{ "type": "genome", "identifier": "GCF_004342585.1", "organism": "Paucimonas lemoignei", "title": "Paucimonas lemoignei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004342585.1", "bioproject": "PRJNA224116", "biosample": "SAMN10363436", "wgs_master": "SLZQ00000000.1", "refseq_category": "reference genome", "taxid": "29443", "species_taxid": "29443", "organism_name": "Paucimonas lemoignei", "infraspecific_name": "strain=DSM 7445", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/11", "asm_name": "ASM434258v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004342585.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/342/585/GCF_004342585.1_ASM434258v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4215120", "genome_size_ungapped": "4215025", "gc_percent": "58.000000", "replicon_count": "0", "scaffold_count": "39", "contig_count": "39", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004342585.1-RS_2024_04_17", "annotation_date": "2024-04-17", "total_gene_count": "3896", "protein_coding_gene_count": "3810", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-11", "dateModified": "2019-03-11", "datePublished": "2019-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Paucimonas lemoignei" ], "sample_taxid": [ "29443" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.187 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)": "4215120", "Number of Sequences": "39", "Longest Sequences (bp)": "741522", "N50 (bp)": "327275", "Gap Ratio (%)": "0.002254", "GCcontent (%)": "57.8", "Number of CDSs": "3827", "Average Protein Length": "323.4", "Coding Ratio (%)": "88.1", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Noviherbaspirillum aridicola", "strain": "strain=NCCP-691", "accession": "GCA_019656455.1", "taxid": 2849687, "species_taxid": 2849687, "relation_to_type": "type", "validated": true, "ani": 79.6153, "matched_fragments": 427, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum malthae", "strain": "strain=CC-AFH3", "accession": "GCA_015352985.1", "taxid": 1260987, "species_taxid": 1260987, "relation_to_type": "type", "validated": true, "ani": 79.529, "matched_fragments": 486, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum chlorophenolicum", "strain": "strain=CPW301", "accession": "GCA_001189955.1", "taxid": 211589, "species_taxid": 211589, "relation_to_type": "type", "validated": true, "ani": 79.474, "matched_fragments": 382, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum chlorophenolicum", "strain": "strain=NBRC 102525", "accession": "GCA_001571165.1", "taxid": 211589, "species_taxid": 211589, "relation_to_type": "type", "validated": true, "ani": 79.3981, "matched_fragments": 378, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum humi", "strain": "strain=U15", "accession": "GCA_900188095.1", "taxid": 1688639, "species_taxid": 1688639, "relation_to_type": "type", "validated": true, "ani": 79.3497, "matched_fragments": 455, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum robiniae", "strain": "strain=HZ10", "accession": "GCA_002213415.1", "taxid": 2014887, "species_taxid": 2014887, "relation_to_type": "type", "validated": true, "ani": 79.3475, "matched_fragments": 416, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum aquaticum", "strain": "strain=IEH 4430", "accession": "GCA_002213425.1", "taxid": 568783, "species_taxid": 568783, "relation_to_type": "type", "validated": true, "ani": 79.3177, "matched_fragments": 372, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum camelliae", "strain": "strain=WT00C", "accession": "GCA_001929405.1", "taxid": 1892903, "species_taxid": 1892903, "relation_to_type": "type", "validated": true, "ani": 79.2365, "matched_fragments": 367, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum galbum", "strain": "strain=17J57-3", "accession": "GCA_010974945.1", "taxid": 2709383, "species_taxid": 2709383, "relation_to_type": "type", "validated": true, "ani": 79.2299, "matched_fragments": 429, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum seropedicae", "strain": "strain=Z67", "accession": "GCA_001040945.1", "taxid": 964, "species_taxid": 964, "relation_to_type": "type", "validated": true, "ani": 79.1965, "matched_fragments": 391, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum seropedicae", "strain": "strain=Z67", "accession": "GCA_013180375.1", "taxid": 964, "species_taxid": 964, "relation_to_type": "type", "validated": true, "ani": 79.1895, "matched_fragments": 375, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum aerium", "strain": "strain=122213-3", "accession": "GCA_008929045.1", "taxid": 2588497, "species_taxid": 2588497, "relation_to_type": "type", "validated": true, "ani": 79.0555, "matched_fragments": 440, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum rubrisubalbicans", "strain": "strain=NBRC 102523", "accession": "GCA_001591225.1", "taxid": 80842, "species_taxid": 80842, "relation_to_type": "type", "validated": true, "ani": 79.0528, "matched_fragments": 368, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas humicola", "strain": "strain=RLT1W51", "accession": "GCA_018304945.1", "taxid": 2825886, "species_taxid": 2825886, "relation_to_type": "type", "validated": true, "ani": 79.0009, "matched_fragments": 400, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum cavernae", "strain": "strain=K2R10-39", "accession": "GCA_003590875.1", "taxid": 2320862, "species_taxid": 2320862, "relation_to_type": "type", "validated": true, "ani": 78.9182, "matched_fragments": 386, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum rhizosphaerae", "strain": "strain=UMS-37", "accession": "GCA_001189965.1", "taxid": 346179, "species_taxid": 346179, "relation_to_type": "type", "validated": true, "ani": 78.8856, "matched_fragments": 383, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum huttiense subsp. putei", "strain": "strain=IAM 15032", "accession": "GCA_000478365.1", "taxid": 230311, "species_taxid": 863372, "relation_to_type": "type", "validated": true, "ani": 78.8812, "matched_fragments": 398, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas fungivorans", "strain": "strain=Ter6", "accession": "GCA_001584145.1", "taxid": 158899, "species_taxid": 158899, "relation_to_type": "type", "validated": true, "ani": 78.8227, "matched_fragments": 380, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia terrae", "strain": "strain=JCM 31606", "accession": "GCA_024753145.1", "taxid": 1811224, "species_taxid": 1811224, "relation_to_type": "type", "validated": true, "ani": 78.7127, "matched_fragments": 378, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia agilis", "strain": "strain=JCM 31605", "accession": "GCA_024756255.1", "taxid": 1811226, "species_taxid": 1811226, "relation_to_type": "type", "validated": true, "ani": 78.6978, "matched_fragments": 369, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia solisilvae", "strain": "strain=JCM 31607", "accession": "GCA_024753215.1", "taxid": 1811225, "species_taxid": 1811225, "relation_to_type": "type", "validated": true, "ani": 78.6777, "matched_fragments": 371, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella dendranthematis", "strain": "strain=AF9R3", "accession": "GCA_012849375.1", "taxid": 2728021, "species_taxid": 2728021, "relation_to_type": "type", "validated": true, "ani": 78.4335, "matched_fragments": 367, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella buxea", "strain": "strain=KCTC 52429", "accession": "GCA_009720835.1", "taxid": 1949069, "species_taxid": 1949069, "relation_to_type": "type", "validated": true, "ani": 78.3087, "matched_fragments": 363, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas arenae", "strain": "strain=Ter10", "accession": "GCA_001584165.1", "taxid": 279058, "species_taxid": 279058, "relation_to_type": "type", "validated": true, "ani": 78.2597, "matched_fragments": 327, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia rubra", "strain": "strain=CCM 8692", "accession": "GCA_011682065.1", "taxid": 2607910, "species_taxid": 2607910, "relation_to_type": "type", "validated": true, "ani": 78.1743, "matched_fragments": 390, "total_fragments": 1385, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004342585.1", "gtdb_species": "s__Paucimonas lemoignei", "ani": 100.0, "matched_fragments": 1383, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas", "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": "GCA_003537575.1", "gtdb_species": "s__Paucimonas sp003537575", "ani": 82.8417, "matched_fragments": 761, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas", "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_003590835.1", "gtdb_species": "s__Paucimonas sp003590835", "ani": 82.1831, "matched_fragments": 738, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas", "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_004114795.1", "gtdb_species": "s__Paucimonas sp004114795", "ani": 82.0122, "matched_fragments": 707, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas", "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_007874125.1", "gtdb_species": "s__Noviherbaspirillum sp007874125", "ani": 79.7473, "matched_fragments": 475, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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": "GCA_017744395.1", "gtdb_species": "s__Herbaspirillum sp017744395", "ani": 79.695, "matched_fragments": 400, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "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_015352985.1", "gtdb_species": "s__Noviherbaspirillum malthae", "ani": 79.5299, "matched_fragments": 485, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_002213415.1", "gtdb_species": "s__Herbaspirillum robiniae", "ani": 79.3255, "matched_fragments": 417, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "98.54", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_009914615.1", "gtdb_species": "s__Herbaspirillum frisingense_B", "ani": 79.2943, "matched_fragments": 391, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "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_001040945.1", "gtdb_species": "s__Herbaspirillum seropedicae", "ani": 79.2079, "matched_fragments": 390, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "96.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_004570315.1", "gtdb_species": "s__Noviherbaspirillum sp004570315", "ani": 79.1462, "matched_fragments": 376, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_008929045.1", "gtdb_species": "s__Noviherbaspirillum aerium", "ani": 79.0408, "matched_fragments": 442, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_000221045.1", "gtdb_species": "s__Collimonas fungivorans_A", "ani": 78.8517, "matched_fragments": 378, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.12", "min_intra_species_ani": "95.12", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001584145.1", "gtdb_species": "s__Collimonas fungivorans", "ani": 78.8112, "matched_fragments": 381, "total_fragments": 1385, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas", "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": -0.222, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 29.5, "optimum_tmp": null, "optimum_ph": null, "genome_size": 5924470.0, "gc_content": 58.9, "coding_genes": 5129.0, "rRNA16S_genes": null, "tRNA_genes": 63.0, "gram_stain": 0.0, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Paucimonas", "lemoignei" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }