{ "type": "genome", "identifier": "GCF_000016525.1", "organism": "Methanobrevibacter smithii ATCC 35061", "title": "Methanobrevibacter smithii ATCC 35061", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Washington University Center for Genome Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000016525.1", "bioproject": "PRJNA224116", "biosample": "SAMN02604313", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "420247", "species_taxid": "2173", "organism_name": "Methanobrevibacter smithii ATCC 35061", "infraspecific_name": "strain=ATCC 35061; PS; DSMZ 861", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2007/06/04", "asm_name": "ASM1652v1", "asm_submitter": "Washington University Center for Genome Sciences", "gbrs_paired_asm": "GCA_000016525.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/016/525/GCF_000016525.1_ASM1652v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "1853160", "genome_size_ungapped": "1853160", "gc_percent": "31.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000016525.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "1815", "protein_coding_gene_count": "1747", "non_coding_gene_count": "45", "pubmed_id": "17563350" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2007-06-04", "dateModified": "2007-06-04", "datePublished": "2007-06-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Methanobrevibacter smithii ATCC 35061" ], "sample_taxid": [ "420247" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.505 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "1853160", "Number of Sequences": "1", "Longest Sequences (bp)": "1853160", "N50 (bp)": "1853160", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "31.0", "Number of CDSs": "1789", "Average Protein Length": "311.5", "Coding Ratio (%)": "90.2", "Number of rRNAs": "4", "Number of tRNAs": "34", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methanobrevibacter smithii", "strain": "strain=ATCC 35061; PS; DSMZ 861", "accession": "GCA_000016525.1", "taxid": 2173, "species_taxid": 2173, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 617, "total_fragments": 617, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methanobrevibacter woesei", "strain": "strain=DSM 11979", "accession": "GCA_003111605.1", "taxid": 190976, "species_taxid": 190976, "relation_to_type": "type", "validated": true, "ani": 80.1496, "matched_fragments": 273, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter oralis", "strain": "strain=DSM 7256", "accession": "GCA_001639275.1", "taxid": 66851, "species_taxid": 66851, "relation_to_type": "type", "validated": true, "ani": 79.7007, "matched_fragments": 281, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter gottschalkii", "strain": "strain=DSM 11977", "accession": "GCA_003814835.1", "taxid": 190974, "species_taxid": 190974, "relation_to_type": "type", "validated": true, "ani": 79.5057, "matched_fragments": 263, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter arboriphilus", "strain": "strain=DH1", "accession": "GCA_002072215.1", "taxid": 39441, "species_taxid": 39441, "relation_to_type": "type", "validated": true, "ani": 76.7783, "matched_fragments": 114, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanobrevibacter cuticularis", "strain": "strain=DSM 11139", "accession": "GCA_001639285.1", "taxid": 47311, "species_taxid": 47311, "relation_to_type": "type", "validated": true, "ani": 76.7182, "matched_fragments": 100, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000016525.1", "gtdb_species": "s__Methanobrevibacter_A smithii", "ani": 100.0, "matched_fragments": 616, "total_fragments": 617, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.32", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.83", "num_clustered_genomes": 24, "status": "conclusive" }, { "accession": "GCF_002252585.1", "gtdb_species": "s__Methanobrevibacter_A smithii_A", "ani": 93.6613, "matched_fragments": 551, "total_fragments": 617, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.61", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_003111605.1", "gtdb_species": "s__Methanobrevibacter_A woesei", "ani": 80.1304, "matched_fragments": 273, "total_fragments": 617, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.82", "min_intra_species_ani": "96.82", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001639275.1", "gtdb_species": "s__Methanobrevibacter_A oralis", "ani": 79.7009, "matched_fragments": 281, "total_fragments": 617, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.83", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003814835.1", "gtdb_species": "s__Methanobrevibacter_A gottschalkii", "ani": 79.5057, 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sp017460025", "ani": 79.0382, "matched_fragments": 179, "total_fragments": 617, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_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_902783085.1", "gtdb_species": "s__Methanobrevibacter_A sp902783085", "ani": 78.1913, "matched_fragments": 220, "total_fragments": 617, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.0, "doubling_h": 1.37, "growth_tmp": 37.0, "optimum_tmp": 38.466, "optimum_ph": 7.15, "genome_size": 1860144.452, "gc_content": 31.16, "coding_genes": 1722.5, "rRNA16S_genes": 2.0, "tRNA_genes": 34.667, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "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": 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": [ "Methanobrevibacter", "smithii", "ATCC", "35061" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }