{ "type": "genome", "identifier": "GCA_013349685.1", "organism": "Rhodospirillaceae bacterium", "title": "Rhodospirillaceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Research Center of Biotechnology RAS", "publication": [ {} ], "properties": { "assembly_accession": "GCA_013349685.1", "bioproject": "PRJNA632036", "biosample": "SAMN14911659", "wgs_master": "DUZE00000000.1", "refseq_category": "na", "taxid": "1898112", "species_taxid": "1898112", "organism_name": "Rhodospirillaceae bacterium", "infraspecific_name": "", "isolate": "MAG_05596_2-02_51", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/16", "asm_name": "ASM1334968v1", "submitter": "Research Center of Biotechnology RAS", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/349/685/GCA_013349685.1_ASM1334968v1", "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": "2020-06-16", "dateModified": "2020-06-16", "datePublished": "2020-06-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodospirillaceae bacterium" ], "sample_taxid": [ "1898112" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean: Eastern Tropical North Pacific" ], "sample_host_location_id": [], "data_size": "0.517 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 89.81, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1831947", "Number of Sequences": "329", "Longest Sequences (bp)": "26063", "N50 (bp)": "6777", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.2", "Number of CDSs": "1555", "Average Protein Length": "281.4", "Coding Ratio (%)": "71.7", "Number of rRNAs": "0", "Number of tRNAs": "28", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Magnetospirillum moscoviense", "strain": "strain=BB-1", "accession": "GCA_001650635.1", "taxid": 1437059, "species_taxid": 1437059, "relation_to_type": "type", "validated": true, "ani": 76.2922, "matched_fragments": 77, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Magnetospirillum caucaseum", "strain": "strain=SO-1", "accession": "GCA_000342045.1", "taxid": 1244869, "species_taxid": 1244869, "relation_to_type": "type", "validated": true, "ani": 76.236, "matched_fragments": 90, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseospirillum parvum", "strain": "strain=930I", "accession": "GCA_900100455.1", "taxid": 83401, "species_taxid": 83401, "relation_to_type": "type", "validated": true, "ani": 76.0832, "matched_fragments": 67, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum argentinense", "strain": "strain=Az39", "accession": "GCA_000632475.2", "taxid": 2970906, "species_taxid": 2970906, "relation_to_type": "type", "validated": true, "ani": 75.9492, "matched_fragments": 74, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum melinis", "strain": "strain=TMCY0552", "accession": "GCA_013340935.1", "taxid": 328839, "species_taxid": 328839, "relation_to_type": "type", "validated": true, "ani": 75.9392, "matched_fragments": 60, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanibaculum indicum", "strain": "strain=P24", "accession": "GCA_000299935.1", "taxid": 526216, "species_taxid": 526216, "relation_to_type": "type", "validated": true, "ani": 75.9016, "matched_fragments": 50, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum melinis", "strain": "strain=TMCY 0552", "accession": "GCA_017876055.1", "taxid": 328839, "species_taxid": 328839, "relation_to_type": "type", "validated": true, "ani": 75.8981, "matched_fragments": 62, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseospira navarrensis", "strain": "strain=DSM 15114", "accession": "GCA_009601025.1", "taxid": 140058, "species_taxid": 140058, "relation_to_type": "type", "validated": true, "ani": 75.8849, "matched_fragments": 62, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum baldaniorum", "strain": "strain=Sp245", "accession": "GCA_000237365.1", "taxid": 1064539, "species_taxid": 1064539, "relation_to_type": "type", "validated": true, "ani": 75.8669, "matched_fragments": 69, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum baldaniorum", "strain": "strain=Sp245", "accession": "GCA_003119195.2", "taxid": 1064539, "species_taxid": 1064539, "relation_to_type": "type", "validated": true, "ani": 75.8483, "matched_fragments": 70, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caenispirillum salinarum", "strain": "strain=AK4", "accession": "GCA_000315795.1", "taxid": 859058, "species_taxid": 859058, "relation_to_type": "type", "validated": true, "ani": 75.8114, "matched_fragments": 65, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanibaculum pacificum", "strain": "strain=MCCC 1A02656", "accession": "GCA_001618175.1", "taxid": 580166, "species_taxid": 580166, "relation_to_type": "type", "validated": true, "ani": 75.7641, "matched_fragments": 52, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oharaeibacter diazotrophicus", "strain": "strain=SM30", "accession": "GCA_011317485.1", "taxid": 1920512, "species_taxid": 1920512, "relation_to_type": "type", "validated": true, "ani": 75.7376, "matched_fragments": 56, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum agricola", "strain": "strain=CC-HIH038", "accession": "GCA_017876095.1", "taxid": 1720247, "species_taxid": 1720247, "relation_to_type": "type", "validated": true, "ani": 75.7358, "matched_fragments": 92, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum doebereinerae", "strain": "strain=GSF71", "accession": "GCA_003989665.1", "taxid": 92933, "species_taxid": 92933, "relation_to_type": "type", "validated": true, "ani": 75.725, "matched_fragments": 83, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella rosea", "strain": "strain=KEMB 2255-458", "accession": "GCA_016806835.2", "taxid": 1817965, "species_taxid": 1817965, "relation_to_type": "type", "validated": true, "ani": 75.6652, "matched_fragments": 71, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oharaeibacter diazotrophicus", "strain": "strain=DSM 102969", "accession": "GCA_004362745.1", "taxid": 1920512, "species_taxid": 1920512, "relation_to_type": "type", "validated": true, "ani": 75.6333, "matched_fragments": 64, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas hellenica", "strain": "strain=LMG 31523", "accession": "GCA_018129085.1", "taxid": 2687306, "species_taxid": 2687306, "relation_to_type": "type", "validated": true, "ani": 75.6121, "matched_fragments": 52, "total_fragments": 439, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 89.81, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_013349695.1", "gtdb_species": "s__GCA-2686765 sp013349695", "ani": 99.5358, "matched_fragments": 398, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__GCA-2686765", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "95.45", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.65", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCA_002725625.1", "gtdb_species": "s__GCA-2725625 sp002725625", "ani": 82.4287, "matched_fragments": 50, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2725625", "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_002686255.1", "gtdb_species": "s__Casp-alpha2 sp002686255", "ani": 77.1941, "matched_fragments": 118, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.76", "min_intra_species_ani": "99.74", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_002938075.1", "gtdb_species": "s__Casp-alpha2 sp002938075", "ani": 77.0317, "matched_fragments": 80, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.63", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.77", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_014382345.1", "gtdb_species": "s__Casp-alpha2 sp014382345", "ani": 76.684, "matched_fragments": 79, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.86", "min_intra_species_ani": "99.86", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_015232025.1", "gtdb_species": "s__JADFZP01 sp015232025", "ani": 76.6459, "matched_fragments": 51, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01", "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_016776525.1", "gtdb_species": "s__JADHTD01 sp016776525", "ani": 76.6418, "matched_fragments": 61, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JADHTD01;g__JADHTD01", "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_016763915.1", "gtdb_species": "s__Casp-alpha2 sp016763915", "ani": 76.5738, "matched_fragments": 51, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2", "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_016187325.1", "gtdb_species": "s__JACPJY01 sp016187325", "ani": 76.5613, "matched_fragments": 86, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01", "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_016202695.1", "gtdb_species": "s__JACQOE01 sp016202695", "ani": 76.5183, "matched_fragments": 63, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01", "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_002781745.1", "gtdb_species": "s__UBA1479 sp002781745", "ani": 76.512, "matched_fragments": 72, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479", "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_001830425.1", "gtdb_species": "s__2-02-FULL-58-16 sp001830425", "ani": 76.4741, "matched_fragments": 88, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009693905.1", "gtdb_species": "s__2-12-FULL-67-15 sp009693905", "ani": 76.4046, "matched_fragments": 56, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.79", "mean_intra_species_af": "0.72", "min_intra_species_af": "0.72", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016793875.1", "gtdb_species": "s__SSA4 sp016793875", "ani": 76.4016, "matched_fragments": 52, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4", "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_014859895.1", "gtdb_species": "s__JACZKS01 sp014859895", "ani": 76.33, "matched_fragments": 99, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01", "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_003354135.1", "gtdb_species": "s__GLO-3 sp003354135", "ani": 76.2049, "matched_fragments": 63, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__GLO-3;g__GLO-3", "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_015232485.1", "gtdb_species": "s__JADFZP01 sp015232485", "ani": 75.9651, "matched_fragments": 66, "total_fragments": 439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.70", "min_intra_species_ani": "95.97", "mean_intra_species_af": "0.70", "min_intra_species_af": "0.69", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.124, "cell_length": 0.412, "doubling_h": 0.931, "growth_tmp": 29.068, "optimum_tmp": 30.167, "optimum_ph": 7.012, "genome_size": 4958622.479, "gc_content": 62.84, "coding_genes": 4573.287, "rRNA16S_genes": 4.82, "tRNA_genes": 64.75, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.839, "range_salinity": 0.666, "facultative_respiration": 0.174, "anaerobic_respiration": 0.158, "aerobic_respiration": 0.666, "mesophilic_range_tmp": 0.916, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.083, "bacillus_cell_shape": 0.509, "coccus_cell_shape": 0.018, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.036, "spiral_cell_shape": 0.436 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhodospirillales_A", "f__JADFTO01", "g__GCA-2686765", "s__GCA-2686765 sp013349695" ], "_genome_taxon": [ "Rhodospirillaceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhodospirillales_A", "f__JADFTO01", "g__GCA-2686765", "s__GCA-2686765 sp013349695", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhodospirillales", "A", "JADFTO01", "GCA-2686765", "GCA-2686765", "sp013349695" ], "_meo": [ { "id": "MEO_0000041", "label": "marine water" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }