{ "type": "genome", "identifier": "GCA_937862955.1", "organism": "uncultured Rhodobacteraceae bacterium", "title": "uncultured Rhodobacteraceae bacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "European Bioinformatics Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_937862955.1", "bioproject": "PRJEB51074", "biosample": "SAMEA14036377", "wgs_master": "CALMDC000000000.1", "refseq_category": "na", "taxid": "157276", "species_taxid": "157276", "organism_name": "uncultured Rhodobacteraceae bacterium", "infraspecific_name": "", "isolate": "SRR8859111_bin.54_CONCOCT_v1.1_MAG", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/01/10", "asm_name": "SRR8859111_bin.54_CONCOCT_v1.1_MAG", "submitter": "European Bioinformatics Institute", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/937/862/955/GCA_937862955.1_SRR8859111_bin.54_CONCOCT_v1.1_MAG", "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": "2023-01-10", "dateModified": "2023-01-10", "datePublished": "2023-01-10", "_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": [ "India" ], "sample_host_location_id": [], "data_size": "0.738 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 68.75, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2708310", "Number of Sequences": "469", "Longest Sequences (bp)": "41610", "N50 (bp)": "7563", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.0", "Number of CDSs": "2280", "Average Protein Length": "285.8", "Coding Ratio (%)": "72.2", "Number of rRNAs": "0", "Number of tRNAs": "34", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sinirhodobacter huangdaonensis", "strain": "strain=CGMCC 1.12963", "accession": "GCA_004022465.1", "taxid": 2501515, "species_taxid": 2501515, "relation_to_type": "type", "validated": true, "ani": 82.7946, "matched_fragments": 531, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter hankyongi", "strain": "strain=BO-81", "accession": "GCA_003664585.1", "taxid": 2294033, "species_taxid": 2294033, "relation_to_type": "type", "validated": true, "ani": 82.7556, "matched_fragments": 528, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter ferrireducens", "strain": "strain=CCTCC AB2012026", "accession": "GCA_004022265.1", "taxid": 1215032, "species_taxid": 1215032, "relation_to_type": "type", "validated": true, "ani": 82.673, "matched_fragments": 528, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter capsulatus", "strain": "strain=DSM 1710", "accession": "GCA_003254295.1", "taxid": 1061, "species_taxid": 1061, "relation_to_type": "type", "validated": true, "ani": 80.8528, "matched_fragments": 462, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava atlantica", "strain": "strain=13D2W-2", "accession": "GCA_000737065.1", "taxid": 1317124, "species_taxid": 1317124, "relation_to_type": "type", "validated": true, "ani": 80.8327, "matched_fragments": 420, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter viridis", "strain": "strain=JA737", "accession": "GCA_003217355.1", "taxid": 1054202, "species_taxid": 1054202, "relation_to_type": "type", "validated": true, "ani": 80.796, "matched_fragments": 453, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava marina", "strain": "strain=11.10-0-13", "accession": "GCA_002020135.1", "taxid": 1915077, "species_taxid": 1915077, "relation_to_type": "type", "validated": true, "ani": 80.4341, "matched_fragments": 426, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeovulum vinaykumarii", "strain": "strain=JA123", "accession": "GCA_900217755.1", "taxid": 407234, "species_taxid": 407234, "relation_to_type": "type", "validated": true, "ani": 79.6273, "matched_fragments": 395, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava nitratireducens", "strain": "strain=25B10_4", "accession": "GCA_001940525.2", "taxid": 1915078, "species_taxid": 1915078, "relation_to_type": "type", "validated": true, "ani": 79.3473, "matched_fragments": 400, "total_fragments": 667, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 68.75, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001856665.1", "gtdb_species": "s__LPB0142 sp001856665", "ani": 98.7183, "matched_fragments": 654, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_014763785.1", "gtdb_species": "s__SZUA-611 sp014763785", "ani": 82.8412, "matched_fragments": 452, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611", "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_003664585.1", "gtdb_species": "s__Paenirhodobacter hankyongi", "ani": 82.7499, "matched_fragments": 528, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter", "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_004022265.1", "gtdb_species": "s__Paenirhodobacter ferrireducens", "ani": 82.6584, "matched_fragments": 529, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "95.14", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002452815.1", "gtdb_species": "s__UBA6796 sp002452815", "ani": 81.8569, "matched_fragments": 502, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005144475.1", "gtdb_species": "s__Rhodobacter capsulatus_C", "ani": 80.8349, "matched_fragments": 455, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "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_003217355.1", "gtdb_species": "s__Rhodobacter viridis", "ani": 80.7968, "matched_fragments": 453, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "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_900217815.1", "gtdb_species": "s__Rhodobacter maris", "ani": 80.7283, "matched_fragments": 458, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "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_000740785.1", "gtdb_species": "s__Paenirhodobacter enshiensis", "ani": 80.3033, "matched_fragments": 370, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter", "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_004022215.1", "gtdb_species": "s__Paenirhodobacter populi", "ani": 79.7081, "matched_fragments": 379, "total_fragments": 667, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.06", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.79", "num_clustered_genomes": 5, "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__LPB0142", "s__LPB0142 sp001856665" ], "_genome_taxon": [ "uncultured", "Rhodobacteraceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhodobacterales", "f__Rhodobacteraceae", "g__LPB0142", "s__LPB0142 sp001856665", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhodobacterales", "Rhodobacteraceae", "LPB0142", "LPB0142", "sp001856665" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }