{ "type": "genome", "identifier": "GCF_003060865.1", "organism": "Gemmobacter aquarius", "title": "Gemmobacter aquarius", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Korea University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003060865.1", "bioproject": "PRJNA224116", "biosample": "SAMN08924525", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2169400", "species_taxid": "2169400", "organism_name": "Gemmobacter aquarius", "infraspecific_name": "strain=HYN0069", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/23", "asm_name": "ASM306086v1", "asm_submitter": "Korea University", "gbrs_paired_asm": "GCA_003060865.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/060/865/GCF_003060865.1_ASM306086v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4206589", "genome_size_ungapped": "4206589", "gc_percent": "64.000000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003060865.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "4136", "protein_coding_gene_count": "3929", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-23", "dateModified": "2018-04-23", "datePublished": "2018-04-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Gemmobacter aquarius" ], "sample_taxid": [ "2169400" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Korea" ], "sample_host_location_id": [], "data_size": "1.152 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4206589", "Number of Sequences": "4", "Longest Sequences (bp)": "3694576", "N50 (bp)": "3694576", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.9", "Number of CDSs": "4137", "Average Protein Length": "304.4", "Coding Ratio (%)": "89.8", "Number of rRNAs": "9", "Number of tRNAs": "56", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gemmobacter aquarius", "strain": "strain=HYN0069", "accession": "GCA_003060865.1", "taxid": 2169400, "species_taxid": 2169400, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1398, "total_fragments": 1400, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Gemmobacter straminiformis", "strain": "strain=CAM-8", "accession": "GCA_014243445.1", "taxid": 2045119, "species_taxid": 2045119, "relation_to_type": "type", "validated": true, "ani": 84.3519, "matched_fragments": 962, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_019130055.1", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 81.4027, "matched_fragments": 799, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_009908265.2", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 81.3808, "matched_fragments": 803, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter ruber", "strain": "strain=CCP-1", "accession": "GCA_009908315.1", "taxid": 1985673, "species_taxid": 1985673, "relation_to_type": "type", "validated": true, "ani": 80.4507, "matched_fragments": 749, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter caeruleus", "strain": "strain=N8", "accession": "GCA_008271655.1", "taxid": 2595004, "species_taxid": 2595004, "relation_to_type": "type", "validated": true, "ani": 79.6684, "matched_fragments": 569, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquatilis", "strain": "strain=DSM 3857", "accession": "GCA_900110025.1", "taxid": 933059, "species_taxid": 933059, "relation_to_type": "type", "validated": true, "ani": 79.3617, "matched_fragments": 593, "total_fragments": 1400, "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": 79.3388, "matched_fragments": 578, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter changlensis", "strain": "strain=DSM 18774", "accession": "GCA_003254335.1", "taxid": 402884, "species_taxid": 402884, "relation_to_type": "type", "validated": true, "ani": 79.1184, "matched_fragments": 563, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter changlensis", "strain": "strain=JA139", "accession": "GCA_003034985.1", "taxid": 402884, "species_taxid": 402884, "relation_to_type": "type", "validated": true, "ani": 79.0822, "matched_fragments": 537, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola sediminis", "strain": "strain=DRYC-M-16", "accession": "GCA_004745575.1", "taxid": 2486418, "species_taxid": 2486418, "relation_to_type": "type", "validated": true, "ani": 79.068, "matched_fragments": 558, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola alkalilacus", "strain": "strain=DJC", "accession": "GCA_003443995.1", "taxid": 2305252, "species_taxid": 2305252, "relation_to_type": "type", "validated": true, "ani": 79.0636, "matched_fragments": 563, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter lanyuensis", "strain": "strain=KCTC 23714", "accession": "GCA_014652355.1", "taxid": 1054497, "species_taxid": 1054497, "relation_to_type": "type", "validated": true, "ani": 78.9661, "matched_fragments": 529, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter nectariphilus", "strain": "strain=DSM 15620", "accession": "GCA_000429765.1", "taxid": 220343, "species_taxid": 220343, "relation_to_type": "type", "validated": true, "ani": 78.3569, "matched_fragments": 442, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cypionkella psychrotolerans", "strain": "strain=PAMC 27389", "accession": "GCA_001294535.1", "taxid": 1678131, "species_taxid": 1678131, "relation_to_type": "type", "validated": true, "ani": 78.1338, "matched_fragments": 447, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter megaterium", "strain": "strain=CGMCC 1.11024", "accession": "GCA_014636395.1", "taxid": 1086013, "species_taxid": 1086013, "relation_to_type": "type", "validated": true, "ani": 77.9092, "matched_fragments": 359, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter megaterium", "strain": "strain=DSM 26375", "accession": "GCA_900156815.1", "taxid": 1086013, "species_taxid": 1086013, "relation_to_type": "type", "validated": true, "ani": 77.9008, "matched_fragments": 355, "total_fragments": 1400, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003060865.1", "gtdb_species": "s__Gemmobacter_B sp003060865", "ani": 100.0, "matched_fragments": 1397, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_014243445.1", "gtdb_species": "s__Gemmobacter_B straminiformis", "ani": 84.3708, "matched_fragments": 960, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_009908265.2", "gtdb_species": "s__Gemmobacter_B sp009908265", "ani": 81.4166, "matched_fragments": 798, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_011059185.1", "gtdb_species": "s__Gemmobacter_B sp011059185", "ani": 80.7957, "matched_fragments": 759, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_000500915.1", "gtdb_species": "s__Gemmobacter_B sp000500915", "ani": 80.7344, "matched_fragments": 664, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_009908315.1", "gtdb_species": "s__Gemmobacter_B sp009908315", "ani": 80.4419, "matched_fragments": 751, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_002256185.1", "gtdb_species": "s__Gemmobacter_B sp002256185", "ani": 79.8956, "matched_fragments": 655, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_008271655.1", "gtdb_species": "s__Gemmobacter caeruleus", "ani": 79.6775, "matched_fragments": 568, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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_001828855.1", "gtdb_species": "s__Cypionkella sp001828855", "ani": 79.6775, "matched_fragments": 625, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_014859945.1", "gtdb_species": "s__UBA1943 sp014859945", "ani": 79.3738, "matched_fragments": 498, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943", "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_011008935.1", "gtdb_species": "s__KMS-5 sp011008935", "ani": 79.1605, "matched_fragments": 592, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5", "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_015999335.1", "gtdb_species": "s__Tabrizicola soli", "ani": 79.1564, "matched_fragments": 568, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola", "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_003443995.1", "gtdb_species": "s__ETT8 sp003443995", "ani": 79.0829, "matched_fragments": 561, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8", "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_003034985.1", "gtdb_species": "s__Cereibacter changlensis", "ani": 79.0722, "matched_fragments": 539, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.78", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003570715.1", "gtdb_species": "s__Gemmobacter lutimaris", "ani": 79.0589, "matched_fragments": 564, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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_000429765.1", "gtdb_species": "s__Wagnerdoeblera nectariphila", "ani": 78.3576, "matched_fragments": 443, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera", "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_900156815.1", "gtdb_species": "s__Wagnerdoeblera megaterium", "ani": 77.9015, "matched_fragments": 355, "total_fragments": 1400, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.264, "cell_length": 0.153, "doubling_h": null, "growth_tmp": 31.0, "optimum_tmp": 29.062, "optimum_ph": 7.017, "genome_size": 4458329.75, "gc_content": 66.2, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.142, "range_salinity": null, "facultative_respiration": 0.375, "anaerobic_respiration": 0.125, "aerobic_respiration": 0.5, "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 }, "_genome_taxon": [ "Gemmobacter", "aquarius" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }