{ "type": "genome", "identifier": "GCF_000420745.1", "organism": "Pseudorhodobacter ferrugineus DSM 5888", "title": "Pseudorhodobacter ferrugineus DSM 5888", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000420745.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441236", "wgs_master": "ATVN00000000.1", "refseq_category": "reference genome", "taxid": "1123027", "species_taxid": "77008", "organism_name": "Pseudorhodobacter ferrugineus DSM 5888", "infraspecific_name": "strain=DSM 5888", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/09", "asm_name": "ASM42074v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000420745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/420/745/GCF_000420745.1_ASM42074v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3430274", "genome_size_ungapped": "3430274", "gc_percent": "58.500000", "replicon_count": "0", "scaffold_count": "42", "contig_count": "42", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000420745.1-RS_2024_04_26", "annotation_date": "2024-04-26", "total_gene_count": "3458", "protein_coding_gene_count": "3341", "non_coding_gene_count": "46", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-09", "dateModified": "2013-07-09", "datePublished": "2013-07-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudorhodobacter ferrugineus DSM 5888" ], "sample_taxid": [ "1123027" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.965 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)": "3430274", "Number of Sequences": "42", "Longest Sequences (bp)": "314308", "N50 (bp)": "164101", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.5", "Number of CDSs": "3407", "Average Protein Length": "299.0", "Coding Ratio (%)": "89.1", "Number of rRNAs": "3", "Number of tRNAs": "40", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudorhodobacter ferrugineus", "strain": "strain=DSM 5888", "accession": "GCA_000420745.1", "taxid": 77008, "species_taxid": 77008, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1121, "total_fragments": 1123, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudorhodobacter wandonensis", "strain": "strain=KCTC 23672", "accession": "GCA_001202035.1", "taxid": 1120568, "species_taxid": 1120568, "relation_to_type": "type", "validated": true, "ani": 81.4847, "matched_fragments": 736, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhodobacter antarcticus", "strain": "strain=CGMCC 1.10836", "accession": "GCA_900110135.1", "taxid": 1077947, "species_taxid": 1077947, "relation_to_type": "type", "validated": true, "ani": 80.6158, "matched_fragments": 687, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhodobacter antarcticus", "strain": "strain=KCTC 23700", "accession": "GCA_001202015.1", "taxid": 1077947, "species_taxid": 1077947, "relation_to_type": "type", "validated": true, "ani": 80.5369, "matched_fragments": 691, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhodobacter turbinis", "strain": "strain=S12M18", "accession": "GCA_005234135.1", "taxid": 2500533, "species_taxid": 2500533, "relation_to_type": "type", "validated": true, "ani": 79.2995, "matched_fragments": 520, "total_fragments": 1123, "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": 77.5541, "matched_fragments": 346, "total_fragments": 1123, "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": 77.446, "matched_fragments": 355, "total_fragments": 1123, "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": 77.362, "matched_fragments": 356, "total_fragments": 1123, "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": 76.9139, "matched_fragments": 279, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actibacterium mucosum", "strain": "strain=KCTC 23349", "accession": "GCA_000647975.1", "taxid": 1087332, "species_taxid": 1087332, "relation_to_type": "type", "validated": true, "ani": 76.6489, "matched_fragments": 154, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter baekdonensis", "strain": "strain=DSM 27375", "accession": "GCA_900102315.1", "taxid": 875171, "species_taxid": 875171, "relation_to_type": "type", "validated": true, "ani": 76.6463, "matched_fragments": 158, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tritonibacter litoralis", "strain": "strain=SM1979", "accession": "GCA_009496005.1", "taxid": 2662264, "species_taxid": 2662264, "relation_to_type": "type", "validated": true, "ani": 76.414, "matched_fragments": 122, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sediminicola", "strain": "strain=JA983", "accession": "GCA_007668225.1", "taxid": 2584941, "species_taxid": 2584941, "relation_to_type": "type", "validated": true, "ani": 76.3623, "matched_fragments": 176, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000420745.1", "gtdb_species": "s__Pseudorhodobacter ferrugineus", "ani": 100.0, "matched_fragments": 1121, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001202035.1", "gtdb_species": "s__Pseudorhodobacter wandonensis", "ani": 81.4847, "matched_fragments": 736, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter", "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_003991405.1", "gtdb_species": "s__Pseudorhodobacter sp003991405", "ani": 81.2655, "matched_fragments": 774, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter", "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_900110135.1", "gtdb_species": "s__Pseudorhodobacter antarcticus", "ani": 80.6118, "matched_fragments": 687, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005234135.1", "gtdb_species": "s__Pseudorhodobacter turbinis", "ani": 79.2995, "matched_fragments": 520, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter", "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_001202025.1", "gtdb_species": "s__Pseudorhodobacter aquimaris", "ani": 79.1919, "matched_fragments": 500, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter", "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_002900965.1", "gtdb_species": "s__ETT8 sp002900965", "ani": 77.5424, "matched_fragments": 309, "total_fragments": 1123, "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": "GCA_009773375.1", "gtdb_species": "s__Cypionkella sp009773375", "ani": 77.3205, "matched_fragments": 325, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella", "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_900110025.1", "gtdb_species": "s__Gemmobacter aquatilis", "ani": 77.2124, "matched_fragments": 337, "total_fragments": 1123, "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_008711135.1", "gtdb_species": "s__LNNU-3342 sp008711135", "ani": 76.5359, "matched_fragments": 152, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LNNU-3342", "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": -0.222, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 26.0, "optimum_tmp": 26.0, "optimum_ph": 7.5, "genome_size": 3431727.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Pseudorhodobacter", "ferrugineus", "DSM", "5888" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }