{ "type": "genome", "identifier": "GCF_000285995.1", "organism": "Actinomyces naeslundii str. Howell 279", "title": "Actinomyces naeslundii str. Howell 279", "description": "na", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000285995.1", "bioproject": "PRJNA224116", "biosample": "SAMN00828754", "wgs_master": "ALJK00000000.1", "refseq_category": "na", "taxid": "1115803", "species_taxid": "1655", "organism_name": "Actinomyces naeslundii str. Howell 279", "infraspecific_name": "strain=Howell 279", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/08/08", "asm_name": "AneasH279v1.0", "asm_submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "GCA_000285995.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/285/995/GCF_000285995.1_AneasH279v1.0", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3114341", "genome_size_ungapped": "3114341", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "243", "contig_count": "243", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-28", "total_gene_count": "2829", "protein_coding_gene_count": "2545", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-08-08", "dateModified": "2012-08-08", "datePublished": "2012-08-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinomyces naeslundii str. Howell 279" ], "sample_taxid": [ "1115803" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not determined" ], "sample_host_location_id": [], "data_size": "0.860 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)": "3114341", "Number of Sequences": "243", "Longest Sequences (bp)": "154895", "N50 (bp)": "23198", "Gap Ratio (%)": "0.000417", "GCcontent (%)": "67.9", "Number of CDSs": "2557", "Average Protein Length": "314.2", "Coding Ratio (%)": "77.4", "Number of rRNAs": "6", "Number of tRNAs": "49", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinomyces naeslundii", "strain": "strain=Howell 279", "accession": "GCA_000285995.1", "taxid": 1655, "species_taxid": 1655, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 906, "total_fragments": 918, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinomyces naeslundii", "strain": "strain=NCTC 10301", "accession": "GCA_001956585.1", "taxid": 1655, "species_taxid": 1655, "relation_to_type": "type", "validated": true, "ani": 99.9282, "matched_fragments": 894, "total_fragments": 918, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinomyces viscosus", "strain": "strain=CCUG 14476", "accession": "GCA_004525795.1", "taxid": 1656, "species_taxid": 1656, "relation_to_type": "type", "validated": true, "ani": 89.54, "matched_fragments": 762, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces johnsonii", "strain": "strain=CCUG 34287", "accession": "GCA_006546835.1", "taxid": 544581, "species_taxid": 544581, "relation_to_type": "type", "validated": true, "ani": 89.5387, "matched_fragments": 787, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces viscosus", "strain": "strain=NCTC10951", "accession": "GCA_900637975.1", "taxid": 1656, "species_taxid": 1656, "relation_to_type": "type", "validated": true, "ani": 89.515, "matched_fragments": 789, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces johnsonii", "strain": "strain=CCUG 34287T", "accession": "GCA_008693165.1", "taxid": 544581, "species_taxid": 544581, "relation_to_type": "type", "validated": true, "ani": 89.4627, "matched_fragments": 787, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces oris", "strain": "strain=FDAARGOS_1051", "accession": "GCA_016127955.1", "taxid": 544580, "species_taxid": 544580, "relation_to_type": "suspected-type", "validated": true, "ani": 89.3806, "matched_fragments": 786, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces oris", "strain": "strain=CCUG 34288", "accession": "GCA_006546825.1", "taxid": 544580, "species_taxid": 544580, "relation_to_type": "suspected-type", "validated": true, "ani": 89.3187, "matched_fragments": 781, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces denticolens", "strain": "strain=DSM 20671", "accession": "GCA_002072185.1", "taxid": 52767, "species_taxid": 52767, "relation_to_type": "type", "validated": true, "ani": 81.4271, "matched_fragments": 428, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces marmotae", "strain": "strain=zg-325", "accession": "GCA_009829655.1", "taxid": 2737173, "species_taxid": 2737173, "relation_to_type": "type", "validated": true, "ani": 81.2994, "matched_fragments": 384, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanitalea stevensii", "strain": "strain=Sa1BUA1", "accession": "GCA_014837105.1", "taxid": 2763072, "species_taxid": 2763072, "relation_to_type": "type", "validated": true, "ani": 78.1397, "matched_fragments": 230, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruania suaedae", "strain": "strain=LR1S40", "accession": "GCA_021049265.1", "taxid": 2897774, "species_taxid": 2897774, "relation_to_type": "type", "validated": true, "ani": 77.2917, "matched_fragments": 149, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinotalea solisilvae", "strain": "strain=KACC 19191", "accession": "GCA_016464425.1", "taxid": 2072922, "species_taxid": 2072922, "relation_to_type": "type", "validated": true, "ani": 76.7799, "matched_fragments": 175, "total_fragments": 918, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001956585.1", "gtdb_species": "s__Actinomyces naeslundii", "ani": 99.9282, "matched_fragments": 894, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.74", "min_intra_species_ani": "96.59", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 23, "status": "conclusive" }, { "accession": "GCF_001937665.1", "gtdb_species": "s__Actinomyces oris_D", "ani": 90.4337, "matched_fragments": 778, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "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_000195595.1", "gtdb_species": "s__Actinomyces sp000195595", "ani": 90.0342, "matched_fragments": 785, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "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_900323545.1", "gtdb_species": "s__Actinomyces sp900323545", "ani": 89.9677, "matched_fragments": 786, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "98.47", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005696555.1", "gtdb_species": "s__Actinomyces oris_E", "ani": 89.5472, "matched_fragments": 775, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.15", "min_intra_species_ani": "98.35", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_006546835.1", "gtdb_species": "s__Actinomyces johnsonii", "ani": 89.5387, "matched_fragments": 787, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "97.12", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900637975.1", "gtdb_species": "s__Actinomyces viscosus", "ani": 89.5243, "matched_fragments": 789, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "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_011752065.1", "gtdb_species": "s__Actinomyces sp011752065", "ani": 89.5206, "matched_fragments": 770, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "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_001937445.1", "gtdb_species": "s__Actinomyces oris_C", "ani": 89.5016, "matched_fragments": 762, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.06", "min_intra_species_ani": "96.78", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001929375.1", "gtdb_species": "s__Actinomyces oris_B", "ani": 89.3637, "matched_fragments": 745, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_006546825.1", "gtdb_species": "s__Actinomyces oris", "ani": 89.3187, "matched_fragments": 781, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "95.25", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_001553935.1", "gtdb_species": "s__Actinomyces oris_A", "ani": 89.1845, "matched_fragments": 770, "total_fragments": 918, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.65", "min_intra_species_ani": "97.48", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.165, "cell_length": 0.258, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.0, "genome_size": 3059524.0, "gc_content": 68.42, "coding_genes": 3229.0, "rRNA16S_genes": 3.0, "tRNA_genes": 51.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Actinomyces", "naeslundii", "str.", "Howell", "279" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }