{ "type": "genome", "identifier": "GCF_900185615.1", "organism": "Photobacterium malacitanum", "title": "Photobacterium malacitanum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "UVEG", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900185615.1", "bioproject": "PRJNA224116", "biosample": "SAMEA104113108", "wgs_master": "FYAK00000000.1", "refseq_category": "reference genome", "taxid": "2204294", "species_taxid": "2204294", "organism_name": "Photobacterium malacitanum", "infraspecific_name": "strain=CECT 9190T", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/06/06", "asm_name": "P.malacitana_CECT9190T_SPAdes_Prokka_EMBL", "asm_submitter": "UVEG", "gbrs_paired_asm": "GCA_900185615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/185/615/GCF_900185615.1_P.malacitana_CECT9190T_SPAdes_Prokka_EMBL", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4380538", "genome_size_ungapped": "4380389", "gc_percent": "40.000000", "replicon_count": "0", "scaffold_count": "55", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900185615.1-RS_2024_08_20", "annotation_date": "2024-08-20", "total_gene_count": "4003", "protein_coding_gene_count": "3751", "non_coding_gene_count": "227", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-06-06", "dateModified": "2017-06-06", "datePublished": "2017-06-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium malacitanum" ], "sample_taxid": [ "2204294" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain" ], "sample_host_location_id": [], "data_size": "1.236 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)": "4380538", "Number of Sequences": "55", "Longest Sequences (bp)": "1130808", "N50 (bp)": "433037", "Gap Ratio (%)": "0.003401", "GCcontent (%)": "39.8", "Number of CDSs": "3801", "Average Protein Length": "323.7", "Coding Ratio (%)": "84.3", "Number of rRNAs": "9", "Number of tRNAs": "184", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium malacitanum", "strain": "strain=CECT 9190", "accession": "GCA_900185615.1", "taxid": 2204294, "species_taxid": 2204294, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1438, "total_fragments": 1439, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium andalusiense", "strain": "strain=CECT 9192", "accession": "GCA_900185625.1", "taxid": 2204296, "species_taxid": 2204296, "relation_to_type": "type", "validated": true, "ani": 93.3171, "matched_fragments": 1292, "total_fragments": 1439, "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": 93.0808, "matched_fragments": 1247, "total_fragments": 1439, "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": 93.0124, "matched_fragments": 1235, "total_fragments": 1439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium aquimaris", "strain": "strain=LC2-065", "accession": "GCA_002954455.1", "taxid": 512643, "species_taxid": 512643, "relation_to_type": "suspected-type", "validated": true, "ani": 92.9803, "matched_fragments": 1278, "total_fragments": 1439, "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": 86.201, "matched_fragments": 1181, "total_fragments": 1439, "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": 86.1607, "matched_fragments": 1164, "total_fragments": 1439, "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": 86.1521, "matched_fragments": 1192, "total_fragments": 1439, "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": 85.9831, "matched_fragments": 1191, "total_fragments": 1439, "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": 85.2977, "matched_fragments": 1046, "total_fragments": 1439, "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": 79.1815, "matched_fragments": 348, "total_fragments": 1439, "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": 78.5763, "matched_fragments": 229, "total_fragments": 1439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio algicola", "strain": "strain=SM1977", "accession": "GCA_009601765.2", "taxid": 2662262, "species_taxid": 2662262, "relation_to_type": "type", "validated": true, "ani": 77.6866, "matched_fragments": 176, "total_fragments": 1439, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900185615.1", "gtdb_species": "s__Photobacterium malacitanum", "ani": 100.0, "matched_fragments": 1438, "total_fragments": 1439, "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": "conclusive" }, { "accession": "GCF_002954455.1", "gtdb_species": "s__Photobacterium aquimaris", "ani": 92.9946, "matched_fragments": 1277, "total_fragments": 1439, "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_003026355.1", "gtdb_species": "s__Photobacterium kishitanii", "ani": 86.1505, "matched_fragments": 1191, "total_fragments": 1439, "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_002954725.1", "gtdb_species": "s__Photobacterium phosphoreum", "ani": 86.0002, "matched_fragments": 1215, "total_fragments": 1439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_900166975.1", "gtdb_species": "s__Photobacterium toruni", "ani": 85.2813, "matched_fragments": 1041, "total_fragments": 1439, "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_900166965.1", "gtdb_species": "s__Photobacterium piscicola", "ani": 84.9424, "matched_fragments": 1120, "total_fragments": 1439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002849605.1", "gtdb_species": "s__Photobacterium carnosum", "ani": 84.651, "matched_fragments": 1020, "total_fragments": 1439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "98.77", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000950415.1", "gtdb_species": "s__Photobacterium leiognathi", "ani": 80.8391, "matched_fragments": 593, "total_fragments": 1439, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.006, "cell_length": 0.34, "doubling_h": 0.223, "growth_tmp": 24.368, "optimum_tmp": 25.035, "optimum_ph": 7.25, "genome_size": 5044823.821, "gc_content": 44.444, "coding_genes": 4615.291, "rRNA16S_genes": 15.0, "tRNA_genes": 173.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.916, "range_salinity": 0.666, "facultative_respiration": 0.666, "anaerobic_respiration": 0.066, "aerobic_respiration": 0.266, "mesophilic_range_tmp": 0.833, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.166, "bacillus_cell_shape": 0.666, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.333, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Photobacterium", "malacitanum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }