{ "type": "genome", "identifier": "GCA_011067185.1", "organism": "Candidatus Afipia apatlaquensis", "title": "Candidatus Afipia apatlaquensis", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "Catedras Conacyt-Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico", "publication": [ {} ], "properties": { "assembly_accession": "GCA_011067185.1", "bioproject": "PRJNA606950", "biosample": "SAMN14117643", "wgs_master": "JAAMRR000000000.1", "refseq_category": "na", "taxid": "2712852", "species_taxid": "2712852", "organism_name": "Candidatus Afipia apatlaquensis", "infraspecific_name": "", "isolate": "IBT-C3", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/07", "asm_name": "ASM1106718v1", "submitter": "Catedras Conacyt-Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/011/067/185/GCA_011067185.1_ASM1106718v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-07", "dateModified": "2020-03-07", "datePublished": "2020-03-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Candidatus Afipia apatlaquensis" ], "sample_taxid": [ "2712852" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mexico: Morelos, Apatlaco basin" ], "sample_host_location_id": [], "data_size": "1.603 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 6.86, "strain_heterogeneity": 71.43, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "5604725", "Number of Sequences": "1705", "Longest Sequences (bp)": "47890", "N50 (bp)": "4194", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.7", "Number of CDSs": "4270", "Average Protein Length": "257.5", "Coding Ratio (%)": "58.9", "Number of rRNAs": "1", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Afipia broomeae", "strain": "strain=ATCC 49717", "accession": "GCA_000314675.2", "taxid": 56946, "species_taxid": 56946, "relation_to_type": "type", "validated": true, "ani": 94.7609, "matched_fragments": 755, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afipia massiliensis", "strain": "strain=DSM 17498", "accession": "GCA_014203115.1", "taxid": 211460, "species_taxid": 211460, "relation_to_type": "type", "validated": true, "ani": 85.4645, "matched_fragments": 683, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afipia birgiae", "strain": "strain=34632", "accession": "GCA_000308295.2", "taxid": 151414, "species_taxid": 151414, "relation_to_type": "type", "validated": true, "ani": 85.3079, "matched_fragments": 665, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afipia clevelandensis", "strain": "strain=ATCC 49720", "accession": "GCA_000336555.1", "taxid": 1034, "species_taxid": 1034, "relation_to_type": "type", "validated": true, "ani": 84.4731, "matched_fragments": 638, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afipia felis", "strain": "strain=ATCC 53690", "accession": "GCA_000314735.2", "taxid": 1035, "species_taxid": 1035, "relation_to_type": "type", "validated": true, "ani": 79.7268, "matched_fragments": 329, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium sediminis", "strain": "strain=S2-20-1", "accession": "GCA_018736085.1", "taxid": 2840469, "species_taxid": 2840469, "relation_to_type": "type", "validated": true, "ani": 79.664, "matched_fragments": 432, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=USDA 76", "accession": "GCA_023278185.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 79.53, "matched_fragments": 445, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium jicamae", "strain": "strain=PAC68", "accession": "GCA_001440395.1", "taxid": 280332, "species_taxid": 280332, "relation_to_type": "type", "validated": true, "ani": 79.494, "matched_fragments": 413, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=USDA 76", "accession": "GCA_000379145.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 79.4201, "matched_fragments": 454, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium viridifuturi", "strain": "strain=SEMIA 690", "accession": "GCA_001238275.1", "taxid": 1654716, "species_taxid": 1654716, "relation_to_type": "type", "validated": true, "ani": 79.3986, "matched_fragments": 433, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium niftali", "strain": "strain=CNPSo 3448", "accession": "GCA_004571025.1", "taxid": 2560055, "species_taxid": 2560055, "relation_to_type": "type", "validated": true, "ani": 79.37, "matched_fragments": 422, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium paxllaeri", "strain": "strain=LMTR 21", "accession": "GCA_001693515.2", "taxid": 190148, "species_taxid": 190148, "relation_to_type": "type", "validated": true, "ani": 79.3654, "matched_fragments": 414, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium altum", "strain": "strain=Pear77", "accession": "GCA_020889705.1", "taxid": 1571202, "species_taxid": 1571202, "relation_to_type": "type", "validated": true, "ani": 79.3632, "matched_fragments": 401, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium acaciae", "strain": "strain=10BB", "accession": "GCA_020889785.1", "taxid": 2683706, "species_taxid": 2683706, "relation_to_type": "type", "validated": true, "ani": 79.3243, "matched_fragments": 419, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cosmicum", "strain": "strain=58S1", "accession": "GCA_007290395.1", "taxid": 1404864, "species_taxid": 1404864, "relation_to_type": "type", "validated": true, "ani": 79.3063, "matched_fragments": 399, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium valentinum", "strain": "strain=LmjM3", "accession": "GCA_001440405.1", "taxid": 1518501, "species_taxid": 1518501, "relation_to_type": "type", "validated": true, "ani": 79.2933, "matched_fragments": 412, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium arachidis", "strain": "strain=CCBAU 051107", "accession": "GCA_015291705.1", "taxid": 858423, "species_taxid": 858423, "relation_to_type": "type", "validated": true, "ani": 79.2736, "matched_fragments": 425, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium arachidis", "strain": "strain=LMG 26795", "accession": "GCA_900116675.1", "taxid": 858423, "species_taxid": 858423, "relation_to_type": "type", "validated": true, "ani": 79.2516, "matched_fragments": 426, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afipia carboxidovorans", "strain": "strain=OM5; ATCC 49405", "accession": "GCA_000021365.1", "taxid": 40137, "species_taxid": 40137, "relation_to_type": "type", "validated": true, "ani": 79.2165, "matched_fragments": 340, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diversitatis", "strain": "strain=CNPSo 4019", "accession": "GCA_016031635.1", "taxid": 2755406, "species_taxid": 2755406, "relation_to_type": "type", "validated": true, "ani": 79.1691, "matched_fragments": 426, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cytisi", "strain": "strain=CTAW11", "accession": "GCA_008123515.1", "taxid": 515489, "species_taxid": 515489, "relation_to_type": "type", "validated": true, "ani": 78.8793, "matched_fragments": 416, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 6.86, "strain_heterogeneity": 71.43 }, "gtdb_result": [ { "accession": "GCF_000314675.2", "gtdb_species": "s__Afipia broomeae", "ani": 94.7763, "matched_fragments": 754, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "97.77", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000497575.1", "gtdb_species": "s__Afipia sp000497575", "ani": 90.1325, "matched_fragments": 716, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "97.37", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.78", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_017474385.1", "gtdb_species": "s__Afipia sp017474385", "ani": 89.2165, "matched_fragments": 569, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "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_001006325.2", "gtdb_species": "s__Afipia massiliensis_A", "ani": 85.4968, "matched_fragments": 649, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "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_014203115.1", "gtdb_species": "s__Afipia massiliensis", "ani": 85.4806, "matched_fragments": 682, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "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_000308295.2", "gtdb_species": "s__Afipia birgiae", "ani": 85.3079, "matched_fragments": 665, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.96", "min_intra_species_ani": "98.31", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000336555.1", "gtdb_species": "s__Afipia clevelandensis", "ani": 84.4731, "matched_fragments": 638, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.84", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017308595.1", "gtdb_species": "s__Afipia sp017308595", "ani": 84.1496, "matched_fragments": 629, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "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_017308575.1", "gtdb_species": "s__Afipia sp001897905", "ani": 82.9603, "matched_fragments": 556, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017308495.1", "gtdb_species": "s__Afipia sp017308495", "ani": 81.7566, "matched_fragments": 461, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia", "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_001908185.1", "gtdb_species": "s__Bradyrhizobium sp001908185", "ani": 79.0118, "matched_fragments": 406, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "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": 28.5, "optimum_tmp": 30.0, "optimum_ph": 6.9, "genome_size": 5009248.083, "gc_content": 60.963, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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__Alphaproteobacteria", "o__Rhizobiales", "f__Xanthobacteraceae", "g__Afipia", "s__Afipia broomeae" ], "_genome_taxon": [ "Candidatus", "Afipia", "apatlaquensis", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Xanthobacteraceae", "g__Afipia", "s__Afipia broomeae", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhizobiales", "Xanthobacteraceae", "Afipia", "Afipia", "broomeae" ], "_meo": [ { "id": "MEO_0000686", "label": "hydrothermal sediment" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }