{ "type": "genome", "identifier": "GCA_937951875.1", "organism": "uncultured Alkalilimnicola sp.", "title": "uncultured Alkalilimnicola sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "European Bioinformatics Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_937951875.1", "bioproject": "PRJEB51072", "biosample": "SAMEA14082021", "wgs_master": "CALGAN000000000.1", "refseq_category": "na", "taxid": "543110", "species_taxid": "543110", "organism_name": "uncultured Alkalilimnicola sp.", "infraspecific_name": "", "isolate": "SRR4028141_bin.101_CONCOCT_v1.1_MAG", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/01/11", "asm_name": "SRR4028141_bin.101_CONCOCT_v1.1_MAG", "submitter": "European Bioinformatics Institute", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/937/951/875/GCA_937951875.1_SRR4028141_bin.101_CONCOCT_v1.1_MAG", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-01-11", "dateModified": "2023-01-11", "datePublished": "2023-01-11", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Alkalilimnicola sp." ], "sample_taxid": [ "543110" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.990 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 12.5, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3594631", "Number of Sequences": "93", "Longest Sequences (bp)": "174592", "N50 (bp)": "62515", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.9", "Number of CDSs": "3257", "Average Protein Length": "320.5", "Coding Ratio (%)": "87.1", "Number of rRNAs": "2", "Number of tRNAs": "48", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thiohalobacter thiocyanaticus", "strain": "strain=Hrh1", "accession": "GCA_003932505.1", "taxid": 585455, "species_taxid": 585455, "relation_to_type": "type", "validated": true, "ani": 77.8966, "matched_fragments": 226, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arhodomonas aquaeolei", "strain": "strain=DSM 8974", "accession": "GCA_000374645.1", "taxid": 2369, "species_taxid": 2369, "relation_to_type": "type", "validated": true, "ani": 77.7513, "matched_fragments": 323, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquisalimonas asiatica", "strain": "strain=CGMCC 1.6291", "accession": "GCA_900110585.1", "taxid": 406100, "species_taxid": 406100, "relation_to_type": "type", "validated": true, "ani": 77.7457, "matched_fragments": 254, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalbus denitrificans", "strain": "strain=DSM 26407", "accession": "GCA_003337735.1", "taxid": 547122, "species_taxid": 547122, "relation_to_type": "type", "validated": true, "ani": 77.6302, "matched_fragments": 298, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Inmirania thermothiophila", "strain": "strain=DSM 100275", "accession": "GCA_003751635.1", "taxid": 1750597, "species_taxid": 1750597, "relation_to_type": "type", "validated": true, "ani": 77.5986, "matched_fragments": 258, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aromaticivorans", "strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 77.5263, "matched_fragments": 307, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hydrolytica", "strain": "strain=DSWY01", "accession": "GCA_021495345.2", "taxid": 2493633, "species_taxid": 2493633, "relation_to_type": "type", "validated": true, "ani": 77.4625, "matched_fragments": 276, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorhodospira neutriphila", "strain": "strain=DSM 15116", "accession": "GCA_016584055.1", "taxid": 168379, "species_taxid": 168379, "relation_to_type": "type", "validated": true, "ani": 77.4429, "matched_fragments": 217, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas carbonaria", "strain": "strain=CIP 111764", "accession": "GCA_904061905.1", "taxid": 2762745, "species_taxid": 2762745, "relation_to_type": "type", "validated": true, "ani": 77.43, "matched_fragments": 333, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sagittaria", "strain": "strain=JCM 18195", "accession": "GCA_900115715.1", "taxid": 1135990, "species_taxid": 1135990, "relation_to_type": "type", "validated": true, "ani": 77.4235, "matched_fragments": 338, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylonatrum kenyense", "strain": "strain=AMT 1", "accession": "GCA_023195885.1", "taxid": 455253, "species_taxid": 455253, "relation_to_type": "type", "validated": true, "ani": 77.4203, "matched_fragments": 175, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Plasticicumulans lactativorans", "strain": "strain=DSM 25287", "accession": "GCA_004341245.1", "taxid": 1133106, "species_taxid": 1133106, "relation_to_type": "type", "validated": true, "ani": 77.3985, "matched_fragments": 356, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 77.3622, "matched_fragments": 315, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spiribacter aquaticus", "strain": "strain=SP30", "accession": "GCA_007625215.1", "taxid": 1935996, "species_taxid": 1935996, "relation_to_type": "type", "validated": true, "ani": 77.3244, "matched_fragments": 138, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas taiwanensis", "strain": "strain=DSM 22914", "accession": "GCA_010093135.1", "taxid": 176598, "species_taxid": 176598, "relation_to_type": "type", "validated": true, "ani": 77.2788, "matched_fragments": 296, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas halophila", "strain": "strain=NBRC 102604", "accession": "GCA_007989465.1", "taxid": 29573, "species_taxid": 29573, "relation_to_type": "type", "validated": true, "ani": 77.2594, "matched_fragments": 247, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas stenophila", "strain": "strain=CECT 7744", "accession": "GCA_014192275.1", "taxid": 795312, "species_taxid": 795312, "relation_to_type": "type", "validated": true, "ani": 77.2471, "matched_fragments": 220, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=FDAARGOS_876", "accession": "GCA_016028635.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "suspected-type", "validated": true, "ani": 77.176, "matched_fragments": 224, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=DSM 50238", "accession": "GCA_024448505.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "type", "validated": true, "ani": 77.1278, "matched_fragments": 224, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lactosivorans", "strain": "strain=KCTC 52281", "accession": "GCA_003254665.1", "taxid": 2185141, "species_taxid": 2185141, "relation_to_type": "type", "validated": true, "ani": 77.0801, "matched_fragments": 251, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marichromatium purpuratum", "strain": "strain=984", "accession": "GCA_000224005.3", "taxid": 37487, "species_taxid": 37487, "relation_to_type": "type", "validated": true, "ani": 77.0268, "matched_fragments": 238, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermithiobacillus tepidarius", "strain": "strain=DSM 3134", "accession": "GCA_000423825.1", "taxid": 929, "species_taxid": 929, "relation_to_type": "type", "validated": true, "ani": 76.9297, "matched_fragments": 196, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=JCM 5962", "accession": "GCA_022496575.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.8256, "matched_fragments": 302, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=CCUG 551", "accession": "GCA_008801675.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.7958, "matched_fragments": 308, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_900167195.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.7466, "matched_fragments": 311, "total_fragments": 1151, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 12.5, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_012523465.1", "gtdb_species": "s__JAAYIK01 sp012523465", "ani": 79.2659, "matched_fragments": 464, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__JAAYIK01", "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_009295635.1", "gtdb_species": "s__S0819 sp009295635", "ani": 78.3498, "matched_fragments": 334, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003149435.1", "gtdb_species": "s__E85 sp003149435", "ani": 78.1862, "matched_fragments": 307, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85", "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_013519935.1", "gtdb_species": "s__WFHF3C12 sp013519935", "ani": 77.9179, "matched_fragments": 332, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__WFHF3C12", "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_004801855.1", "gtdb_species": "s__Pseudomonas_K sp004801855", "ani": 77.8646, "matched_fragments": 338, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000014785.1", "gtdb_species": "s__Alkalilimnicola ehrlichii", "ani": 77.8529, "matched_fragments": 243, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Alkalilimnicola", "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_011371455.1", "gtdb_species": "s__DRQN01 sp011371455", "ani": 77.7633, "matched_fragments": 156, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.38", "min_intra_species_ani": "97.35", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000374645.1", "gtdb_species": "s__Arhodomonas aquaeolei", "ani": 77.7418, "matched_fragments": 324, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas", "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_003664325.1", "gtdb_species": "s__Alkalilimnicola mobilis", "ani": 77.7091, "matched_fragments": 234, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Alkalilimnicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.61", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003751635.1", "gtdb_species": "s__Inmirania thermothiophila", "ani": 77.6069, "matched_fragments": 258, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania", "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_007126095.1", "gtdb_species": "s__Aquisalimonas sp007126095", "ani": 77.4641, "matched_fragments": 232, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.73", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_012044895.1", "gtdb_species": "s__Aquisalimonas sp012044895", "ani": 77.4158, "matched_fragments": 266, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas", "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_900115715.1", "gtdb_species": "s__Pseudomonas_K sagittaria", "ani": 77.3646, "matched_fragments": 346, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K", "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_009799925.1", "gtdb_species": "s__Pseudomonas_E sp009799925", "ani": 77.1749, "matched_fragments": 297, "total_fragments": 1151, "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_003254665.1", "gtdb_species": "s__Halomonas lactosivorans", "ani": 77.0894, "matched_fragments": 252, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_018240295.1", "gtdb_species": "s__Plasticicumulans sp003962905", "ani": 77.0639, "matched_fragments": 310, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.50", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002391525.1", "gtdb_species": "s__Competibacter_A sp002391525", "ani": 76.7304, "matched_fragments": 180, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.79", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003527885.1", "gtdb_species": "s__Competibacter_A sp003527885", "ani": 76.3069, "matched_fragments": 89, "total_fragments": 1151, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A", "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": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Nitrococcales", "f__AK92", "g__JAAYIK01", "s__JAAYIK01 sp937951875" ], "_genome_taxon": [ "uncultured", "Alkalilimnicola", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Nitrococcales", "f__AK92", "g__JAAYIK01", "s__JAAYIK01 sp937951875", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Nitrococcales", "AK92", "JAAYIK01", "JAAYIK01", "sp937951875" ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }