{ "type": "genome", "identifier": "GCF_014838735.1", "organism": "Limosilactobacillus portuensis", "title": "Limosilactobacillus portuensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "UCIBIO/REQUIMTE, Faculty of Pharmacy, University of Porto", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014838735.1", "bioproject": "PRJNA224116", "biosample": "SAMN15159667", "wgs_master": "JABUXQ000000000.1", "refseq_category": "na", "taxid": "2742601", "species_taxid": "2742601", "organism_name": "Limosilactobacillus portuensis", "infraspecific_name": "strain=c11Ua_112_M", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/10/01", "asm_name": "ASM1483873v1", "asm_submitter": "UCIBIO/REQUIMTE, Faculty of Pharmacy, University of Porto", "gbrs_paired_asm": "GCA_014838735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/838/735/GCF_014838735.1_ASM1483873v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2115452", "genome_size_ungapped": "2115452", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "169", "contig_count": "169", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-30", "total_gene_count": "2188", "protein_coding_gene_count": "1998", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-10-01", "dateModified": "2020-10-01", "datePublished": "2020-10-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Limosilactobacillus portuensis" ], "sample_taxid": [ "2742601" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Portugal: Porto" ], "sample_host_location_id": [], "data_size": "0.608 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)": "2115452", "Number of Sequences": "169", "Longest Sequences (bp)": "162854", "N50 (bp)": "64968", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.7", "Number of CDSs": "2088", "Average Protein Length": "285.9", "Coding Ratio (%)": "84.6", "Number of rRNAs": "2", "Number of tRNAs": "63", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Limosilactobacillus portuensis", "strain": "strain=c11Ua_112_M", "accession": "GCA_014838735.1", "taxid": 2742601, "species_taxid": 2742601, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 658, "total_fragments": 660, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Limosilactobacillus urinaemulieris", "strain": "strain=c9Ua_26_M", "accession": "GCA_014838745.1", "taxid": 2742600, "species_taxid": 2742600, "relation_to_type": "type", "validated": true, "ani": 93.0487, "matched_fragments": 531, "total_fragments": 660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus vaginalis", "strain": "strain=ATCC 49540", "accession": "GCA_000159435.1", "taxid": 1633, "species_taxid": 1633, "relation_to_type": "type", "validated": true, "ani": 91.5352, "matched_fragments": 510, "total_fragments": 660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus vaginalis", "strain": "strain=DSM 5837", "accession": "GCA_001435915.1", "taxid": 1633, "species_taxid": 1633, "relation_to_type": "type", "validated": true, "ani": 91.4883, "matched_fragments": 463, "total_fragments": 660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus avistercoris", "strain": "strain=Sa3CUN2", "accession": "GCA_014836425.1", "taxid": 2762243, "species_taxid": 2762243, "relation_to_type": "type", "validated": true, "ani": 83.7324, "matched_fragments": 395, "total_fragments": 660, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limosilactobacillus fastidiosus", "strain": "strain=WF-MO7-1", "accession": "GCA_014145505.1", "taxid": 2759855, "species_taxid": 2759855, "relation_to_type": "type", "validated": true, "ani": 82.9609, "matched_fragments": 376, "total_fragments": 660, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014838735.1", "gtdb_species": "s__Limosilactobacillus portuensis", "ani": 100.0, "matched_fragments": 658, "total_fragments": 660, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.50", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_014838745.1", "gtdb_species": "s__Limosilactobacillus urinaemulieris", "ani": 93.0683, "matched_fragments": 530, "total_fragments": 660, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.61", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000159435.1", "gtdb_species": "s__Limosilactobacillus vaginalis", "ani": 91.5352, "matched_fragments": 510, "total_fragments": 660, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "96.39", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.86", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_014836425.1", "gtdb_species": "s__Limosilactobacillus sp014836425", "ani": 83.7462, "matched_fragments": 395, "total_fragments": 660, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "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_014145505.1", "gtdb_species": "s__Limosilactobacillus fastidiosus", "ani": 82.9492, "matched_fragments": 375, "total_fragments": 660, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900156885.1", "gtdb_species": "s__Limosilactobacillus sp900156885", "ani": 79.26, "matched_fragments": 158, "total_fragments": 660, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Limosilactobacillus", "portuensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }