{ "type": "genome", "identifier": "GCF_004331955.1", "organism": "Roseitalea porphyridii", "title": "Roseitalea porphyridii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chung-Ang University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004331955.1", "bioproject": "PRJNA224116", "biosample": "SAMN11037189", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1852022", "species_taxid": "1852022", "organism_name": "Roseitalea porphyridii", "infraspecific_name": "strain=MA7-20", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/07", "asm_name": "ASM433195v1", "asm_submitter": "Chung-Ang University", "gbrs_paired_asm": "GCA_004331955.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/331/955/GCF_004331955.1_ASM433195v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3539672", "genome_size_ungapped": "3539672", "gc_percent": "66.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004331955.1-RS_2024_05_19", "annotation_date": "2024-05-19", "total_gene_count": "3486", "protein_coding_gene_count": "3412", "non_coding_gene_count": "49", "pubmed_id": "27902230" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-07", "dateModified": "2019-03-07", "datePublished": "2019-03-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Roseitalea porphyridii" ], "sample_taxid": [ "1852022" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.960 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3539672", "Number of Sequences": "1", "Longest Sequences (bp)": "3539672", "N50 (bp)": "3539672", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.6", "Number of CDSs": "3457", "Average Protein Length": "311.7", "Coding Ratio (%)": "91.3", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Oricola indica", "strain": "strain=JL-62", "accession": "GCA_019966595.1", "taxid": 2872591, "species_taxid": 2872591, "relation_to_type": "type", "validated": true, "ani": 78.7618, "matched_fragments": 453, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hoeflea olei", "strain": "strain=JC234", "accession": "GCA_001703635.1", "taxid": 1480615, "species_taxid": 1480615, "relation_to_type": "type", "validated": true, "ani": 78.7407, "matched_fragments": 445, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor pacificus", "strain": "strain=pht-3B", "accession": "GCA_000300335.1", "taxid": 1231180, "species_taxid": 1231180, "relation_to_type": "type", "validated": true, "ani": 78.6112, "matched_fragments": 430, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella pollutisoli", "strain": "strain=KCTC 52677", "accession": "GCA_024609765.1", "taxid": 2250594, "species_taxid": 2250594, "relation_to_type": "type", "validated": true, "ani": 78.5921, "matched_fragments": 436, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor alexandrii", "strain": "strain=Z3-1", "accession": "GCA_004000215.1", "taxid": 2448161, "species_taxid": 2448161, "relation_to_type": "type", "validated": true, "ani": 78.5633, "matched_fragments": 479, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquibium microcysteis", "strain": "strain=NIBR3", "accession": "GCA_014495845.1", "taxid": 675281, "species_taxid": 675281, "relation_to_type": "type", "validated": true, "ani": 78.4123, "matched_fragments": 473, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquibium oceanicum", "strain": "strain=B7", "accession": "GCA_001889605.1", "taxid": 1670800, "species_taxid": 1670800, "relation_to_type": "type", "validated": true, "ani": 78.3714, "matched_fragments": 385, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Zhengella mangrovi", "strain": "strain=X9-2-2", "accession": "GCA_002727065.1", "taxid": 1982044, "species_taxid": 1982044, "relation_to_type": "type", "validated": true, "ani": 78.366, "matched_fragments": 374, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium intechi", "strain": "strain=BD68", "accession": "GCA_002879535.2", "taxid": 537601, "species_taxid": 537601, "relation_to_type": "type", "validated": true, "ani": 78.2501, "matched_fragments": 372, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium tamadayense", "strain": "strain=DSM 28320", "accession": "GCA_003863365.1", "taxid": 425306, "species_taxid": 425306, "relation_to_type": "type", "validated": true, "ani": 78.2492, "matched_fragments": 426, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aminobacter aganoensis", "strain": "strain=DSM 7051", "accession": "GCA_014206975.1", "taxid": 83264, "species_taxid": 83264, "relation_to_type": "type", "validated": true, "ani": 78.2412, "matched_fragments": 404, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor soli", "strain": "strain=ZZ-1", "accession": "GCA_001050155.1", "taxid": 1670619, "species_taxid": 1670619, "relation_to_type": "type", "validated": true, "ani": 78.2186, "matched_fragments": 415, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquibium carbonis", "strain": "strain=B2.3", "accession": "GCA_003970795.1", "taxid": 2495581, "species_taxid": 2495581, "relation_to_type": "type", "validated": true, "ani": 78.1949, "matched_fragments": 420, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium erdmanii", "strain": "strain=USDA 3471", "accession": "GCA_000472705.1", "taxid": 1777866, "species_taxid": 1777866, "relation_to_type": "type", "validated": true, "ani": 78.1886, "matched_fragments": 386, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium caraganae", "strain": "strain=LMG 24397", "accession": "GCA_016836705.1", "taxid": 483206, "species_taxid": 483206, "relation_to_type": "type", "validated": true, "ani": 78.1702, "matched_fragments": 400, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium azooxidifex", "strain": "strain=DSM 100211", "accession": "GCA_014196765.1", "taxid": 1636188, "species_taxid": 1636188, "relation_to_type": "type", "validated": true, "ani": 78.1505, "matched_fragments": 374, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella granuli", "strain": "strain=DSM 18401", "accession": "GCA_004341885.1", "taxid": 323621, "species_taxid": 323621, "relation_to_type": "type", "validated": true, "ani": 78.1226, "matched_fragments": 403, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium camelthorni", "strain": "strain=CCNWXJ 40-4", "accession": "GCA_011045125.1", "taxid": 475069, "species_taxid": 475069, "relation_to_type": "type", "validated": true, "ani": 78.1209, "matched_fragments": 383, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium sanjuanii", "strain": "strain=BSA136", "accession": "GCA_002529485.1", "taxid": 2037900, "species_taxid": 2037900, "relation_to_type": "type", "validated": true, "ani": 78.0578, "matched_fragments": 374, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aurantimonas endophytica", "strain": "strain=KCTC 52296", "accession": "GCA_024105745.1", "taxid": 1522175, "species_taxid": 1522175, "relation_to_type": "type", "validated": true, "ani": 78.034, "matched_fragments": 368, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium metallidurans", "strain": "strain=STM 2683", "accession": "GCA_000350085.1", "taxid": 489722, "species_taxid": 489722, "relation_to_type": "type", "validated": true, "ani": 78.0237, "matched_fragments": 402, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella yambaruensis", "strain": "strain=DSM 18801", "accession": "GCA_022899355.1", "taxid": 415996, "species_taxid": 415996, "relation_to_type": "type", "validated": true, "ani": 77.964, "matched_fragments": 424, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella sumterensis", "strain": "strain=MEC087", "accession": "GCA_004514425.2", "taxid": 1967501, "species_taxid": 1967501, "relation_to_type": "type", "validated": true, "ani": 77.9421, "matched_fragments": 334, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hoeflea marina", "strain": "strain=DSM 16791", "accession": "GCA_003182275.1", "taxid": 274592, "species_taxid": 274592, "relation_to_type": "type", "validated": true, "ani": 77.9362, "matched_fragments": 417, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquamicrobium lusatiense", "strain": "strain=DSM 11099", "accession": "GCA_014201615.1", "taxid": 89772, "species_taxid": 89772, "relation_to_type": "type", "validated": true, "ani": 77.9091, "matched_fragments": 283, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium wenxiniae", "strain": "strain=WYCCWR 10195", "accession": "GCA_002284535.1", "taxid": 2014805, "species_taxid": 2014805, "relation_to_type": "type", "validated": true, "ani": 77.82, "matched_fragments": 391, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella daejeonensis", "strain": "strain=JCM 16236", "accession": "GCA_024281235.1", "taxid": 659017, "species_taxid": 659017, "relation_to_type": "type", "validated": true, "ani": 77.7527, "matched_fragments": 296, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hoeflea halophila", "strain": "strain=KCTC 23107", "accession": "GCA_900220985.1", "taxid": 714899, "species_taxid": 714899, "relation_to_type": "type", "validated": true, "ani": 77.7273, "matched_fragments": 286, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor indicus", "strain": "strain=C115", "accession": "GCA_000300515.1", "taxid": 721133, "species_taxid": 721133, "relation_to_type": "type", "validated": true, "ani": 77.445, "matched_fragments": 232, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium redzepovicii", "strain": "strain=18T", "accession": "GCA_019793435.1", "taxid": 2867518, "species_taxid": 2867518, "relation_to_type": "type", "validated": true, "ani": 77.4264, "matched_fragments": 315, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phyllobacterium salinisoli", "strain": "strain=LLAN61", "accession": "GCA_003335045.1", "taxid": 1899321, "species_taxid": 1899321, "relation_to_type": "type", "validated": true, "ani": 77.3937, "matched_fragments": 273, "total_fragments": 1179, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004331955.1", "gtdb_species": "s__Roseitalea porphyridii", "ani": 100.0, "matched_fragments": 1179, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea", "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_003149475.2", "gtdb_species": "s__Roseitalea stylonematis", "ani": 83.3606, "matched_fragments": 832, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCA_017642895.1", "gtdb_species": "s__Roseitalea sp017642895", "ani": 82.3831, "matched_fragments": 804, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014904745.1", "gtdb_species": "s__Oricola sp014904745", "ani": 79.3043, "matched_fragments": 533, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola", "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_000759435.1", "gtdb_species": "s__Hoeflea sp000759435", "ani": 78.8722, "matched_fragments": 466, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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_002698425.1", "gtdb_species": "s__Oricola sp002698425", "ani": 78.8174, "matched_fragments": 517, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola", "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_000300335.1", "gtdb_species": "s__Nitratireductor pacificus", "ani": 78.6311, "matched_fragments": 428, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor", "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_014860725.1", "gtdb_species": "s__Aquamicrobium_A sp014860725", "ani": 78.5476, "matched_fragments": 257, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A", "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_007922615.2", "gtdb_species": "s__Nitratireductor_D sp007922615", "ani": 78.4317, "matched_fragments": 429, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D", "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_900469965.1", "gtdb_species": "s__Mycoplana sp900469965", "ani": 78.393, "matched_fragments": 396, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_001889605.1", "gtdb_species": "s__Mesorhizobium_E oceanicum", "ani": 78.3827, "matched_fragments": 385, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E", "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_905339215.1", "gtdb_species": "s__DUSC01 sp008933895", "ani": 78.2174, "matched_fragments": 402, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.82", "min_intra_species_ani": "99.82", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014873545.1", "gtdb_species": "s__OAS926 sp014873545", "ani": 78.1717, "matched_fragments": 418, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__OAS926", "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_018829385.1", "gtdb_species": "s__Hoeflea sp018829385", "ani": 78.1551, "matched_fragments": 251, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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_012911015.1", "gtdb_species": "s__Aliihoeflea sp012911015", "ani": 78.1395, "matched_fragments": 379, "total_fragments": 1179, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea", "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": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Roseitalea", "porphyridii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }