{ "type": "genome", "identifier": "GCA_905479055.1", "organism": "uncultured Rhodobacteraceae bacterium", "title": "uncultured Rhodobacteraceae bacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY", "publication": [ {} ], "properties": { "assembly_accession": "GCA_905479055.1", "bioproject": "PRJEB38290", "biosample": "SAMEA8498487", "wgs_master": "CAJQLC000000000.1", "refseq_category": "na", "taxid": "157276", "species_taxid": "157276", "organism_name": "uncultured Rhodobacteraceae bacterium", "infraspecific_name": "", "isolate": "0.2_20180517_Bin_163_sub_1", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/15", "asm_name": "0.2_20180517_Bin_163_sub_1", "submitter": "MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/479/055/GCA_905479055.1_0.2_20180517_Bin_163_sub_1", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-15", "dateModified": "2021-04-15", "datePublished": "2021-04-15", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Rhodobacteraceae bacterium" ], "sample_taxid": [ "157276" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "North Sea" ], "sample_host_location_id": [], "data_size": "0.993 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 86.57, "contamination": 0.52, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3455422", "Number of Sequences": "343", "Longest Sequences (bp)": "50716", "N50 (bp)": "12498", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.6", "Number of CDSs": "3003", "Average Protein Length": "304.9", "Coding Ratio (%)": "79.5", "Number of rRNAs": "0", "Number of tRNAs": "25", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseovarius lutimaris", "strain": "strain=DSM 28463", "accession": "GCA_900115165.1", "taxid": 1005928, "species_taxid": 1005928, "relation_to_type": "type", "validated": true, "ani": 76.7422, "matched_fragments": 80, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagimonas phthalicica", "strain": "strain=DSM 26923", "accession": "GCA_004364805.1", "taxid": 1037362, "species_taxid": 1037362, "relation_to_type": "type", "validated": true, "ani": 76.1035, "matched_fragments": 70, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter marinus", "strain": "strain=DSM 23422", "accession": "GCA_900116285.1", "taxid": 394264, "species_taxid": 394264, "relation_to_type": "type", "validated": true, "ani": 75.9693, "matched_fragments": 65, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius nubinhibens", "strain": "strain=ISM", "accession": "GCA_000152625.1", "taxid": 314263, "species_taxid": 314263, "relation_to_type": "type", "validated": true, "ani": 75.9158, "matched_fragments": 83, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudophaeobacter leonis", "strain": "strain=306", "accession": "GCA_002087335.1", "taxid": 1144477, "species_taxid": 1144477, "relation_to_type": "type", "validated": true, "ani": 75.8587, "matched_fragments": 83, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Zongyanglinia marina", "strain": "strain=DSW4-44", "accession": "GCA_005771405.1", "taxid": 2578117, "species_taxid": 2578117, "relation_to_type": "type", "validated": true, "ani": 75.835, "matched_fragments": 55, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseobacter ponti", "strain": "strain=DSM 106830", "accession": "GCA_012932215.1", "taxid": 1891787, "species_taxid": 1891787, "relation_to_type": "type", "validated": true, "ani": 75.8169, "matched_fragments": 64, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter fulva", "strain": "strain=con5", "accession": "GCA_018798885.1", "taxid": 2840474, "species_taxid": 2840474, "relation_to_type": "type", "validated": true, "ani": 75.8166, "matched_fragments": 65, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola nitratireducens", "strain": "strain=DSM 29619", "accession": "GCA_900112545.1", "taxid": 517719, "species_taxid": 517719, "relation_to_type": "type", "validated": true, "ani": 75.8164, "matched_fragments": 55, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Zongyanglinia huanghaiensis", "strain": "strain=CY05", "accession": "GCA_009753675.1", "taxid": 2682100, "species_taxid": 2682100, "relation_to_type": "type", "validated": true, "ani": 75.8106, "matched_fragments": 58, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola nitratireducens", "strain": "strain=CGMCC 1.7292", "accession": "GCA_900109195.1", "taxid": 517719, "species_taxid": 517719, "relation_to_type": "type", "validated": true, "ani": 75.8097, "matched_fragments": 54, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseobacter cerasinus", "strain": "strain=AI77", "accession": "GCA_009811755.1", "taxid": 2602289, "species_taxid": 2602289, "relation_to_type": "type", "validated": true, "ani": 75.7877, "matched_fragments": 63, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter litoralis", "strain": "strain=DSM 17584", "accession": "GCA_900103185.1", "taxid": 335975, "species_taxid": 335975, "relation_to_type": "type", "validated": true, "ani": 75.7756, "matched_fragments": 60, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leisingera caerulea", "strain": "strain=DSM 24564", "accession": "GCA_000473325.1", "taxid": 506591, "species_taxid": 506591, "relation_to_type": "type", "validated": true, "ani": 75.7704, "matched_fragments": 58, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagivirga dicentrarchi", "strain": "strain=YLY04", "accession": "GCA_003316635.1", "taxid": 2250573, "species_taxid": 2250573, "relation_to_type": "type", "validated": true, "ani": 75.7365, "matched_fragments": 72, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudophaeobacter flagellatus", "strain": "strain=MA21411-1", "accession": "GCA_021228235.1", "taxid": 2899119, "species_taxid": 2899119, "relation_to_type": "type", "validated": true, "ani": 75.7036, "matched_fragments": 75, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeobacter italicus", "strain": "strain=CECT 7645", "accession": "GCA_001258055.1", "taxid": 481446, "species_taxid": 481446, "relation_to_type": "type", "validated": true, "ani": 75.6943, "matched_fragments": 63, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeobacter italicus", "strain": "strain=DSM 26436", "accession": "GCA_900113345.1", "taxid": 481446, "species_taxid": 481446, "relation_to_type": "type", "validated": true, "ani": 75.6943, "matched_fragments": 63, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria profundi", "strain": "strain=ZGT108", "accession": "GCA_001507545.1", "taxid": 1685378, "species_taxid": 1685378, "relation_to_type": "type", "validated": true, "ani": 75.6327, "matched_fragments": 63, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yoonia sediminilitoris", "strain": "strain=CECT 8284", "accession": "GCA_003337495.1", "taxid": 1286148, "species_taxid": 1286148, "relation_to_type": "type", "validated": true, "ani": 75.4568, "matched_fragments": 59, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yoonia sediminilitoris", "strain": "strain=DSM 29955", "accession": "GCA_003058085.1", "taxid": 1286148, "species_taxid": 1286148, "relation_to_type": "type", "validated": true, "ani": 75.4568, "matched_fragments": 59, "total_fragments": 972, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 86.57, "contamination": 0.52, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_002684375.1", "gtdb_species": "s__CPC320 sp002684375", "ani": 98.7869, "matched_fragments": 793, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "98.26", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.72", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCA_002336405.1", "gtdb_species": "s__CPC320 sp002336405", "ani": 86.9816, "matched_fragments": 689, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "97.78", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.51", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_001642945.1", "gtdb_species": "s__LGRT01 sp001642945", "ani": 77.1792, "matched_fragments": 70, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.88", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_900115165.1", "gtdb_species": "s__Roseovarius lutimaris", "ani": 76.7961, "matched_fragments": 78, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius", "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_003205515.1", "gtdb_species": "s__Litorivita pollutaquae", "ani": 76.2283, "matched_fragments": 69, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorivita", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.23", "min_intra_species_ani": "98.23", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900110775.1", "gtdb_species": "s__Litorimicrobium taeanense", "ani": 76.154, "matched_fragments": 81, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium", "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_017854855.1", "gtdb_species": "s__Sulfitobacter sp017854855", "ani": 76.0522, "matched_fragments": 64, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter", "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_000152625.1", "gtdb_species": "s__Roseovarius nubinhibens", "ani": 75.9335, "matched_fragments": 82, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.78", "min_intra_species_ani": "96.50", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_004216475.1", "gtdb_species": "s__GCA-004216475 sp004216475", "ani": 75.9061, "matched_fragments": 58, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475", "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_012932215.1", "gtdb_species": "s__Roseobacter ponti", "ani": 75.8384, "matched_fragments": 63, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter", "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_900109195.1", "gtdb_species": "s__Pseudooceanicola nitratireducens", "ani": 75.8351, "matched_fragments": 53, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "97.09", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_006064855.1", "gtdb_species": "s__Sulfitobacter sp006064855", "ani": 75.8152, "matched_fragments": 66, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter", "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_009811755.1", "gtdb_species": "s__Roseobacter cerasinus", "ani": 75.8091, "matched_fragments": 62, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter", "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_000620505.1", "gtdb_species": "s__Ascidiaceihabitans sp000620505", "ani": 75.7723, "matched_fragments": 73, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans", "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_001458355.1", "gtdb_species": "s__Thalassobius gelatinovorus", "ani": 75.7256, "matched_fragments": 74, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900143615.1", "gtdb_species": "s__Shimia sp900143615", "ani": 75.704, "matched_fragments": 76, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia", "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_002366795.1", "gtdb_species": "s__UBA3069 sp002366795", "ani": 75.5948, "matched_fragments": 70, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069", "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_003058085.1", "gtdb_species": "s__Yoonia sediminilitoris", "ani": 75.4568, "matched_fragments": 59, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900112755.1", "gtdb_species": "s__Sulfitobacter brevis", "ani": 75.2827, "matched_fragments": 66, "total_fragments": 972, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter", "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": -0.184, "cell_length": 0.194, "doubling_h": 0.42, "growth_tmp": 28.315, "optimum_tmp": 28.94, "optimum_ph": 7.466, "genome_size": 3336110.0, "gc_content": 56.805, "coding_genes": 3231.0, "rRNA16S_genes": 2.828, "tRNA_genes": 51.0, "gram_stain": 0.004, "sporulation": 0.015, "motility": 0.413, "range_salinity": 0.909, "facultative_respiration": 0.086, "anaerobic_respiration": 0.05, "aerobic_respiration": 0.862, "mesophilic_range_tmp": 0.92, "thermophilic_range_tmp": 0.04, "psychrophilic_range_tmp": 0.04, "bacillus_cell_shape": 0.843, "coccus_cell_shape": 0.04, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.116, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhodobacterales", "f__Rhodobacteraceae", "g__CPC320", "s__CPC320 sp002684375" ], "_genome_taxon": [ "uncultured", "Rhodobacteraceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhodobacterales", "f__Rhodobacteraceae", "g__CPC320", "s__CPC320 sp002684375", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhodobacterales", "Rhodobacteraceae", "CPC320", "CPC320", "sp002684375" ], "_meo": [ { "id": "MEO_0000041", "label": "marine water" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }