{ "type": "genome", "identifier": "GCA_005239965.1", "organism": "Methylobacter tundripaludum", "title": "Methylobacter tundripaludum", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Trento", "publication": [ {} ], "properties": { "assembly_accession": "GCA_005239965.1", "bioproject": "PRJNA414404", "biosample": "SAMN08774407", "wgs_master": "SBAV00000000.1", "refseq_category": "na", "taxid": "173365", "species_taxid": "173365", "organism_name": "Methylobacter tundripaludum", "infraspecific_name": "", "isolate": "Bin_16_1", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/05/09", "asm_name": "ASM523996v1", "submitter": "University of Trento", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/005/239/965/GCA_005239965.1_ASM523996v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-05-09", "dateModified": "2019-05-09", "datePublished": "2019-05-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylobacter tundripaludum" ], "sample_taxid": [ "173365" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Italy: Trento, Comano Thermal Spring" ], "sample_host_location_id": [], "data_size": "1.120 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 85.09, "contamination": 0.46, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3903614", "Number of Sequences": "553", "Longest Sequences (bp)": "34027", "N50 (bp)": "8590", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "46.0", "Number of CDSs": "3326", "Average Protein Length": "295.9", "Coding Ratio (%)": "75.6", "Number of rRNAs": "0", "Number of tRNAs": "32", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Crenothrix polyspora", "strain": "", "accession": "GCA_900163755.1", "taxid": 360316, "species_taxid": 360316, "relation_to_type": "reftype", "validated": true, "ani": 79.0618, "matched_fragments": 375, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacter tundripaludum", "strain": "strain=SV96", "accession": "GCA_000190755.3", "taxid": 173365, "species_taxid": 173365, "relation_to_type": "type", "validated": true, "ani": 77.1405, "matched_fragments": 181, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylicorpusculum oleiharenae", "strain": "strain=XLMV4", "accession": "GCA_009828925.2", "taxid": 1338687, "species_taxid": 1338687, "relation_to_type": "type", "validated": true, "ani": 77.095, "matched_fragments": 70, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylovulum miyakonense", "strain": "strain=HT12", "accession": "GCA_000384075.1", "taxid": 645578, "species_taxid": 645578, "relation_to_type": "type", "validated": true, "ani": 76.874, "matched_fragments": 116, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacter marinus", "strain": "strain=A45", "accession": "GCA_000383855.1", "taxid": 34058, "species_taxid": 34058, "relation_to_type": "type", "validated": true, "ani": 76.6046, "matched_fragments": 97, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylovulum psychrotolerans", "strain": "strain=Sph1", "accession": "GCA_002923755.1", "taxid": 1704499, "species_taxid": 1704499, "relation_to_type": "type", "validated": true, "ani": 76.5083, "matched_fragments": 105, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomicrobium lacus", "strain": "strain=LW14", "accession": "GCA_000527095.1", "taxid": 136992, "species_taxid": 136992, "relation_to_type": "type", "validated": true, "ani": 76.1962, "matched_fragments": 72, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomonas denitrificans", "strain": "strain=FJG1", "accession": "GCA_000785705.2", "taxid": 1538553, "species_taxid": 1538553, "relation_to_type": "type", "validated": true, "ani": 76.1396, "matched_fragments": 57, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylosarcina fibrata", "strain": "strain=AML-C10", "accession": "GCA_000372865.1", "taxid": 105972, "species_taxid": 105972, "relation_to_type": "type", "validated": true, "ani": 75.8784, "matched_fragments": 66, "total_fragments": 1013, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 85.09, "contamination": 0.46, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_005239965.1", "gtdb_species": "s__Crenothrix sp005239965", "ani": 100.0, "matched_fragments": 991, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Crenothrix", "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_900163745.1", "gtdb_species": "s__Crenothrix polyspora_B", "ani": 81.6074, "matched_fragments": 512, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Crenothrix", "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_900163755.1", "gtdb_species": "s__Crenothrix polyspora", "ani": 79.0791, "matched_fragments": 373, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Crenothrix", "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_002862125.1", "gtdb_species": "s__KS41 sp002862125", "ani": 77.1991, "matched_fragments": 139, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41", "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_000190755.2", "gtdb_species": "s__Methylobacter_A tundripaludum", "ani": 77.1403, "matched_fragments": 181, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.80", "min_intra_species_ani": "95.64", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.80", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_004299305.1", "gtdb_species": "s__Methylobacter_A sp004299305", "ani": 77.0519, "matched_fragments": 141, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_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_004322395.1", "gtdb_species": "s__Methylobacter_A sp004322395", "ani": 76.9526, "matched_fragments": 150, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_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_002256465.1", "gtdb_species": "s__KS41 sp002256465", "ani": 76.9109, "matched_fragments": 69, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41", "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_016784875.1", "gtdb_species": "s__Methylobacter_A sp016784875", "ani": 76.8002, "matched_fragments": 93, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_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_903873045.1", "gtdb_species": "s__KS41 sp903873045", "ani": 76.7964, "matched_fragments": 122, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41", "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_000745375.1", "gtdb_species": "s__Methylobacter whittenburyi", "ani": 76.7214, "matched_fragments": 95, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "98.36", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_003158415.1", "gtdb_species": "s__KS41 sp003158415", "ani": 76.6951, "matched_fragments": 109, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41", "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_013140465.1", "gtdb_species": "s__KS41 sp013140465", "ani": 76.6249, "matched_fragments": 109, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41", "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_013141505.1", "gtdb_species": "s__Methyloglobulus sp013141505", "ani": 76.6065, "matched_fragments": 105, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloglobulus", "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_903839795.1", "gtdb_species": "s__KS41 sp903839795", "ani": 76.5941, "matched_fragments": 94, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41", "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_006788925.1", "gtdb_species": "s__Methylotuvimicrobium kenyense", "ani": 76.107, "matched_fragments": 51, "total_fragments": 1013, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium", "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": -0.097, "cell_length": 0.278, "doubling_h": 1.943, "growth_tmp": 22.0, "optimum_tmp": 23.0, "optimum_ph": 6.85, "genome_size": 4698225.8, "gc_content": 49.49, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Methylococcales", "f__Methylomonadaceae", "g__Crenothrix", "s__Crenothrix sp005239965" ], "_genome_taxon": [ "Methylobacter", "tundripaludum", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Methylococcales", "f__Methylomonadaceae", "g__Crenothrix", "s__Crenothrix sp005239965", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Methylococcales", "Methylomonadaceae", "Crenothrix", "Crenothrix", "sp005239965" ], "_meo": [ { "id": "MEO_0000029", "label": "hot spring" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }