{ "type": "genome", "identifier": "GCF_900070325.1", "organism": "Herbinix luporum", "title": "Herbinix luporum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CEBITEC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900070325.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3518679", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1679721", "species_taxid": "1679721", "organism_name": "Herbinix luporum", "infraspecific_name": "strain=SD1D", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/09/14", "asm_name": "SD1D", "asm_submitter": "CEBITEC", "gbrs_paired_asm": "GCA_900070325.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/070/325/GCF_900070325.1_SD1D", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2609352", "genome_size_ungapped": "2609352", "gc_percent": "35.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900070325.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "2442", "protein_coding_gene_count": "2340", "non_coding_gene_count": "69", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-09-14", "dateModified": "2015-09-14", "datePublished": "2015-09-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Herbinix luporum" ], "sample_taxid": [ "1679721" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "0.728 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)": "2609352", "Number of Sequences": "1", "Longest Sequences (bp)": "2609352", "N50 (bp)": "2609352", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.3", "Number of CDSs": "2379", "Average Protein Length": "318.1", "Coding Ratio (%)": "87.0", "Number of rRNAs": "8", "Number of tRNAs": "53", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Herbinix luporum", "strain": "strain=SD1D", "accession": "GCA_900070325.1", "taxid": 1679721, "species_taxid": 1679721, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 869, "total_fragments": 869, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Herbinix hemicellulosilytica", "strain": "", "accession": "GCA_002904165.1", "taxid": 1564487, "species_taxid": 1564487, "relation_to_type": "type", "validated": true, "ani": 78.4743, "matched_fragments": 244, "total_fragments": 869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbinix hemicellulosilytica", "strain": "strain=DSM 29228", "accession": "GCA_003315275.1", "taxid": 1564487, "species_taxid": 1564487, "relation_to_type": "type", "validated": true, "ani": 78.1945, "matched_fragments": 233, "total_fragments": 869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variimorphobacter saccharofermentans", "strain": "strain=MD1", "accession": "GCA_014174405.1", "taxid": 2755051, "species_taxid": 2755051, "relation_to_type": "type", "validated": true, "ani": 78.1303, "matched_fragments": 125, "total_fragments": 869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaerosporobacter mobilis", "strain": "strain=DSM 15930", "accession": "GCA_900142955.1", "taxid": 264463, "species_taxid": 264463, "relation_to_type": "type", "validated": true, "ani": 77.4575, "matched_fragments": 50, "total_fragments": 869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mobilitalea sibirica", "strain": "strain=DSM 26468", "accession": "GCA_015999265.1", "taxid": 1462919, "species_taxid": 1462919, "relation_to_type": "type", "validated": true, "ani": 77.2421, "matched_fragments": 129, "total_fragments": 869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaerocolumna aminovalerica", "strain": "strain=DSM 1283", "accession": "GCA_900115365.1", "taxid": 1527, "species_taxid": 1527, "relation_to_type": "type", "validated": true, "ani": 76.6879, "matched_fragments": 70, "total_fragments": 869, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] populeti", "strain": "strain=743A", "accession": "GCA_900112775.1", "taxid": 37658, "species_taxid": 37658, "relation_to_type": "type", "validated": true, "ani": 76.5001, "matched_fragments": 51, "total_fragments": 869, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900070325.1", "gtdb_species": "s__Mobilitalea luporum", "ani": 100.0, "matched_fragments": 869, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.78", "min_intra_species_ani": "99.78", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_002904165.1", "gtdb_species": "s__Mobilitalea hemicellulosilytica", "ani": 78.4838, "matched_fragments": 242, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_014174405.1", "gtdb_species": "s__Mobilitalea sp014174405", "ani": 78.0588, "matched_fragments": 124, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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_004294845.1", "gtdb_species": "s__Mobilitalea sp004294845", "ani": 78.0466, "matched_fragments": 243, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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_012523775.1", "gtdb_species": "s__Mobilitalea sp012523775", "ani": 77.8747, "matched_fragments": 213, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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_012522735.1", "gtdb_species": "s__Mobilitalea sp012522735", "ani": 77.7606, "matched_fragments": 222, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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_012837605.1", "gtdb_species": "s__Mobilitalea sp012837605", "ani": 77.662, "matched_fragments": 183, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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_012519905.1", "gtdb_species": "s__Mobilitalea sp012519905", "ani": 77.6001, "matched_fragments": 213, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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_012518975.1", "gtdb_species": "s__Mobilitalea sp012518975", "ani": 77.5278, "matched_fragments": 198, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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_900142955.1", "gtdb_species": "s__Anaerosporobacter mobilis", "ani": 77.506, "matched_fragments": 51, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter", "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_012518935.1", "gtdb_species": "s__Mobilitalea sp012518935", "ani": 77.3707, "matched_fragments": 211, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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_900115365.1", "gtdb_species": "s__Anaerocolumna aminovalerica", "ani": 76.6879, "matched_fragments": 70, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.17", "min_intra_species_ani": "99.14", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_012839295.1", "gtdb_species": "s__Mobilitalea sp012839295", "ani": 76.5844, "matched_fragments": 83, "total_fragments": 869, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea", "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": 55.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 2609351.333, "gc_content": 35.3, "coding_genes": 2320.5, "rRNA16S_genes": 4.0, "tRNA_genes": 53.0, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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": [ "Herbinix", "luporum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }