{ "type": "genome", "identifier": "GCF_000695255.1", "organism": "Photobacterium galatheae", "title": "Photobacterium galatheae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Technical University of Denmark", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000695255.1", "bioproject": "PRJNA224116", "biosample": "SAMN02729099", "wgs_master": "JMIB00000000.1", "refseq_category": "na", "taxid": "1654360", "species_taxid": "1654360", "organism_name": "Photobacterium galatheae", "infraspecific_name": "strain=S2753", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/05/20", "asm_name": "Phalotolerans2753", "asm_submitter": "Technical University of Denmark", "gbrs_paired_asm": "GCA_000695255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/695/255/GCF_000695255.1_Phalotolerans2753", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4533138", "genome_size_ungapped": "4533138", "gc_percent": "49.500000", "replicon_count": "0", "scaffold_count": "80", "contig_count": "80", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-25", "total_gene_count": "4133", "protein_coding_gene_count": "3984", "non_coding_gene_count": "108", "pubmed_id": "24926051" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-05-20", "dateModified": "2014-05-20", "datePublished": "2014-05-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Photobacterium galatheae" ], "sample_taxid": [ "1654360" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Solomon Islands" ], "sample_host_location_id": [], "data_size": "1.291 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4533138", "Number of Sequences": "80", "Longest Sequences (bp)": "339038", "N50 (bp)": "141239", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.5", "Number of CDSs": "4030", "Average Protein Length": "319.8", "Coding Ratio (%)": "85.3", "Number of rRNAs": "3", "Number of tRNAs": "97", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Photobacterium galatheae", "strain": "strain=S2753", "accession": "GCA_000695255.1", "taxid": 1654360, "species_taxid": 1654360, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1472, "total_fragments": 1480, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium galatheae", "strain": "strain=DSM 100496", "accession": "GCA_023653475.1", "taxid": 1654360, "species_taxid": 1654360, "relation_to_type": "type", "validated": true, "ani": 99.9915, "matched_fragments": 1472, "total_fragments": 1480, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Photobacterium arenosum", "strain": "strain=CAU 1568", "accession": "GCA_014841115.1", "taxid": 2774143, "species_taxid": 2774143, "relation_to_type": "type", "validated": true, "ani": 81.8489, "matched_fragments": 709, "total_fragments": 1480, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium halotolerans", "strain": "strain=DSM 18316", "accession": "GCA_000425165.1", "taxid": 265726, "species_taxid": 265726, "relation_to_type": "type", "validated": true, "ani": 81.5609, "matched_fragments": 729, "total_fragments": 1480, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium salinisoli", "strain": "strain=LAM9072", "accession": "GCA_003614885.1", "taxid": 1616783, "species_taxid": 1616783, "relation_to_type": "type", "validated": true, "ani": 81.5169, "matched_fragments": 732, "total_fragments": 1480, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tarriae", "strain": "strain=2521-89", "accession": "GCA_002216685.1", "taxid": 2014742, "species_taxid": 2014742, "relation_to_type": "type", "validated": true, "ani": 78.0532, "matched_fragments": 120, "total_fragments": 1480, "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": 77.959, "matched_fragments": 111, "total_fragments": 1480, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio albus", "strain": "strain=E4404", "accession": "GCA_003144035.1", "taxid": 2200953, "species_taxid": 2200953, "relation_to_type": "type", "validated": true, "ani": 77.6086, "matched_fragments": 134, "total_fragments": 1480, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio fujianensis", "strain": "strain=FJ201301", "accession": "GCA_002749895.1", "taxid": 1974215, "species_taxid": 1974215, "relation_to_type": "type", "validated": true, "ani": 77.5755, "matched_fragments": 69, "total_fragments": 1480, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000695255.1", "gtdb_species": "s__Photobacterium galatheae", "ani": 100.0, "matched_fragments": 1472, "total_fragments": 1480, "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": "conclusive" }, { "accession": "GCF_018199995.1", "gtdb_species": "s__Photobacterium sp018199995", "ani": 82.3028, "matched_fragments": 834, "total_fragments": 1480, "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_014841115.1", "gtdb_species": "s__Photobacterium sp014841115", "ani": 81.8489, "matched_fragments": 709, "total_fragments": 1480, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000972145.1", "gtdb_species": "s__Photobacterium halotolerans_A", "ani": 81.5781, "matched_fragments": 723, "total_fragments": 1480, "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_000425165.1", "gtdb_species": "s__Photobacterium halotolerans", "ani": 81.5664, "matched_fragments": 728, "total_fragments": 1480, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.78", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003614885.1", "gtdb_species": "s__Photobacterium sp003614885", "ani": 81.5263, "matched_fragments": 731, "total_fragments": 1480, "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_002196515.1", "gtdb_species": "s__Vibrio gazogenes_A", "ani": 77.6255, "matched_fragments": 76, "total_fragments": 1480, "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_018860525.1", "gtdb_species": "s__Vibrio hepatarius_B", "ani": 77.6012, "matched_fragments": 72, "total_fragments": 1480, "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": 24.368, "optimum_tmp": 25.035, "optimum_ph": 7.25, "genome_size": 4524183.0, "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", "galatheae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }