{ "type": "genome", "identifier": "GCF_001439845.1", "organism": "Pseudomonas lactis", "title": "Pseudomonas lactis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zentralinstitut fuer Ernaehrungs- und Lebensmittelforschung (ZIEL), WZW, TUM", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001439845.1", "bioproject": "PRJNA224116", "biosample": "SAMN03332052", "wgs_master": "JYLO00000000.1", "refseq_category": "reference genome", "taxid": "1615674", "species_taxid": "1615674", "organism_name": "Pseudomonas lactis", "infraspecific_name": "strain=DSM 29167", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/11/06", "asm_name": "MG336", "asm_submitter": "Zentralinstitut fuer Ernaehrungs- und Lebensmittelforschung (ZIEL), WZW, TUM", "gbrs_paired_asm": "GCA_001439845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/439/845/GCF_001439845.1_MG336", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6733097", "genome_size_ungapped": "6733097", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "42", "contig_count": "42", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001439845.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "6174", "protein_coding_gene_count": "6003", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-11-06", "dateModified": "2015-11-06", "datePublished": "2015-11-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas lactis" ], "sample_taxid": [ "1615674" ], "sample_host_organism": [ "not collected" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Southern Germany" ], "sample_host_location_id": [], "data_size": "1.889 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)": "6733097", "Number of Sequences": "42", "Longest Sequences (bp)": "670499", "N50 (bp)": "392630", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.0", "Number of CDSs": "6104", "Average Protein Length": "325.4", "Coding Ratio (%)": "88.5", "Number of rRNAs": "4", "Number of tRNAs": "62", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas lactis", "strain": "strain=DSM 29167", "accession": "GCA_001439845.1", "taxid": 1615674, "species_taxid": 1615674, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2221, "total_fragments": 2222, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas salmasensis", "strain": "strain=SWRI126", "accession": "GCA_014268375.2", "taxid": 2745514, "species_taxid": 2745514, "relation_to_type": "type", "validated": true, "ani": 95.541, "matched_fragments": 1839, "total_fragments": 2222, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas paracarnis", "strain": "strain=V5/DAB/2/5", "accession": "GCA_904063055.1", "taxid": 2750625, "species_taxid": 2750625, "relation_to_type": "type", "validated": true, "ani": 94.9746, "matched_fragments": 1779, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas paralactis", "strain": "strain=DSM 29164", "accession": "GCA_001439735.1", "taxid": 1615673, "species_taxid": 1615673, "relation_to_type": "type", "validated": true, "ani": 90.8594, "matched_fragments": 1724, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas libanensis", "strain": "strain=DSM 17149", "accession": "GCA_001439685.1", "taxid": 75588, "species_taxid": 75588, "relation_to_type": "type", "validated": true, "ani": 90.2121, "matched_fragments": 1661, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas marginalis", "strain": "strain=DSM 13124", "accession": "GCA_007858155.1", "taxid": 298, "species_taxid": 298, "relation_to_type": "suspected-type", "validated": true, "ani": 87.9424, "matched_fragments": 1555, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azotoformans", "strain": "strain=NBRC 12693", "accession": "GCA_002091515.1", "taxid": 47878, "species_taxid": 47878, "relation_to_type": "suspected-type", "validated": true, "ani": 87.8314, "matched_fragments": 1570, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pergaminensis", "strain": "strain=1008", "accession": "GCA_024112395.1", "taxid": 2853159, "species_taxid": 2853159, "relation_to_type": "type", "validated": true, "ani": 87.7688, "matched_fragments": 1580, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lactucae", "strain": "strain=MAFF 301380", "accession": "GCA_016937615.1", "taxid": 2813360, "species_taxid": 2813360, "relation_to_type": "type", "validated": true, "ani": 87.6227, "matched_fragments": 1431, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lurida", "strain": "strain=LMG 21995", "accession": "GCA_002563895.1", "taxid": 244566, "species_taxid": 244566, "relation_to_type": "type", "validated": true, "ani": 87.5572, "matched_fragments": 1562, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=DSM 50090", "accession": "GCA_007858165.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 87.4198, "matched_fragments": 1598, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas spelaei", "strain": "strain=CCM 7893", "accession": "GCA_009724245.1", "taxid": 1055469, "species_taxid": 1055469, "relation_to_type": "type", "validated": true, "ani": 85.5825, "matched_fragments": 1500, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas karstica", "strain": "strain=CCM 7891", "accession": "GCA_009707515.1", "taxid": 1055468, "species_taxid": 1055468, "relation_to_type": "type", "validated": true, "ani": 84.9929, "matched_fragments": 1304, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas vranovensis", "strain": "strain=DSM 16006", "accession": "GCA_000425805.1", "taxid": 321661, "species_taxid": 321661, "relation_to_type": "type", "validated": true, "ani": 81.486, "matched_fragments": 970, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas azotifigens", "strain": "strain=DSM 17556", "accession": "GCA_000425625.1", "taxid": 291995, "species_taxid": 291995, "relation_to_type": "type", "validated": true, "ani": 78.8639, "matched_fragments": 588, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas rhizoryzae", "strain": "strain=RY24", "accession": "GCA_005250615.1", "taxid": 2571129, "species_taxid": 2571129, "relation_to_type": "type", "validated": true, "ani": 78.3835, "matched_fragments": 529, "total_fragments": 2222, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001439845.1", "gtdb_species": "s__Pseudomonas_E lactis", "ani": 100.0, "matched_fragments": 2221, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.24", "min_intra_species_ani": "95.50", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.81", "num_clustered_genomes": 30, "status": "conclusive" }, { "accession": "GCF_904063055.1", "gtdb_species": "s__Pseudomonas_E paracarnis", "ani": 94.9746, "matched_fragments": 1779, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.75", "min_intra_species_ani": "95.59", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 86, "status": "-" }, { "accession": "GCF_001902145.1", "gtdb_species": "s__Pseudomonas_E fluorescens_BV", "ani": 94.4724, "matched_fragments": 1734, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.76", "min_intra_species_ani": "95.23", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_001439735.1", "gtdb_species": "s__Pseudomonas_E paralactis", "ani": 90.8462, "matched_fragments": 1726, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.61", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000263715.2", "gtdb_species": "s__Pseudomonas_E synxantha_A", "ani": 90.3891, "matched_fragments": 1697, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.66", "min_intra_species_ani": "97.33", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001439685.1", "gtdb_species": "s__Pseudomonas_E libanensis", "ani": 90.2305, "matched_fragments": 1659, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.7053, "mean_intra_species_ani": "97.93", "min_intra_species_ani": "95.87", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009659625.1", "gtdb_species": "s__Pseudomonas_E haemolytica", "ani": 90.0809, "matched_fragments": 1691, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_900105675.1", "gtdb_species": "s__Pseudomonas_E synxantha", "ani": 89.7524, "matched_fragments": 1750, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.7053, "mean_intra_species_ani": "98.15", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.84", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_003851495.1", "gtdb_species": "s__Pseudomonas_E fluorescens_BB", "ani": 89.7411, "matched_fragments": 1677, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.3929, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "97.70", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003851685.1", "gtdb_species": "s__Pseudomonas_E sp003851685", "ani": 88.3213, "matched_fragments": 1634, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_002934065.1", "gtdb_species": "s__Pseudomonas_E orientalis_A", "ani": 88.1734, "matched_fragments": 1586, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.15", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_009707325.1", "gtdb_species": "s__Pseudomonas_E sp002263605", "ani": 88.0302, "matched_fragments": 1521, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001439695.1", "gtdb_species": "s__Pseudomonas_E veronii", "ani": 87.8268, "matched_fragments": 1506, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.82", "num_clustered_genomes": 43, "status": "-" }, { "accession": "GCF_900103345.1", "gtdb_species": "s__Pseudomonas_E azotoformans", "ani": 87.7967, "matched_fragments": 1579, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "95.87", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_900107155.1", "gtdb_species": "s__Pseudomonas_E salomonii", "ani": 87.6954, "matched_fragments": 1646, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "96.43", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_019139815.1", "gtdb_species": "s__Pseudomonas_E sp900005815", "ani": 87.6589, "matched_fragments": 1486, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.55", "min_intra_species_ani": "99.31", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003852315.1", "gtdb_species": "s__Pseudomonas_E sp003014915", "ani": 87.5811, "matched_fragments": 1592, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "96.20", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_017980685.1", "gtdb_species": "s__Pseudomonas_E iridis", "ani": 82.7797, "matched_fragments": 1185, "total_fragments": 2222, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.83", "min_intra_species_ani": "96.38", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.767, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 6732552.5, "gc_content": 60.02, "coding_genes": 5204.79, "rRNA16S_genes": 5.319, "tRNA_genes": 67.35, "gram_stain": 0.0, "sporulation": 0.013, "motility": 0.975, "range_salinity": 0.666, "facultative_respiration": 0.021, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.978, "mesophilic_range_tmp": 0.926, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.073, "bacillus_cell_shape": 0.988, "coccus_cell_shape": 0.011, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudomonas", "lactis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }