", "validated": true, "ani": 76.8473, "matched_fragments": 57, "total_fragments": 1247, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Syntrophotalea acetylenivorans", "strain": "strain=SFB93", "accession": "GCA_001887775.1", "taxid": 1842532, "species_taxid": 1842532, "relation_to_type": "type", "validated": true, "ani": 76.5234, "matched_fragments": 63, "total_fragments": 1247, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geothermobacter hydrogeniphilus", "strain": "strain=EPR-M", "accession": "GCA_002093115.1", "taxid": 1969733, "species_taxid": 1969733, "relation_to_type": "type", "validated": true, "ani": 76.3672, "matched_fragments": 58, "total_fragments": 1247, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 92.19, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000167355.1", "gtdb_species": "s__Desulfuromonas acetoxidans", "ani": 100.0, "matched_fragments": 1244, "total_fragments": 1247, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Desulfuromonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCA_002869685.1", "gtdb_species": "s__Desulfuromonas sp002869685", "ani": 81.2553, "matched_fragments": 523, "total_fragments": 1247, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Desulfuromonas", "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_900101955.1", "gtdb_species": "s__Pseudodesulfuromonas thiophila", "ani": 77.6498, "matched_fragments": 147, "total_fragments": 1247, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Pseudodesulfuromonas", "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_016936455.1", "gtdb_species": "s__Pseudodesulfuromonas sp016936455", "ani": 77.6013, "matched_fragments": 160, "total_fragments": 1247, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Pseudodesulfuromonas", "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_001751155.1", "gtdb_species": "s__Desulfuromonas sp001751155", "ani": 77.1469, "matched_fragments": 72, "total_fragments": 1247, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Desulfuromonas", "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_002084705.1", "gtdb_species": "s__Desulfuromonas sp002084705", "ani": 76.8192, "matched_fragments": 74, "total_fragments": 1247, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Desulfuromonas", "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_013152145.1", "gtdb_species": "s__Malonomonas sp013152145", "ani": 75.7708, "matched_fragments": 50, "total_fragments": 1247, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Malonomonas", "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": -0.155, "cell_length": 0.287, "doubling_h": null, "growth_tmp": 26.714, "optimum_tmp": 22.166, "optimum_ph": 7.3, "genome_size": 3476713.666, "gc_content": 61.195, "coding_genes": 3459.0, "rRNA16S_genes": 2.0, "tRNA_genes": 55.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "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": 0.666, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.333, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Desulfuromonas", "acetoxidans", "DSM", "684" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }