{ "type": "genome", "identifier": "GCF_003026365.1", "organism": "Photobacterium angustum", "title": "Photobacterium angustum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "FDA/CFSAN", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003026365.1", "bioproject": "PRJNA224116", "biosample": "SAMN07327724", "wgs_master": "PYOM00000000.1", "refseq_category": "na", "taxid": "661", "species_taxid": "661", "organism_name": "Photobacterium angustum", "infraspecific_name": "strain=ATCC 25915", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/31", "asm_name": "ASM302636v1", "asm_submitter": "FDA/CFSAN", "gbrs_paired_asm": "GCA_003026365.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/026/365/GCF_003026365.1_ASM302636v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4969311", "genome_size_ungapped": "4969311", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "66", "contig_count": "66", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003026365.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "4524", "protein_coding_gene_count": "4297", "non_coding_gene_count": "168", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-31", "dateModified": "2018-03-31", "datePublished": "2018-03-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium angustum" ], "sample_taxid": [ "661" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA", "USA:HI" ], "sample_host_location_id": [], "data_size": "1.411 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)": "4969311", "Number of Sequences": "66", "Longest Sequences (bp)": "435642", "N50 (bp)": "201170", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.6", "Number of CDSs": "4356", "Average Protein Length": "316.8", "Coding Ratio (%)": "83.3", "Number of rRNAs": "6", "Number of tRNAs": "146", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium angustum", "strain": "strain=ATCC 25915", "accession": "GCA_003026365.1", "taxid": 661, "species_taxid": 661, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1627, "total_fragments": 1630, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium angustum", "strain": "strain=ATCC 25915", "accession": "GCA_000950005.1", "taxid": 661, "species_taxid": 661, "relation_to_type": "type", "validated": true, "ani": 99.9641, "matched_fragments": 1577, "total_fragments": 1630, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium leiognathi", "strain": "strain=ATCC 25521", "accession": "GCA_003026235.1", "taxid": 553611, "species_taxid": 553611, "relation_to_type": "type", "validated": true, "ani": 84.7043, "matched_fragments": 1099, "total_fragments": 1630, "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": 84.609, "matched_fragments": 1109, "total_fragments": 1630, "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": 84.1088, "matched_fragments": 961, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium aquimaris", "strain": "strain=DSM 23343", "accession": "GCA_003025415.1", "taxid": 512643, "species_taxid": 512643, "relation_to_type": "suspected-type", "validated": true, "ani": 80.6835, "matched_fragments": 631, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium kishitanii", "strain": "strain=ATCC:BAA-1194", "accession": "GCA_003026355.1", "taxid": 318456, "species_taxid": 318456, "relation_to_type": "type", "validated": true, "ani": 80.6747, "matched_fragments": 631, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium kishitanii", "strain": "strain=pjapo.1.1", "accession": "GCA_003025975.1", "taxid": 318456, "species_taxid": 318456, "relation_to_type": "type", "validated": true, "ani": 80.5834, "matched_fragments": 634, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium aquimaris", "strain": "strain=GCSL-P109", "accession": "GCA_001676085.1", "taxid": 512643, "species_taxid": 512643, "relation_to_type": "suspected-type", "validated": true, "ani": 80.5681, "matched_fragments": 643, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium andalusiense", "strain": "strain=CECT 9192", "accession": "GCA_900185625.1", "taxid": 2204296, "species_taxid": 2204296, "relation_to_type": "type", "validated": true, "ani": 80.5576, "matched_fragments": 619, "total_fragments": 1630, "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": 80.524, "matched_fragments": 589, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium kishitanii", "strain": "strain=ATCC BAA-1194", "accession": "GCA_000950095.1", "taxid": 318456, "species_taxid": 318456, "relation_to_type": "type", "validated": true, "ani": 80.5148, "matched_fragments": 630, "total_fragments": 1630, "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": 80.3498, "matched_fragments": 584, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium iliopiscarium", "strain": "strain=ATCC 51760", "accession": "GCA_000950265.1", "taxid": 56192, "species_taxid": 56192, "relation_to_type": "type", "validated": true, "ani": 80.28, "matched_fragments": 586, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium sanguinicancri", "strain": "strain=CECT 7579", "accession": "GCA_024346675.1", "taxid": 875932, "species_taxid": 875932, "relation_to_type": "type", "validated": true, "ani": 79.253, "matched_fragments": 377, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliivibrio fischeri", "strain": "strain=DSM 507", "accession": "GCA_023983475.1", "taxid": 668, "species_taxid": 668, "relation_to_type": "suspected-type", "validated": true, "ani": 78.2429, "matched_fragments": 244, "total_fragments": 1630, "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": 77.9611, "matched_fragments": 158, "total_fragments": 1630, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003026365.1", "gtdb_species": "s__Photobacterium angustum", "ani": 100.0, "matched_fragments": 1627, "total_fragments": 1630, "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": "conclusive" }, { "accession": "GCF_003026105.1", "gtdb_species": "s__Photobacterium sp003026105", "ani": 94.211, "matched_fragments": 1359, "total_fragments": 1630, "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_000153325.1", "gtdb_species": "s__Photobacterium sp000153325", "ani": 93.4041, "matched_fragments": 1392, "total_fragments": 1630, "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_000950415.1", "gtdb_species": "s__Photobacterium leiognathi", "ani": 84.6218, "matched_fragments": 1108, "total_fragments": 1630, "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": 84.1308, "matched_fragments": 957, "total_fragments": 1630, "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_003026355.1", "gtdb_species": "s__Photobacterium kishitanii", "ani": 80.6664, "matched_fragments": 631, "total_fragments": 1630, "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_900185615.1", "gtdb_species": "s__Photobacterium malacitanum", "ani": 80.6638, "matched_fragments": 615, "total_fragments": 1630, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.08", "min_intra_species_ani": "95.06", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002954455.1", "gtdb_species": "s__Photobacterium aquimaris", "ani": 80.6425, "matched_fragments": 643, "total_fragments": 1630, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "95.34", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900166975.1", "gtdb_species": "s__Photobacterium toruni", "ani": 80.4159, "matched_fragments": 591, "total_fragments": 1630, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.006, "cell_length": 0.34, "doubling_h": 0.223, "growth_tmp": 28.0, "optimum_tmp": 26.0, "optimum_ph": 7.25, "genome_size": 4860589.0, "gc_content": 39.7, "coding_genes": 4615.291, "rRNA16S_genes": 15.0, "tRNA_genes": 173.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 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