{ "type": "genome", "identifier": "GCF_000820505.1", "organism": "Geoalkalibacter ferrihydriticus DSM 17813", "title": "Geoalkalibacter ferrihydriticus DSM 17813", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Minnesota", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000820505.1", "bioproject": "PRJNA224116", "biosample": "SAMN03097396", "wgs_master": "JWJD00000000.1", "refseq_category": "na", "taxid": "1121915", "species_taxid": "392333", "organism_name": "Geoalkalibacter ferrihydriticus DSM 17813", "infraspecific_name": "strain=DSM 17813", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/01/16", "asm_name": "ASM82050v1", "asm_submitter": "University of Minnesota", "gbrs_paired_asm": "GCA_000820505.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/820/505/GCF_000820505.1_ASM82050v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3839692", "genome_size_ungapped": "3839681", "gc_percent": "58.000000", "replicon_count": "0", "scaffold_count": "23", "contig_count": "23", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-25", "total_gene_count": "3496", "protein_coding_gene_count": "3414", "non_coding_gene_count": "55", "pubmed_id": "25767222" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-01-16", "dateModified": "2015-01-16", "datePublished": "2015-01-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Geoalkalibacter ferrihydriticus DSM 17813" ], "sample_taxid": [ "1121915" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia: Lake Khadyn, Tuva Region" ], "sample_host_location_id": [], "data_size": "1.082 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)": "3839692", "Number of Sequences": "23", "Longest Sequences (bp)": "1394064", "N50 (bp)": "602663", "Gap Ratio (%)": "0.003438", "GCcontent (%)": "57.9", "Number of CDSs": "3498", "Average Protein Length": "325.2", "Coding Ratio (%)": "88.9", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Geoalkalibacter ferrihydriticus", "strain": "strain=DSM 17813", "accession": "GCA_000820505.1", "taxid": 392333, "species_taxid": 392333, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1266, "total_fragments": 1268, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Geoalkalibacter ferrihydriticus", "strain": "strain=DSM 17813", "accession": "GCA_900103065.1", "taxid": 392333, "species_taxid": 392333, "relation_to_type": "type", "validated": true, "ani": 99.9881, "matched_fragments": 1254, "total_fragments": 1268, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Geoalkalibacter halelectricus", "strain": "strain=SAP-1", "accession": "GCA_025263685.1", "taxid": 2847045, "species_taxid": 2847045, "relation_to_type": "type", "validated": true, "ani": 81.1868, "matched_fragments": 856, "total_fragments": 1268, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geoalkalibacter subterraneus", "strain": "strain=Red1", "accession": "GCA_000827125.1", "taxid": 483547, "species_taxid": 483547, "relation_to_type": "type", "validated": true, "ani": 77.9923, "matched_fragments": 284, "total_fragments": 1268, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas versatilis", "strain": "strain=NIT-T3", "accession": "GCA_019704135.1", "taxid": 2802975, "species_taxid": 2802975, "relation_to_type": "type", "validated": true, "ani": 77.5826, "matched_fragments": 272, "total_fragments": 1268, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas soudanensis", "strain": "strain=WTL", "accession": "GCA_001278055.1", "taxid": 1603606, "species_taxid": 1603606, "relation_to_type": "type", "validated": true, "ani": 77.181, "matched_fragments": 194, "total_fragments": 1268, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geothermobacter ehrlichii", "strain": "strain=SS015", "accession": "GCA_008124615.1", "taxid": 213224, "species_taxid": 213224, "relation_to_type": "type", "validated": true, "ani": 76.8085, "matched_fragments": 152, "total_fragments": 1268, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Syntrophotalea acetylenica", "strain": "strain=DSM 3246", "accession": "GCA_001888165.1", "taxid": 29542, "species_taxid": 29542, "relation_to_type": "type", "validated": true, "ani": 76.753, "matched_fragments": 93, "total_fragments": 1268, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas thiophila", "strain": "strain=DSM 8987", "accession": "GCA_900101955.1", "taxid": 57664, "species_taxid": 57664, "relation_to_type": "type", "validated": true, "ani": 76.7215, "matched_fragments": 104, "total_fragments": 1268, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas acetoxidans", "strain": "strain=DSM 684", "accession": "GCA_000167355.1", "taxid": 891, "species_taxid": 891, "relation_to_type": "type", "validated": true, "ani": 76.6312, "matched_fragments": 50, "total_fragments": 1268, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000820505.1", "gtdb_species": "s__Geoalkalibacter ferrihydriticus", "ani": 100.0, "matched_fragments": 1266, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geoalkalibacteraceae;g__Geoalkalibacter", "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": "conclusive" }, { "accession": "GCF_000827125.1", "gtdb_species": "s__Geoalkalibacter_A subterraneus", "ani": 77.9919, "matched_fragments": 284, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geoalkalibacteraceae;g__Geoalkalibacter_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_001278055.1", "gtdb_species": "s__Deferrimonas soudanensis", "ani": 77.2705, "matched_fragments": 192, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__WTL;g__Deferrimonas", "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_014860175.1", "gtdb_species": "s__JACZKF01 sp014860175", "ani": 77.0595, "matched_fragments": 143, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JACZKF01;g__JACZKF01", "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_002898515.1", "gtdb_species": "s__PPFX01 sp002898515", "ani": 76.8606, "matched_fragments": 137, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01", "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_008124615.1", "gtdb_species": "s__Geothermobacter ehrlichii", "ani": 76.7928, "matched_fragments": 153, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter", "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_001888165.1", "gtdb_species": "s__Syntrophotalea acetylenica", "ani": 76.7782, "matched_fragments": 92, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002093115.1", "gtdb_species": "s__PPFX01 sp002093115", "ani": 76.7296, "matched_fragments": 123, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01", "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": 76.6984, "matched_fragments": 104, "total_fragments": 1268, "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_002435955.1", "gtdb_species": "s__Syntrophotalea sp002435955", "ani": 76.6229, "matched_fragments": 97, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea", "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_001799485.1", "gtdb_species": "s__UBA12091 sp001799485", "ani": 76.5637, "matched_fragments": 115, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2197;g__UBA12091", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_003246035.1", "gtdb_species": "s__SZUA-401 sp003246035", "ani": 76.3837, "matched_fragments": 57, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__SZUA-401;g__SZUA-401", "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_012974445.1", "gtdb_species": "s__JAAXQG01 sp012974445", "ani": 76.3571, "matched_fragments": 88, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JAAXQG01;g__JAAXQG01", "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_003695205.1", "gtdb_species": "s__Geothermobacter sp003695205", "ani": 76.0641, "matched_fragments": 78, "total_fragments": 1268, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter", "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": -0.523, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 35.0, "optimum_tmp": 30.0, "optimum_ph": 7.0, "genome_size": 3839829.5, "gc_content": 57.94, "coding_genes": 3309.667, "rRNA16S_genes": 3.0, "tRNA_genes": 52.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": 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": [ "Geoalkalibacter", "ferrihydriticus", "DSM", "17813" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }