{ "type": "genome", "identifier": "GCF_007860175.1", "organism": "Rubripirellula reticaptiva", "title": "Rubripirellula reticaptiva", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Radboud Universiteit Nijmegen", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007860175.1", "bioproject": "PRJNA224116", "biosample": "SAMN10954033", "wgs_master": "SJPX00000000.1", "refseq_category": "reference genome", "taxid": "2528013", "species_taxid": "2528013", "organism_name": "Rubripirellula reticaptiva", "infraspecific_name": "strain=Poly59", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/08/07", "asm_name": "ASM786017v1", "asm_submitter": "Radboud Universiteit Nijmegen", "gbrs_paired_asm": "GCA_007860175.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/860/175/GCF_007860175.1_ASM786017v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7852560", "genome_size_ungapped": "7851960", "gc_percent": "55.000000", "replicon_count": "0", "scaffold_count": "13", "contig_count": "13", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007860175.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "5915", "protein_coding_gene_count": "5797", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-08-07", "dateModified": "2019-08-07", "datePublished": "2019-08-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Rubripirellula reticaptiva" ], "sample_taxid": [ "2528013" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Heiligendamm" ], "sample_host_location_id": [], "data_size": "2.215 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)": "7852560", "Number of Sequences": "13", "Longest Sequences (bp)": "1778767", "N50 (bp)": "1192914", "Gap Ratio (%)": "0.007654", "GCcontent (%)": "54.8", "Number of CDSs": "5878", "Average Protein Length": "387.0", "Coding Ratio (%)": "86.9", "Number of rRNAs": "2", "Number of tRNAs": "71", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rubripirellula reticaptiva", "strain": "strain=Poly59", "accession": "GCA_007860175.1", "taxid": 2528013, "species_taxid": 2528013, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2610, "total_fragments": 2610, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rubripirellula tenax", "strain": "strain=Poly51", "accession": "GCA_007860125.1", "taxid": 2528015, "species_taxid": 2528015, "relation_to_type": "type", "validated": true, "ani": 79.6106, "matched_fragments": 827, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rubripirellula lacrimiformis", "strain": "strain=K22.7", "accession": "GCA_007741535.1", "taxid": 1930273, "species_taxid": 1930273, "relation_to_type": "type", "validated": true, "ani": 78.5399, "matched_fragments": 640, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rubripirellula amarantea", "strain": "strain=Pla22", "accession": "GCA_007859865.1", "taxid": 2527999, "species_taxid": 2527999, "relation_to_type": "type", "validated": true, "ani": 78.0999, "matched_fragments": 265, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crateriforma conspicua", "strain": "strain=Mal65", "accession": "GCA_007752935.1", "taxid": 2527996, "species_taxid": 2527996, "relation_to_type": "type", "validated": true, "ani": 77.3765, "matched_fragments": 215, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopirellula baltica", "strain": "strain=1", "accession": "GCA_000196115.1", "taxid": 265606, "species_taxid": 265606, "relation_to_type": "type", "validated": true, "ani": 77.3735, "matched_fragments": 214, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rubripirellula obstinata", "strain": "strain=CECT 8602", "accession": "GCA_001642955.1", "taxid": 406547, "species_taxid": 406547, "relation_to_type": "type", "validated": true, "ani": 77.2311, "matched_fragments": 263, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopirellula bahusiensis", "strain": "strain=SWK21", "accession": "GCA_002727185.1", "taxid": 2014065, "species_taxid": 2014065, "relation_to_type": "type", "validated": true, "ani": 77.1186, "matched_fragments": 220, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopirellula maiorica", "strain": "strain=SM1", "accession": "GCA_000346295.1", "taxid": 1265734, "species_taxid": 1265734, "relation_to_type": "type", "validated": true, "ani": 76.9569, "matched_fragments": 241, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopirellula europaea", "strain": "strain=6C", "accession": "GCA_000338295.1", "taxid": 1263866, "species_taxid": 1263866, "relation_to_type": "type", "validated": true, "ani": 76.9396, "matched_fragments": 216, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novipirellula galeiformis", "strain": "strain=Pla52o", "accession": "GCA_007860095.1", "taxid": 2528004, "species_taxid": 2528004, "relation_to_type": "type", "validated": true, "ani": 76.5031, "matched_fragments": 209, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stieleria neptunia", "strain": "strain=Enr13", "accession": "GCA_007754155.1", "taxid": 2527979, "species_taxid": 2527979, "relation_to_type": "type", "validated": true, "ani": 76.5024, "matched_fragments": 246, "total_fragments": 2610, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_007860175.1", "gtdb_species": "s__Rubripirellula reticaptiva", "ani": 100.0, "matched_fragments": 2610, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula", "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_007860125.1", "gtdb_species": "s__Rubripirellula tenax", "ani": 79.6041, "matched_fragments": 833, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula", "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_007741535.1", "gtdb_species": "s__Rubripirellula sp007741535", "ani": 78.5428, "matched_fragments": 639, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula", "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_007859865.1", "gtdb_species": "s__Rubripirellula amarantea", "ani": 78.0999, "matched_fragments": 265, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula", "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_012290005.1", "gtdb_species": "s__Crateriforma spongiae", "ani": 77.3837, "matched_fragments": 209, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.43", "min_intra_species_ani": "98.43", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001642955.1", "gtdb_species": "s__Rubripirellula obstinata", "ani": 77.2379, "matched_fragments": 264, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002727185.1", "gtdb_species": "s__Rhodopirellula bahusiensis", "ani": 77.1297, "matched_fragments": 219, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula", "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_000346295.1", "gtdb_species": "s__Novipirellula maiorica", "ani": 76.953, "matched_fragments": 239, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula", "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_000338295.1", "gtdb_species": "s__Rhodopirellula europaea", "ani": 76.9399, "matched_fragments": 216, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.18", "min_intra_species_ani": "96.16", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_007860045.1", "gtdb_species": "s__Stieleria varia", "ani": 76.6376, "matched_fragments": 217, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria", "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_007754155.1", "gtdb_species": "s__Stieleria neptunia", "ani": 76.5093, "matched_fragments": 245, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria", "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_007860095.1", "gtdb_species": "s__Novipirellula galeiformis", "ani": 76.4934, "matched_fragments": 210, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula", "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_014154935.1", "gtdb_species": "s__Stieleria sp014154935", "ani": 76.4044, "matched_fragments": 253, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria", "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_008035925.1", "gtdb_species": "s__Stieleria maiorica", "ani": 76.1027, "matched_fragments": 240, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria", "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_010367455.1", "gtdb_species": "s__Laterigemmans baculatus", "ani": 75.8106, "matched_fragments": 94, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans", "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": "GCA_002428205.1", "gtdb_species": "s__UBA6163 sp002428205", "ani": 75.746, "matched_fragments": 96, "total_fragments": 2610, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": 25.0, "optimum_ph": null, "genome_size": 6578739.0, "gc_content": 54.108, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Rubripirellula", "reticaptiva" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }