{ "type": "genome", "identifier": "GCF_000420145.1", "organism": "Paracoccus zeaxanthinifaciens ATCC 21588", "title": "Paracoccus zeaxanthinifaciens ATCC 21588", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000420145.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441598", "wgs_master": "ATUJ00000000.1", "refseq_category": "reference genome", "taxid": "1266998", "species_taxid": "187400", "organism_name": "Paracoccus zeaxanthinifaciens ATCC 21588", "infraspecific_name": "strain=ATCC 21588", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/09", "asm_name": "ASM42014v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000420145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/420/145/GCF_000420145.1_ASM42014v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3049695", "genome_size_ungapped": "3049695", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000420145.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "3019", "protein_coding_gene_count": "2919", "non_coding_gene_count": "56", "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": [ "Paracoccus zeaxanthinifaciens ATCC 21588" ], "sample_taxid": [ "1266998" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.826 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)": "3049695", "Number of Sequences": "35", "Longest Sequences (bp)": "367886", "N50 (bp)": "237387", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.2", "Number of CDSs": "2946", "Average Protein Length": "319.1", "Coding Ratio (%)": "92.5", "Number of rRNAs": "2", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paracoccus zeaxanthinifaciens", "strain": "strain=ATCC 21588", "accession": "GCA_000420145.1", "taxid": 187400, "species_taxid": 187400, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 997, "total_fragments": 999, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paracoccus liaowanqingii", "strain": "strain=2251", "accession": "GCA_004683865.2", "taxid": 2560053, "species_taxid": 2560053, "relation_to_type": "type", "validated": true, "ani": 84.1597, "matched_fragments": 724, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aestuarii", "strain": "strain=DSM 19484", "accession": "GCA_003594815.1", "taxid": 453842, "species_taxid": 453842, "relation_to_type": "type", "validated": true, "ani": 84.0642, "matched_fragments": 651, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus indicus", "strain": "strain=IO390502", "accession": "GCA_003056335.1", "taxid": 2079229, "species_taxid": 2079229, "relation_to_type": "type", "validated": true, "ani": 83.7247, "matched_fragments": 729, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus hibiscisoli", "strain": "strain=CCTCC AB2016182", "accession": "GCA_005048265.1", "taxid": 2023261, "species_taxid": 2023261, "relation_to_type": "type", "validated": true, "ani": 83.6803, "matched_fragments": 721, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus sediminilitoris", "strain": "strain=DSL-16", "accession": "GCA_003259195.1", "taxid": 2202419, "species_taxid": 2202419, "relation_to_type": "type", "validated": true, "ani": 83.2367, "matched_fragments": 723, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus homiensis", "strain": "strain=DSM 17862", "accession": "GCA_900111675.1", "taxid": 364199, "species_taxid": 364199, "relation_to_type": "type", "validated": true, "ani": 82.9626, "matched_fragments": 652, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus siganidrum", "strain": "strain=M26", "accession": "GCA_003709565.1", "taxid": 1276757, "species_taxid": 1276757, "relation_to_type": "type", "validated": true, "ani": 82.9026, "matched_fragments": 685, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus siganidrum", "strain": "strain=DSM 26381", "accession": "GCA_003594835.1", "taxid": 1276757, "species_taxid": 1276757, "relation_to_type": "type", "validated": true, "ani": 82.8362, "matched_fragments": 635, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus tibetensis", "strain": "strain=CGMCC 1.8925", "accession": "GCA_900102505.1", "taxid": 336292, "species_taxid": 336292, "relation_to_type": "type", "validated": true, "ani": 82.7756, "matched_fragments": 668, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus shandongensis", "strain": "strain=wg2", "accession": "GCA_017315735.1", "taxid": 2816048, "species_taxid": 2816048, "relation_to_type": "type", "validated": true, "ani": 82.5766, "matched_fragments": 624, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus nototheniae", "strain": "strain=I-41R45", "accession": "GCA_004335005.1", "taxid": 2489002, "species_taxid": 2489002, "relation_to_type": "type", "validated": true, "ani": 82.3449, "matched_fragments": 688, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus fontiphilus", "strain": "strain=MVW-1", "accession": "GCA_017356265.1", "taxid": 1815556, "species_taxid": 1815556, "relation_to_type": "type", "validated": true, "ani": 82.3182, "matched_fragments": 626, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus lichenicola", "strain": "strain=YIM 132242", "accession": "GCA_009708075.1", "taxid": 2665644, "species_taxid": 2665644, "relation_to_type": "type", "validated": true, "ani": 82.2986, "matched_fragments": 600, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aerius", "strain": "strain=KCTC 42845", "accession": "GCA_016757275.1", "taxid": 1915382, "species_taxid": 1915382, "relation_to_type": "type", "validated": true, "ani": 82.078, "matched_fragments": 619, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aerius", "strain": "strain=KCTC 42845", "accession": "GCA_014656455.1", "taxid": 1915382, "species_taxid": 1915382, "relation_to_type": "type", "validated": true, "ani": 82.0418, "matched_fragments": 618, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus everestensis", "strain": "strain=S8-55", "accession": "GCA_021491915.1", "taxid": 2903900, "species_taxid": 2903900, "relation_to_type": "type", "validated": true, "ani": 81.2792, "matched_fragments": 563, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus salsus", "strain": "strain=EGI L200073", "accession": "GCA_021556615.1", "taxid": 2911061, "species_taxid": 2911061, "relation_to_type": "type", "validated": true, "ani": 81.1024, "matched_fragments": 587, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus tegillarcae", "strain": "strain=BM15", "accession": "GCA_002847305.1", "taxid": 1529068, "species_taxid": 1529068, "relation_to_type": "type", "validated": true, "ani": 79.3131, "matched_fragments": 476, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000420145.1", "gtdb_species": "s__Paracoccus zeaxanthinifaciens", "ani": 100.0, "matched_fragments": 997, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_018860625.1", "gtdb_species": "s__Paracoccus sp018860625", "ani": 90.1901, "matched_fragments": 868, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_004683865.2", "gtdb_species": "s__Paracoccus liaowanqingii", "ani": 84.159, "matched_fragments": 725, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.54", "min_intra_species_ani": "96.54", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003594815.1", "gtdb_species": "s__Paracoccus aestuarii", "ani": 84.0518, "matched_fragments": 652, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_005048225.1", "gtdb_species": "s__Paracoccus gahaiensis", "ani": 83.8005, "matched_fragments": 722, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_006151785.1", "gtdb_species": "s__Paracoccus marcusii", "ani": 83.7883, "matched_fragments": 666, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.50", "min_intra_species_ani": "96.78", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.75", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_003056335.1", "gtdb_species": "s__Paracoccus indicus", "ani": 83.7535, "matched_fragments": 727, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_005048265.1", "gtdb_species": "s__Paracoccus hibiscisoli", "ani": 83.6643, "matched_fragments": 723, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.40", "min_intra_species_ani": "96.40", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003259195.1", "gtdb_species": "s__Paracoccus sediminilitoris", "ani": 83.2487, "matched_fragments": 722, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.17", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900111675.1", "gtdb_species": "s__Paracoccus homiensis", "ani": 82.9401, "matched_fragments": 655, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_003709565.1", "gtdb_species": "s__Paracoccus siganidrum", "ani": 82.9331, "matched_fragments": 683, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900102505.1", "gtdb_species": "s__Paracoccus tibetensis", "ani": 82.7613, "matched_fragments": 670, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_017356265.1", "gtdb_species": "s__Paracoccus fontiphilus", "ani": 82.313, "matched_fragments": 626, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_900631945.1", "gtdb_species": "s__Paracoccus haematequi", "ani": 82.2036, "matched_fragments": 612, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_014656455.1", "gtdb_species": "s__Paracoccus aerius", "ani": 82.0452, "matched_fragments": 618, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.225, "cell_length": 0.052, "doubling_h": 0.322, "growth_tmp": 30.0, "optimum_tmp": 27.5, "optimum_ph": 7.854, "genome_size": 3055520.0, "gc_content": 67.295, "coding_genes": 3755.444, "rRNA16S_genes": 3.0, "tRNA_genes": 52.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.117, "range_salinity": null, "facultative_respiration": 0.062, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.937, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.647, "coccus_cell_shape": 0.294, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.058, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Paracoccus", "zeaxanthinifaciens", "ATCC", "21588" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }