{ "type": "genome", "identifier": "GCF_000176795.1", "organism": "Photobacterium damselae subsp. damselae CIP 102761", "title": "Photobacterium damselae subsp. damselae CIP 102761", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Los Alamos National Laboratory (LANL), National Microbial Pathogen Data Resource (NMPDR)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000176795.1", "bioproject": "PRJNA224116", "biosample": "SAMN02393816", "wgs_master": "ADBS00000000.1", "refseq_category": "na", "taxid": "675817", "species_taxid": "38293", "organism_name": "Photobacterium damselae subsp. damselae CIP 102761", "infraspecific_name": "strain=CIP 102761", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2009/11/13", "asm_name": "ASM17679v1", "asm_submitter": "Los Alamos National Laboratory (LANL), National Microbial Pathogen Data Resource (NMPDR)", "gbrs_paired_asm": "GCA_000176795.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/176/795/GCF_000176795.1_ASM17679v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5046328", "genome_size_ungapped": "5046301", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-03", "total_gene_count": "4588", "protein_coding_gene_count": "4269", "non_coding_gene_count": "230", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2009-11-13", "dateModified": "2009-11-13", "datePublished": "2009-11-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium damselae subsp. damselae CIP 102761" ], "sample_taxid": [ "675817" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.423 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)": "5046328", "Number of Sequences": "8", "Longest Sequences (bp)": "3236779", "N50 (bp)": "3236779", "Gap Ratio (%)": "0.000535", "GCcontent (%)": "40.7", "Number of CDSs": "4424", "Average Protein Length": "319.5", "Coding Ratio (%)": "84.0", "Number of rRNAs": "35", "Number of tRNAs": "190", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium damselae subsp. damselae", "strain": "strain=CIP 102761", "accession": "GCA_000176795.1", "taxid": 85581, "species_taxid": 38293, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1671, "total_fragments": 1677, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium damselae", "strain": "strain=NCTC11647", "accession": "GCA_900454585.1", "taxid": 38293, "species_taxid": 38293, "relation_to_type": "type", "validated": true, "ani": 99.9781, "matched_fragments": 1644, "total_fragments": 1677, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium damselae", "strain": "strain=ATCC 33539", "accession": "GCA_003026815.1", "taxid": 38293, "species_taxid": 38293, "relation_to_type": "type", "validated": true, "ani": 99.9552, "matched_fragments": 1572, "total_fragments": 1677, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio inusitatus", "strain": "strain=LMG 23434", "accession": "GCA_024346935.1", "taxid": 413402, "species_taxid": 413402, "relation_to_type": "type", "validated": true, "ani": 80.4037, "matched_fragments": 145, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio pelagius", "strain": "strain=ATCC 25916", "accession": "GCA_024347575.1", "taxid": 28169, "species_taxid": 28169, "relation_to_type": "type", "validated": true, "ani": 79.9923, "matched_fragments": 186, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium leiognathi", "strain": "strain=ATCC 25521", "accession": "GCA_003026235.1", "taxid": 553611, "species_taxid": 553611, "relation_to_type": "type", "validated": true, "ani": 79.8604, "matched_fragments": 455, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium leiognathi", "strain": "strain=ATCC 25521", "accession": "GCA_000950415.1", "taxid": 553611, "species_taxid": 553611, "relation_to_type": "type", "validated": true, "ani": 79.8046, "matched_fragments": 455, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio panuliri", "strain": "strain=JCM 19500", "accession": "GCA_009938205.1", "taxid": 1381081, "species_taxid": 1381081, "relation_to_type": "type", "validated": true, "ani": 79.7642, "matched_fragments": 173, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium toruni", "strain": "strain=CECT 9189", "accession": "GCA_024529955.1", "taxid": 1935446, "species_taxid": 1935446, "relation_to_type": "type", "validated": true, "ani": 79.6875, "matched_fragments": 457, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium lucens", "strain": "strain=CAIM 1937", "accession": "GCA_009873615.1", "taxid": 2562949, "species_taxid": 2562949, "relation_to_type": "type", "validated": true, "ani": 79.6736, "matched_fragments": 429, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio panuliri", "strain": "strain=LBS 2", "accession": "GCA_008830195.1", "taxid": 1381081, "species_taxid": 1381081, "relation_to_type": "type", "validated": true, "ani": 79.4111, "matched_fragments": 171, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium marinum", "strain": "strain=AK15", "accession": "GCA_000331515.1", "taxid": 1056511, "species_taxid": 1056511, "relation_to_type": "type", "validated": true, "ani": 79.3256, "matched_fragments": 264, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio nitrifigilis", "strain": "strain=NFV-1", "accession": "GCA_015686695.1", "taxid": 2789781, "species_taxid": 2789781, "relation_to_type": "type", "validated": true, "ani": 79.2667, "matched_fragments": 163, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium angustum", "strain": "strain=ATCC 25915", "accession": "GCA_003026365.1", "taxid": 661, "species_taxid": 661, "relation_to_type": "type", "validated": true, "ani": 79.262, "matched_fragments": 430, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium angustum", "strain": "strain=ATCC 25915", "accession": "GCA_000950005.1", "taxid": 661, "species_taxid": 661, "relation_to_type": "type", "validated": true, "ani": 79.1551, "matched_fragments": 431, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium phosphoreum", "strain": "strain=ATCC 11040", "accession": "GCA_000949955.1", "taxid": 659, "species_taxid": 659, "relation_to_type": "type", "validated": true, "ani": 78.8398, "matched_fragments": 387, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio inusitatus", "strain": "strain=NBRC 102082", "accession": "GCA_006538525.1", "taxid": 413402, "species_taxid": 413402, "relation_to_type": "type", "validated": true, "ani": 78.8157, "matched_fragments": 130, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium indicum", "strain": "strain=ATCC 19614", "accession": "GCA_003026215.1", "taxid": 81447, "species_taxid": 81447, "relation_to_type": "type", "validated": true, "ani": 78.6136, "matched_fragments": 356, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium frigidiphilum", "strain": "strain=JCM 12947", "accession": "GCA_003025615.1", "taxid": 264736, "species_taxid": 264736, "relation_to_type": "type", "validated": true, "ani": 78.5755, "matched_fragments": 342, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio variabilis", "strain": "strain=CAIM 1454", "accession": "GCA_003263785.1", "taxid": 990271, "species_taxid": 990271, "relation_to_type": "type", "validated": true, "ani": 78.564, "matched_fragments": 162, "total_fragments": 1677, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003026815.1", "gtdb_species": "s__Photobacterium damselae", "ani": 99.9552, "matched_fragments": 1572, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.68", "min_intra_species_ani": "96.10", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.75", "num_clustered_genomes": 54, "status": "conclusive" }, { "accession": "GCF_000940995.1", "gtdb_species": "s__Photobacterium gaetbulicola", "ani": 80.045, "matched_fragments": 255, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "95.81", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000950415.1", "gtdb_species": "s__Photobacterium leiognathi", "ani": 79.808, "matched_fragments": 452, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.11", "min_intra_species_ani": "96.59", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_009873615.1", "gtdb_species": "s__Photobacterium lucens", "ani": 79.6785, "matched_fragments": 428, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.83", "min_intra_species_ani": "97.58", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003026105.1", "gtdb_species": "s__Photobacterium sp003026105", "ani": 79.6678, "matched_fragments": 414, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.17", "min_intra_species_ani": "99.06", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_003026495.1", "gtdb_species": "s__Photobacterium sanctipauli", "ani": 79.4453, "matched_fragments": 280, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "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_000331515.1", "gtdb_species": "s__Photobacterium marinum", "ani": 79.3318, "matched_fragments": 264, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.66", "min_intra_species_ani": "96.66", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003026365.1", "gtdb_species": "s__Photobacterium angustum", "ani": 79.2519, "matched_fragments": 430, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.76", "min_intra_species_ani": "95.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 27, "status": "-" }, { "accession": "GCF_001650345.1", "gtdb_species": "s__Photobacterium jeanii", "ani": 79.1663, "matched_fragments": 349, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "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_003026455.1", "gtdb_species": "s__Photobacterium rosenbergii", "ani": 79.1528, "matched_fragments": 273, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.32", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000153325.1", "gtdb_species": "s__Photobacterium sp000153325", "ani": 79.14, "matched_fragments": 422, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "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_900233005.1", "gtdb_species": "s__Vibrio tapetis", "ani": 79.0769, "matched_fragments": 169, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_001077885.1", "gtdb_species": "s__Photobacterium swingsii", "ani": 78.9865, "matched_fragments": 345, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000695685.1", "gtdb_species": "s__Vibrio fortis", "ani": 78.9249, "matched_fragments": 170, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.41", "min_intra_species_ani": "96.21", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003026355.1", "gtdb_species": "s__Photobacterium kishitanii", "ani": 78.8308, "matched_fragments": 409, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.67", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_006538525.1", "gtdb_species": "s__Vibrio inusitatus", "ani": 78.786, "matched_fragments": 129, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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_003026285.1", "gtdb_species": "s__Photobacterium profundum", "ani": 78.7275, "matched_fragments": 347, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003026215.1", "gtdb_species": "s__Photobacterium indicum", "ani": 78.6137, "matched_fragments": 355, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "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_000775715.1", "gtdb_species": "s__Vibrio tubiashii_A", "ani": 78.6052, "matched_fragments": 158, "total_fragments": 1677, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "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": -0.006, "cell_length": 0.34, "doubling_h": 0.223, "growth_tmp": 26.333, "optimum_tmp": 25.0, "optimum_ph": 7.25, "genome_size": 4596290.182, "gc_content": 42.986, "coding_genes": 3827.25, "rRNA16S_genes": 15.0, "tRNA_genes": 177.667, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 1.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "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": [ "Photobacterium", "damselae", "subsp.", "damselae", "CIP", "102761" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }