{ "type": "genome", "identifier": "GCF_000485925.1", "organism": "Siccibacter turicensis", "title": "Siccibacter turicensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "OARSA, CFSAN", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000485925.1", "bioproject": "PRJNA224116", "biosample": "SAMN02319256", "wgs_master": "AVPP00000000.1", "refseq_category": "na", "taxid": "357233", "species_taxid": "357233", "organism_name": "Siccibacter turicensis", "infraspecific_name": "strain=z508", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/10/29", "asm_name": "Etur508", "asm_submitter": "OARSA, CFSAN", "gbrs_paired_asm": "GCA_000485925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/485/925/GCF_000485925.1_Etur508", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4183714", "genome_size_ungapped": "4183714", "gc_percent": "58.000000", "replicon_count": "0", "scaffold_count": "291", "contig_count": "291", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000485925.1-RS_2024_12_23", "annotation_date": "2024-12-23", "total_gene_count": "4171", "protein_coding_gene_count": "3954", "non_coding_gene_count": "79", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-10-29", "dateModified": "2013-10-29", "datePublished": "2013-10-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Siccibacter turicensis" ], "sample_taxid": [ "357233" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.189 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4183714", "Number of Sequences": "291", "Longest Sequences (bp)": "72712", "N50 (bp)": "27330", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.0", "Number of CDSs": "3686", "Average Protein Length": "303.8", "Coding Ratio (%)": "80.3", "Number of rRNAs": "3", "Number of tRNAs": "66", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Siccibacter turicensis", "strain": "strain=LMG 23730", "accession": "GCA_000463155.2", "taxid": 357233, "species_taxid": 357233, "relation_to_type": "type", "validated": true, "ani": 99.9941, "matched_fragments": 1252, "total_fragments": 1254, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Siccibacter colletis", "strain": "strain=1383", "accession": "GCA_000696575.1", "taxid": 1505757, "species_taxid": 1505757, "relation_to_type": "type", "validated": true, "ani": 86.6251, "matched_fragments": 1070, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter malonaticus", "strain": "strain=LMG 23826", "accession": "GCA_001277215.2", "taxid": 413503, "species_taxid": 413503, "relation_to_type": "type", "validated": true, "ani": 81.927, "matched_fragments": 838, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter malonaticus", "strain": "strain=LMG 23826", "accession": "GCA_000409305.1", "taxid": 413503, "species_taxid": 413503, "relation_to_type": "type", "validated": true, "ani": 81.9239, "matched_fragments": 823, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter dublinensis subsp. lactaridi", "strain": "strain=LMG 23825", "accession": "GCA_000409345.1", "taxid": 413499, "species_taxid": 413497, "relation_to_type": "type", "validated": true, "ani": 81.8543, "matched_fragments": 846, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter dublinensis subsp. lausannensis", "strain": "strain=LMG 23824", "accession": "GCA_000409365.1", "taxid": 413500, "species_taxid": 413497, "relation_to_type": "type", "validated": true, "ani": 81.7734, "matched_fragments": 843, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter dublinensis subsp. dublinensis", "strain": "strain=LMG 23823", "accession": "GCA_000409225.1", "taxid": 413498, "species_taxid": 413497, "relation_to_type": "type", "validated": true, "ani": 81.6818, "matched_fragments": 821, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter sakazakii", "strain": "strain=ATCC 29544", "accession": "GCA_001971035.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 81.616, "matched_fragments": 786, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 81.603, "matched_fragments": 765, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter muytjensii", "strain": "strain=ATCC 51329", "accession": "GCA_001277195.1", "taxid": 413501, "species_taxid": 413501, "relation_to_type": "type", "validated": true, "ani": 81.5082, "matched_fragments": 822, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter muytjensii", "strain": "strain=ATCC 51329", "accession": "GCA_000409285.1", "taxid": 413501, "species_taxid": 413501, "relation_to_type": "type", "validated": true, "ani": 81.4965, "matched_fragments": 808, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter asburiae", "strain": "strain=FDAARGOS_892", "accession": "GCA_016027695.1", "taxid": 61645, "species_taxid": 61645, "relation_to_type": "type", "validated": true, "ani": 81.4661, "matched_fragments": 722, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_024390995.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 81.443, "matched_fragments": 762, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter asburiae", "strain": "strain=ATCC 35953", "accession": "GCA_001521715.1", "taxid": 61645, "species_taxid": 61645, "relation_to_type": "type", "validated": true, "ani": 81.3948, "matched_fragments": 726, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pluralibacter gergoviae", "strain": "strain=NBRC 105706", "accession": "GCA_001598855.1", "taxid": 61647, "species_taxid": 61647, "relation_to_type": "type", "validated": true, "ani": 81.3185, "matched_fragments": 721, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Franconibacter helveticus", "strain": "strain=LMG 23732", "accession": "GCA_000463115.2", "taxid": 357240, "species_taxid": 357240, "relation_to_type": "type", "validated": true, "ani": 81.2134, "matched_fragments": 756, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei", "strain": "strain=FDAARGOS 1433", "accession": "GCA_019048245.1", "taxid": 158836, "species_taxid": 158836, "relation_to_type": "suspected-type", "validated": true, "ani": 81.2115, "matched_fragments": 762, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Franconibacter helveticus", "strain": "strain=513", "accession": "GCA_000485945.1", "taxid": 357240, "species_taxid": 357240, "relation_to_type": "type", "validated": true, "ani": 81.0909, "matched_fragments": 717, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 81.0494, "matched_fragments": 744, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Atlantibacter hermannii", "strain": "strain=FDAARGOS_888", "accession": "GCA_016027855.1", "taxid": 565, "species_taxid": 565, "relation_to_type": "type", "validated": true, "ani": 80.879, "matched_fragments": 658, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yokenella regensburgei", "strain": "strain=NCTC11966", "accession": "GCA_900460805.1", "taxid": 158877, "species_taxid": 158877, "relation_to_type": "type", "validated": true, "ani": 80.7865, "matched_fragments": 677, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yokenella regensburgei", "strain": "strain=ATCC 49455", "accession": "GCA_000735455.1", "taxid": 158877, "species_taxid": 158877, "relation_to_type": "type", "validated": true, "ani": 80.6907, "matched_fragments": 655, "total_fragments": 1254, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000463155.2", "gtdb_species": "s__Siccibacter turicensis", "ani": 99.9941, "matched_fragments": 1252, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "97.87", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_000696575.1", "gtdb_species": "s__Siccibacter colletis", "ani": 86.6251, "matched_fragments": 1070, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter", "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_001277215.2", "gtdb_species": "s__Cronobacter malonaticus", "ani": 81.927, "matched_fragments": 838, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.11", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 62, "status": "-" }, { "accession": "GCA_000027065.2", "gtdb_species": "s__Cronobacter turicensis", "ani": 81.8942, "matched_fragments": 837, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.17", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_001277175.1", "gtdb_species": "s__Cronobacter universalis", "ani": 81.87, "matched_fragments": 843, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.62", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000982825.1", "gtdb_species": "s__Cronobacter sakazakii", "ani": 81.8302, "matched_fragments": 819, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.00", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 440, "status": "-" }, { "accession": "GCF_002208095.1", "gtdb_species": "s__Enterobacter cloacae_M", "ani": 81.5394, "matched_fragments": 753, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.7528, "mean_intra_species_ani": "98.28", "min_intra_species_ani": "96.89", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 84, "status": "-" }, { "accession": "GCF_000164865.1", "gtdb_species": "s__Enterobacter_B lignolyticus", "ani": 81.4441, "matched_fragments": 715, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.80", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007570865.1", "gtdb_species": "s__Atlantibacter subterranea", "ani": 81.3299, "matched_fragments": 737, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "98.44", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001598855.1", "gtdb_species": "s__Pluralibacter gergoviae", "ani": 81.3259, "matched_fragments": 720, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pluralibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_009907385.1", "gtdb_species": "s__Atlantibacter hermannii_A", "ani": 81.2555, "matched_fragments": 738, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter", "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_014193285.1", "gtdb_species": "s__Atlantibacter sp002345315", "ani": 81.2442, "matched_fragments": 741, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000463115.2", "gtdb_species": "s__Franconibacter helveticus", "ani": 81.2315, "matched_fragments": 754, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Franconibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.04", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000321045.1", "gtdb_species": "s__Phytobacter massiliensis", "ani": 81.0477, "matched_fragments": 726, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter", "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_002469605.1", "gtdb_species": "s__UBA7405 sp002469605", "ani": 80.9661, "matched_fragments": 583, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405", "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_019237635.1", "gtdb_species": "s__Enterobacter_B sp019237635", "ani": 80.9197, "matched_fragments": 643, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_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_900635495.1", "gtdb_species": "s__Atlantibacter hermannii", "ani": 80.797, "matched_fragments": 663, "total_fragments": 1254, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.90", "num_clustered_genomes": 28, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.0, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 27.0, "optimum_ph": null, "genome_size": 4239459.0, "gc_content": 57.8, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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": [ "Siccibacter", "turicensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }