{ "type": "genome", "identifier": "GCF_000428785.1", "organism": "Conchiformibius kuhniae DSM 17694", "title": "Conchiformibius kuhniae DSM 17694", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000428785.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441546", "wgs_master": "AUAP00000000.1", "refseq_category": "na", "taxid": "1121351", "species_taxid": "211502", "organism_name": "Conchiformibius kuhniae DSM 17694", "infraspecific_name": "strain=DSM 17694", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/15", "asm_name": "ASM42878v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000428785.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/428/785/GCF_000428785.1_ASM42878v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2118625", "genome_size_ungapped": "2113141", "gc_percent": "56.000000", "replicon_count": "0", "scaffold_count": "50", "contig_count": "56", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000428785.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "2120", "protein_coding_gene_count": "2020", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-15", "dateModified": "2013-07-15", "datePublished": "2013-07-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Conchiformibius kuhniae DSM 17694" ], "sample_taxid": [ "1121351" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.579 MB", "sample_ph_range": { "min": 8.0, "max": 8.0 }, "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)": "2118625", "Number of Sequences": "50", "Longest Sequences (bp)": "419397", "N50 (bp)": "108101", "Gap Ratio (%)": "0.258847", "GCcontent (%)": "56.2", "Number of CDSs": "1970", "Average Protein Length": "309.0", "Coding Ratio (%)": "86.2", "Number of rRNAs": "2", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Conchiformibius kuhniae", "strain": "strain=DSM 17694", "accession": "GCA_000428785.1", "taxid": 211502, "species_taxid": 211502, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 675, "total_fragments": 681, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Conchiformibius kuhniae", "strain": "strain=17694", "accession": "GCA_022871025.1", "taxid": 211502, "species_taxid": 211502, "relation_to_type": "type", "validated": true, "ani": 99.8539, "matched_fragments": 680, "total_fragments": 681, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Conchiformibius steedae", "strain": "strain=DSM 2580", "accession": "GCA_023547005.1", "taxid": 153493, "species_taxid": 153493, "relation_to_type": "type", "validated": true, "ani": 82.0257, "matched_fragments": 486, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Conchiformibius steedae", "strain": "strain=DSM 2580", "accession": "GCA_000620925.1", "taxid": 153493, "species_taxid": 153493, "relation_to_type": "type", "validated": true, "ani": 82.0095, "matched_fragments": 485, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Conchiformibius steedae", "strain": "strain=DSM 2580", "accession": "GCA_014054725.1", "taxid": 153493, "species_taxid": 153493, "relation_to_type": "type", "validated": true, "ani": 81.8542, "matched_fragments": 486, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella bonacorsii", "strain": "strain=Marseille-Q4569", "accession": "GCA_016623605.1", "taxid": 2796361, "species_taxid": 2796361, "relation_to_type": "type", "validated": true, "ani": 78.0688, "matched_fragments": 268, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella oralis", "strain": "strain=DSM 18271", "accession": "GCA_014054985.1", "taxid": 505, "species_taxid": 505, "relation_to_type": "type", "validated": true, "ani": 78.0156, "matched_fragments": 268, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella oralis", "strain": "strain=ATCC 51147", "accession": "GCA_000160435.1", "taxid": 505, "species_taxid": 505, "relation_to_type": "type", "validated": true, "ani": 77.9958, "matched_fragments": 268, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria dumasiana", "strain": "strain=LMG 30012", "accession": "GCA_022870885.1", "taxid": 1931275, "species_taxid": 1931275, "relation_to_type": "type", "validated": true, "ani": 77.7126, "matched_fragments": 203, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Uruburuella testudinis", "strain": "strain=CCUG 63373m", "accession": "GCA_022870865.1", "taxid": 1282863, "species_taxid": 1282863, "relation_to_type": "type", "validated": true, "ani": 77.5898, "matched_fragments": 223, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria meningitidis", "strain": "strain=PartJ-Nmeningitidis-RM8376", "accession": "GCA_022869645.1", "taxid": 487, "species_taxid": 487, "relation_to_type": "type", "validated": true, "ani": 77.4892, "matched_fragments": 186, "total_fragments": 681, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000428785.1", "gtdb_species": "s__Conchiformibius kuhniae", "ani": 100.0, "matched_fragments": 675, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius", "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_014054725.1", "gtdb_species": "s__Conchiformibius steedae", "ani": 81.8908, "matched_fragments": 483, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000190695.1", "gtdb_species": "s__Kingella_A denitrificans", "ani": 78.3219, "matched_fragments": 252, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "96.04", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_905373195.1", "gtdb_species": "s__Kingella_B oralis_A", "ani": 78.305, "matched_fragments": 150, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_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": "GCF_002237445.1", "gtdb_species": "s__Neisseria sp002237445", "ani": 78.2384, "matched_fragments": 229, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001592185.1", "gtdb_species": "s__Neisseria denitrificans", "ani": 78.0536, "matched_fragments": 174, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "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": "GCF_000745955.1", "gtdb_species": "s__Alysiella crassa", "ani": 78.051, "matched_fragments": 248, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014054985.1", "gtdb_species": "s__Kingella_B oralis", "ani": 77.9998, "matched_fragments": 267, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014055025.1", "gtdb_species": "s__Neisseria bacilliformis", "ani": 77.9916, "matched_fragments": 251, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "96.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900451175.1", "gtdb_species": "s__Neisseria potus", "ani": 77.9508, "matched_fragments": 239, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "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_004341385.1", "gtdb_species": "s__Neisseria suis", "ani": 77.908, "matched_fragments": 241, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.29", "min_intra_species_ani": "97.17", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002108505.1", "gtdb_species": "s__Neisseria dumasiana", "ani": 77.8167, "matched_fragments": 197, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.54", "min_intra_species_ani": "97.26", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003044455.1", "gtdb_species": "s__Neisseria bergeri", "ani": 77.6021, "matched_fragments": 184, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.18", "min_intra_species_ani": "96.14", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_000220865.1", "gtdb_species": "s__Neisseria macacae", "ani": 77.5142, "matched_fragments": 202, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 96.509, "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_900638555.1", "gtdb_species": "s__Neisseria meningitidis", "ani": 77.4923, "matched_fragments": 187, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0389, "mean_intra_species_ani": "97.78", "min_intra_species_ani": "97.16", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.86", "num_clustered_genomes": 2138, "status": "-" }, { "accession": "GCF_016025525.2", "gtdb_species": "s__Eikenella sp016025525", "ani": 77.4706, "matched_fragments": 222, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella", "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_900638685.1", "gtdb_species": "s__Neisseria weaveri", "ani": 77.424, "matched_fragments": 154, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_901482445.1", "gtdb_species": "s__Neisseria lactamica", "ani": 77.3597, "matched_fragments": 206, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.73", "min_intra_species_ani": "97.33", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 36, "status": "-" }, { "accession": "GCF_013267835.1", "gtdb_species": "s__Neisseria sp000186165", "ani": 77.3222, "matched_fragments": 154, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0019, "mean_intra_species_ani": "96.64", "min_intra_species_ani": "96.07", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_000227275.1", "gtdb_species": "s__Neisseria sp000227275", "ani": 77.26, "matched_fragments": 202, "total_fragments": 681, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 96.3387, "mean_intra_species_ani": "97.52", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.431, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 8.0, "optimum_ph": null, "genome_size": 2118516.0, "gc_content": 56.2, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": 1.0, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Conchiformibius", "kuhniae", "DSM", "17694" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }