{ "type": "genome", "identifier": "GCA_026400845.1", "organism": "Alphaproteobacteria bacterium", "title": "Alphaproteobacteria bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Jill Banfield's Lab at Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_026400845.1", "bioproject": "PRJNA852163", "biosample": "SAMN30026342", "wgs_master": "JAPLOH000000000.1", "refseq_category": "na", "taxid": "1913988", "species_taxid": "1913988", "organism_name": "Alphaproteobacteria bacterium", "infraspecific_name": "", "isolate": "LacPavin_0419_WC53_MAG_67_8", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/11/24", "asm_name": "ASM2640084v1", "submitter": "Jill Banfield's Lab at Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/400/845/GCA_026400845.1_ASM2640084v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-11-24", "dateModified": "2022-11-24", "datePublished": "2022-11-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Alphaproteobacteria bacterium" ], "sample_taxid": [ "1913988" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France: Besse-et-Saint-Anastaise, Lac Pavin" ], "sample_host_location_id": [], "data_size": "1.489 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.61, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "5398449", "Number of Sequences": "369", "Longest Sequences (bp)": "117190", "N50 (bp)": "22097", "Gap Ratio (%)": "0.075725", "GCcontent (%)": "67.4", "Number of CDSs": "4917", "Average Protein Length": "311.7", "Coding Ratio (%)": "85.2", "Number of rRNAs": "0", "Number of tRNAs": "44", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodovastum atsumiense", "strain": "strain=G2-11", "accession": "GCA_937425535.1", "taxid": 504468, "species_taxid": 504468, "relation_to_type": "type", "validated": true, "ani": 78.0944, "matched_fragments": 494, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidisphaera rubrifaciens", "strain": "strain=HS-AP3", "accession": "GCA_000964365.1", "taxid": 50715, "species_taxid": 50715, "relation_to_type": "type", "validated": true, "ani": 77.648, "matched_fragments": 240, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidiphilium multivorum", "strain": "strain=AIU301", "accession": "GCA_000964345.1", "taxid": 62140, "species_taxid": 62140, "relation_to_type": "type", "validated": true, "ani": 77.5573, "matched_fragments": 282, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Endobacter medicaginis", "strain": "strain=LMG 26838", "accession": "GCA_013376135.1", "taxid": 1181271, "species_taxid": 1181271, "relation_to_type": "type", "validated": true, "ani": 77.5269, "matched_fragments": 175, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopila globiformis", "strain": "strain=DSM 161", "accession": "GCA_002937115.1", "taxid": 1071, "species_taxid": 1071, "relation_to_type": "type", "validated": true, "ani": 77.4223, "matched_fragments": 408, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas coralli", "strain": "strain=M0104", "accession": "GCA_009829925.1", "taxid": 2545983, "species_taxid": 2545983, "relation_to_type": "type", "validated": true, "ani": 77.4189, "matched_fragments": 399, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidiphilium multivorum", "strain": "strain=AIU301", "accession": "GCA_000202835.1", "taxid": 62140, "species_taxid": 62140, "relation_to_type": "type", "validated": true, "ani": 77.3615, "matched_fragments": 312, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas cervicalis", "strain": "strain=ATCC 49957", "accession": "GCA_000164635.1", "taxid": 204525, "species_taxid": 204525, "relation_to_type": "type", "validated": true, "ani": 77.3537, "matched_fragments": 416, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas gilardii subsp. rosea", "strain": "strain=NCTC13290", "accession": "GCA_900455865.1", "taxid": 243956, "species_taxid": 257708, "relation_to_type": "type", "validated": true, "ani": 77.223, "matched_fragments": 346, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas alkaliterrae", "strain": "strain=DSM 25895", "accession": "GCA_014199195.1", "taxid": 1452450, "species_taxid": 1452450, "relation_to_type": "type", "validated": true, "ani": 77.1972, "matched_fragments": 444, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Siccirubricoccus deserti", "strain": "strain=CGMCC 1.15936", "accession": "GCA_014644195.1", "taxid": 2013562, "species_taxid": 2013562, "relation_to_type": "type", "validated": true, "ani": 77.1949, "matched_fragments": 446, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas rhizosphaerae", "strain": "strain=YW11", "accession": "GCA_002631185.1", "taxid": 1335062, "species_taxid": 1335062, "relation_to_type": "type", "validated": true, "ani": 77.1904, "matched_fragments": 440, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Siccirubricoccus deserti", "strain": "strain=SYSU D8009", "accession": "GCA_014283215.1", "taxid": 2013562, "species_taxid": 2013562, "relation_to_type": "type", "validated": true, "ani": 77.1827, "matched_fragments": 453, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas rubea", "strain": "strain=MO17", "accession": "GCA_016106015.1", "taxid": 2748666, "species_taxid": 2748666, "relation_to_type": "type", "validated": true, "ani": 77.1101, "matched_fragments": 344, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Endobacter medicaginis", "strain": "strain=CECT 8088", "accession": "GCA_014192375.1", "taxid": 1181271, "species_taxid": 1181271, "relation_to_type": "type", "validated": true, "ani": 77.079, "matched_fragments": 280, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas marmotae", "strain": "strain=1318", "accession": "GCA_017654485.1", "taxid": 2768161, "species_taxid": 2768161, "relation_to_type": "type", "validated": true, "ani": 77.0079, "matched_fragments": 326, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Falsiroseomonas frigidaquae", "strain": "strain=JCM 15073", "accession": "GCA_012163145.1", "taxid": 487318, "species_taxid": 487318, "relation_to_type": "type", "validated": true, "ani": 77.0074, "matched_fragments": 416, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseococcus pinisoli", "strain": "strain=XZZS9", "accession": "GCA_018413645.1", "taxid": 2835040, "species_taxid": 2835040, "relation_to_type": "type", "validated": true, "ani": 76.9866, "matched_fragments": 345, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas deserti", "strain": "strain=M3", "accession": "GCA_001982615.1", "taxid": 1817963, "species_taxid": 1817963, "relation_to_type": "type", "validated": true, "ani": 76.9679, "matched_fragments": 440, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas haemaphysalidis", "strain": "strain=546", "accession": "GCA_017355405.1", "taxid": 2768162, "species_taxid": 2768162, "relation_to_type": "type", "validated": true, "ani": 76.9384, "matched_fragments": 372, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidocella facilis", "strain": "strain=ATCC 35904", "accession": "GCA_000687875.1", "taxid": 525, "species_taxid": 525, "relation_to_type": "type", "validated": true, "ani": 76.9237, "matched_fragments": 221, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas wenyumeiae", "strain": "strain=Z23", "accession": "GCA_003696345.1", "taxid": 2478470, "species_taxid": 2478470, "relation_to_type": "type", "validated": true, "ani": 76.8049, "matched_fragments": 381, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseococcus thiosulfatophilus", "strain": "strain=RB-3", "accession": "GCA_017311575.1", "taxid": 35813, "species_taxid": 35813, "relation_to_type": "type", "validated": true, "ani": 76.7751, "matched_fragments": 330, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter diazotrophicus", "strain": "strain=PAl 5", "accession": "GCA_000067045.1", "taxid": 33996, "species_taxid": 33996, "relation_to_type": "type", "validated": true, "ani": 76.7457, "matched_fragments": 172, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter diazotrophicus", "strain": "strain=LMG 7603", "accession": "GCA_014174315.1", "taxid": 33996, "species_taxid": 33996, "relation_to_type": "type", "validated": true, "ani": 76.6687, "matched_fragments": 182, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidisoma silvae", "strain": "strain=HW T2.11", "accession": "GCA_020618775.1", "taxid": 2802396, "species_taxid": 2802396, "relation_to_type": "type", "validated": true, "ani": 76.637, "matched_fragments": 215, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter diazotrophicus", "strain": "strain=PAl 5; ATCC 49037", "accession": "GCA_000021325.1", "taxid": 33996, "species_taxid": 33996, "relation_to_type": "type", "validated": true, "ani": 76.5684, "matched_fragments": 187, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidisoma cellulosilyticum", "strain": "strain=HW T5.17", "accession": "GCA_020621385.1", "taxid": 2802395, "species_taxid": 2802395, "relation_to_type": "type", "validated": true, "ani": 76.4021, "matched_fragments": 226, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Komagataeibacter melaceti", "strain": "strain=AV382", "accession": "GCA_003403295.1", "taxid": 2766577, "species_taxid": 2766577, "relation_to_type": "type", "validated": true, "ani": 76.2748, "matched_fragments": 116, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Komagataeibacter europaeus", "strain": "strain=type strain:LMG 18890", "accession": "GCA_000285295.1", "taxid": 33995, "species_taxid": 33995, "relation_to_type": "suspected-type", "validated": true, "ani": 76.2518, "matched_fragments": 110, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Komagataeibacter oboediens", "strain": "strain=LMG 18849", "accession": "GCA_003207815.1", "taxid": 65958, "species_taxid": 65958, "relation_to_type": "type", "validated": true, "ani": 76.0679, "matched_fragments": 90, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella stibiiresistens", "strain": "strain=SB22", "accession": "GCA_000576635.1", "taxid": 913326, "species_taxid": 913326, "relation_to_type": "type", "validated": true, "ani": 75.8424, "matched_fragments": 239, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aureimonas leprariae", "strain": "strain=YIM 132180", "accession": "GCA_008802405.1", "taxid": 2615207, "species_taxid": 2615207, "relation_to_type": "type", "validated": true, "ani": 75.7666, "matched_fragments": 186, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomonas johnsonii", "strain": "strain=MHS-2", "accession": "GCA_000685275.1", "taxid": 81031, "species_taxid": 81031, "relation_to_type": "type", "validated": true, "ani": 75.372, "matched_fragments": 64, "total_fragments": 1614, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.61, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903865895.1", "gtdb_species": "s__CAIYPH01 sp903865895", "ani": 88.0902, "matched_fragments": 1187, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01", "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_903928045.1", "gtdb_species": "s__CAIYPH01 sp903928045", "ani": 86.5576, "matched_fragments": 853, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.76", "min_intra_species_af": "0.76", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_903845065.1", "gtdb_species": "s__CAIYPH01 sp903845065", "ani": 80.9576, "matched_fragments": 889, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01", "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_903928895.1", "gtdb_species": "s__CAIYPH01 sp903928895", "ani": 80.8991, "matched_fragments": 905, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_001899585.1", "gtdb_species": "s__70-18 sp001899585", "ani": 79.2227, "matched_fragments": 733, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018971455.1", "gtdb_species": "s__REEB85 sp018971455", "ani": 78.9848, "matched_fragments": 321, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85", "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_003133265.1", "gtdb_species": "s__PALSA-911 sp003133265", "ani": 78.0876, "matched_fragments": 377, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911", "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_903918195.1", "gtdb_species": "s__BOG-930 sp903918195", "ani": 78.0685, "matched_fragments": 408, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002937115.1", "gtdb_species": "s__Rhodopila globiformis", "ani": 77.3798, "matched_fragments": 414, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila", "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_014192375.1", "gtdb_species": "s__Endobacter medicaginis", "ani": 77.0729, "matched_fragments": 280, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Endobacter", "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": "-" }, { "accession": "GCA_903944925.1", "gtdb_species": "s__Rhodopila sp903944925", "ani": 76.7992, "matched_fragments": 344, "total_fragments": 1614, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Acetobacterales", "f__Acetobacteraceae", "g__CAIYPH01", "s__CAIYPH01 sp026400845" ], "_genome_taxon": [ "Alphaproteobacteria", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Acetobacterales", "f__Acetobacteraceae", "g__CAIYPH01", "s__CAIYPH01 sp026400845", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Acetobacterales", "Acetobacteraceae", "CAIYPH01", "CAIYPH01", "sp026400845" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }