{ "type": "genome", "identifier": "GCF_001043915.1", "organism": "Methylobacterium aquaticum", "title": "Methylobacterium aquaticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIR-Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001043915.1", "bioproject": "PRJNA224116", "biosample": "SAMN03401149", "wgs_master": "LABX00000000.1", "refseq_category": "reference genome", "taxid": "270351", "species_taxid": "270351", "organism_name": "Methylobacterium aquaticum", "infraspecific_name": "strain=DSM 16371", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/06/30", "asm_name": "ASM104391v1", "asm_submitter": "CSIR-Institute of Microbial Technology", "gbrs_paired_asm": "GCA_001043915.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/043/915/GCF_001043915.1_ASM104391v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7425331", "genome_size_ungapped": "7425331", "gc_percent": "70.000000", "replicon_count": "0", "scaffold_count": "512", "contig_count": "512", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001043915.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "6996", "protein_coding_gene_count": "6604", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-06-30", "dateModified": "2015-06-30", "datePublished": "2015-06-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylobacterium aquaticum" ], "sample_taxid": [ "270351" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain: Seville" ], "sample_host_location_id": [], "data_size": "2.022 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7425331", "Number of Sequences": "512", "Longest Sequences (bp)": "131309", "N50 (bp)": "32100", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.9", "Number of CDSs": "6532", "Average Protein Length": "303.1", "Coding Ratio (%)": "80.0", "Number of rRNAs": "4", "Number of tRNAs": "67", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylobacterium aquaticum", "strain": "strain=DSM 16371", "accession": "GCA_001043915.1", "taxid": 270351, "species_taxid": 270351, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2236, "total_fragments": 2255, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylobacterium tarhaniae", "strain": "strain=DSM 25844", "accession": "GCA_001043955.1", "taxid": 1187852, "species_taxid": 1187852, "relation_to_type": "type", "validated": true, "ani": 90.0222, "matched_fragments": 1380, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium frigidaeris", "strain": "strain=JCM 32048", "accession": "GCA_022179185.1", "taxid": 2038277, "species_taxid": 2038277, "relation_to_type": "type", "validated": true, "ani": 89.8573, "matched_fragments": 1573, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium currus", "strain": "strain=PR1016A", "accession": "GCA_003058325.1", "taxid": 2051553, "species_taxid": 2051553, "relation_to_type": "type", "validated": true, "ani": 89.73, "matched_fragments": 1592, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium frigidaeris", "strain": "strain=IER25-16", "accession": "GCA_002759055.1", "taxid": 2038277, "species_taxid": 2038277, "relation_to_type": "type", "validated": true, "ani": 89.4814, "matched_fragments": 1025, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium platani", "strain": "strain=PMB02", "accession": "GCA_001653715.1", "taxid": 427683, "species_taxid": 427683, "relation_to_type": "type", "validated": true, "ani": 89.4707, "matched_fragments": 1527, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium platani", "strain": "strain=JCM 14648", "accession": "GCA_001043885.1", "taxid": 427683, "species_taxid": 427683, "relation_to_type": "type", "validated": true, "ani": 89.4672, "matched_fragments": 1375, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium terrae", "strain": "strain=17Sr1-28", "accession": "GCA_003173755.1", "taxid": 2202827, "species_taxid": 2202827, "relation_to_type": "type", "validated": true, "ani": 89.4191, "matched_fragments": 1483, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium terricola", "strain": "strain=17Sr1-39", "accession": "GCA_006151805.1", "taxid": 2583531, "species_taxid": 2583531, "relation_to_type": "type", "validated": true, "ani": 89.2611, "matched_fragments": 1585, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium indicum", "strain": "strain=SE2.11", "accession": "GCA_001043895.1", "taxid": 1775910, "species_taxid": 1775910, "relation_to_type": "type", "validated": true, "ani": 88.973, "matched_fragments": 1436, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium ajmalii", "strain": "strain=IF7SW-B2", "accession": "GCA_016613415.1", "taxid": 2738439, "species_taxid": 2738439, "relation_to_type": "type", "validated": true, "ani": 88.8995, "matched_fragments": 1484, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium variabile", "strain": "strain=DSM 16961", "accession": "GCA_001043975.1", "taxid": 298794, "species_taxid": 298794, "relation_to_type": "type", "validated": true, "ani": 88.7743, "matched_fragments": 1428, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium nonmethylotrophicum", "strain": "strain=6HR-1", "accession": "GCA_004745635.1", "taxid": 1141884, "species_taxid": 1141884, "relation_to_type": "type", "validated": true, "ani": 88.6613, "matched_fragments": 1574, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium oryzihabitans", "strain": "strain=TER-1", "accession": "GCA_004004555.2", "taxid": 2499852, "species_taxid": 2499852, "relation_to_type": "type", "validated": true, "ani": 84.284, "matched_fragments": 1290, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium crusticola", "strain": "strain=KCTC 52305", "accession": "GCA_022179145.1", "taxid": 1697972, "species_taxid": 1697972, "relation_to_type": "type", "validated": true, "ani": 83.8501, "matched_fragments": 1367, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium haplocladii", "strain": "strain=DSM 24195", "accession": "GCA_022179265.1", "taxid": 1176176, "species_taxid": 1176176, "relation_to_type": "type", "validated": true, "ani": 79.949, "matched_fragments": 693, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium haplocladii", "strain": "strain=NBRC 107714", "accession": "GCA_007992175.1", "taxid": 1176176, "species_taxid": 1176176, "relation_to_type": "type", "validated": true, "ani": 79.9017, "matched_fragments": 731, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ancylobacter dichloromethanicus", "strain": "strain=VKM B-2484", "accession": "GCA_018390645.1", "taxid": 518825, "species_taxid": 518825, "relation_to_type": "type", "validated": true, "ani": 77.6231, "matched_fragments": 474, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium norvegicum", "strain": "strain=10.2.2", "accession": "GCA_004919685.1", "taxid": 1085774, "species_taxid": 1085774, "relation_to_type": "type", "validated": true, "ani": 76.8027, "matched_fragments": 355, "total_fragments": 2255, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001043915.1", "gtdb_species": "s__Methylobacterium aquaticum", "ani": 100.0, "matched_fragments": 2236, "total_fragments": 2255, "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": "GCA_019216885.1", "gtdb_species": "s__Methylobacterium sp019216885", "ani": 90.3815, "matched_fragments": 1637, "total_fragments": 2255, "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_016804325.1", "gtdb_species": "s__Methylobacterium aquaticum_C", "ani": 90.3413, "matched_fragments": 1629, "total_fragments": 2255, "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_001043955.1", "gtdb_species": "s__Methylobacterium tarhaniae", "ani": 89.9821, "matched_fragments": 1385, "total_fragments": 2255, "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_003173775.1", "gtdb_species": "s__Methylobacterium sp003173775", "ani": 89.8901, "matched_fragments": 1505, "total_fragments": 2255, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.16", "min_intra_species_ani": "95.16", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003058325.1", "gtdb_species": "s__Methylobacterium currus", "ani": 89.7562, "matched_fragments": 1592, "total_fragments": 2255, "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_001653715.1", "gtdb_species": "s__Methylobacterium platani", "ani": 89.4192, "matched_fragments": 1531, "total_fragments": 2255, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011043735.1", "gtdb_species": "s__Methylobacterium sp011043735", "ani": 89.3067, "matched_fragments": 1592, "total_fragments": 2255, "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_001043895.1", "gtdb_species": "s__Methylobacterium indicum", "ani": 88.9455, "matched_fragments": 1439, "total_fragments": 2255, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "98.07", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_004745635.1", "gtdb_species": "s__Methylobacterium sp004745635", "ani": 88.6737, "matched_fragments": 1572, "total_fragments": 2255, "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_004004555.2", "gtdb_species": "s__Methylobacterium sp004004555", "ani": 84.2924, "matched_fragments": 1285, "total_fragments": 2255, "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_008040035.1", "gtdb_species": "s__Methylobacterium sp008040035", "ani": 80.109, "matched_fragments": 727, "total_fragments": 2255, "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_014191355.1", "gtdb_species": "s__Methylobacterium sp014191355", "ani": 79.9945, "matched_fragments": 831, "total_fragments": 2255, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.204, "cell_length": 0.795, "doubling_h": 0.623, "growth_tmp": 27.0, "optimum_tmp": 28.0, "optimum_ph": 6.0, "genome_size": 6993198.571, "gc_content": 70.772, "coding_genes": 6813.667, "rRNA16S_genes": 11.0, "tRNA_genes": 97.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": 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": [ "Methylobacterium", "aquaticum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }