{ "type": "genome", "identifier": "GCF_003173715.1", "organism": "Methylobacterium durans", "title": "Methylobacterium durans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Seoul Women's University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003173715.1", "bioproject": "PRJNA224116", "biosample": "SAMN09235291", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2202825", "species_taxid": "2202825", "organism_name": "Methylobacterium durans", "infraspecific_name": "strain=17SD2-17", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/29", "asm_name": "ASM317371v1", "asm_submitter": "Seoul Women's University", "gbrs_paired_asm": "GCA_003173715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/173/715/GCF_003173715.1_ASM317371v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6788375", "genome_size_ungapped": "6788375", "gc_percent": "68.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-05", "total_gene_count": "6603", "protein_coding_gene_count": "6036", "non_coding_gene_count": "73", "pubmed_id": "31541329" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-29", "dateModified": "2018-05-29", "datePublished": "2018-05-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylobacterium durans" ], "sample_taxid": [ "2202825" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Seoul" ], "sample_host_location_id": [], "data_size": "1.842 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)": "6788375", "Number of Sequences": "1", "Longest Sequences (bp)": "6788375", "N50 (bp)": "6788375", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.7", "Number of CDSs": "6917", "Average Protein Length": "271.5", "Coding Ratio (%)": "83.0", "Number of rRNAs": "12", "Number of tRNAs": "68", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylobacterium durans", "strain": "strain=17SD2-17", "accession": "GCA_003173715.1", "taxid": 2202825, "species_taxid": 2202825, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2259, "total_fragments": 2262, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylobacterium segetis", "strain": "strain=17J42-1", "accession": "GCA_004348265.1", "taxid": 2488750, "species_taxid": 2488750, "relation_to_type": "type", "validated": true, "ani": 89.1048, "matched_fragments": 1354, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium oxalidis", "strain": "strain=DSM 24028", "accession": "GCA_022179505.1", "taxid": 944322, "species_taxid": 944322, "relation_to_type": "type", "validated": true, "ani": 88.0886, "matched_fragments": 1475, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium oxalidis", "strain": "strain=NBRC 107715", "accession": "GCA_007992195.1", "taxid": 944322, "species_taxid": 944322, "relation_to_type": "type", "validated": true, "ani": 88.084, "matched_fragments": 1469, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium soli", "strain": "strain=YIM 48816", "accession": "GCA_008806385.1", "taxid": 553447, "species_taxid": 553447, "relation_to_type": "type", "validated": true, "ani": 83.8052, "matched_fragments": 1242, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium soli", "strain": "strain=KCTC 22810", "accession": "GCA_022179555.1", "taxid": 553447, "species_taxid": 553447, "relation_to_type": "type", "validated": true, "ani": 83.6449, "matched_fragments": 964, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium dankookense", "strain": "strain=DSM 22415", "accession": "GCA_022179165.1", "taxid": 560405, "species_taxid": 560405, "relation_to_type": "type", "validated": true, "ani": 83.268, "matched_fragments": 1067, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium hispanicum", "strain": "strain=DSM 16372", "accession": "GCA_022179285.1", "taxid": 270350, "species_taxid": 270350, "relation_to_type": "type", "validated": true, "ani": 82.9156, "matched_fragments": 1083, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium symbioticum", "strain": "strain=SB0023/3", "accession": "GCA_902141845.1", "taxid": 2584084, "species_taxid": 2584084, "relation_to_type": "type", "validated": true, "ani": 82.7346, "matched_fragments": 1061, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium cerastii", "strain": "strain=DSM 23679", "accession": "GCA_022179125.1", "taxid": 932741, "species_taxid": 932741, "relation_to_type": "type", "validated": true, "ani": 82.5219, "matched_fragments": 984, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium iners", "strain": "strain=DSM 19015", "accession": "GCA_022179305.1", "taxid": 418707, "species_taxid": 418707, "relation_to_type": "type", "validated": true, "ani": 82.0472, "matched_fragments": 928, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium tardum", "strain": "strain=DSM 19566", "accession": "GCA_023546765.1", "taxid": 374432, "species_taxid": 374432, "relation_to_type": "type", "validated": true, "ani": 81.3611, "matched_fragments": 1046, "total_fragments": 2262, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003173715.1", "gtdb_species": "s__Methylobacterium durans", "ani": 100.0, "matched_fragments": 2258, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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_004348265.1", "gtdb_species": "s__Methylobacterium segetis", "ani": 89.0987, "matched_fragments": 1356, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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_007992195.1", "gtdb_species": "s__Methylobacterium oxalidis", "ani": 88.0899, "matched_fragments": 1470, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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_008806345.1", "gtdb_species": "s__Methylobacterium sp008806345", "ani": 84.2787, "matched_fragments": 1192, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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_008806385.1", "gtdb_species": "s__Methylobacterium soli", "ani": 83.7773, "matched_fragments": 1246, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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_902141855.1", "gtdb_species": "s__Methylobacterium dankookense", "ani": 83.1144, "matched_fragments": 1143, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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_902141845.1", "gtdb_species": "s__Methylobacterium symbioticum", "ani": 82.7429, "matched_fragments": 1059, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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_001422885.1", "gtdb_species": "s__Methylobacterium sp001422885", "ani": 81.7766, "matched_fragments": 987, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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_900112625.1", "gtdb_species": "s__Methylobacterium sp900112625", "ani": 81.6815, "matched_fragments": 1048, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.34", "min_intra_species_ani": "98.23", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_900234795.1", "gtdb_species": "s__Methylobacterium extorquens", "ani": 81.6726, "matched_fragments": 1034, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.03", "min_intra_species_ani": "96.19", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.73", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_900103195.1", "gtdb_species": "s__Methylobacterium sp900103195", "ani": 81.2312, "matched_fragments": 984, "total_fragments": 2262, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.81", "min_intra_species_ani": "96.81", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.014, "cell_length": 0.425, "doubling_h": 0.623, "growth_tmp": 28.448, "optimum_tmp": 27.246, "optimum_ph": 6.721, "genome_size": 6004081.51, "gc_content": 68.2, "coding_genes": 6044.758, "rRNA16S_genes": 6.142, "tRNA_genes": 64.375, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.833, "range_salinity": 0.333, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.935, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.064, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Methylobacterium", "durans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }