{ "type": "genome", "identifier": "GCF_030815255.1", "organism": "Hathewaya limosa", "title": "Hathewaya limosa", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_030815255.1", "bioproject": "PRJNA224116", "biosample": "SAMN35367918", "wgs_master": "JAUSWN000000000.1", "refseq_category": "reference genome", "taxid": "1536", "species_taxid": "1536", "organism_name": "Hathewaya limosa", "infraspecific_name": "strain=DSM 1400", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/08/18", "asm_name": "ASM3081525v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_030815255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/815/255/GCF_030815255.1_ASM3081525v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3052708", "genome_size_ungapped": "3052708", "gc_percent": "27.500000", "replicon_count": "0", "scaffold_count": "55", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_030815255.1-RS_2024_04_07", "annotation_date": "2024-04-07", "total_gene_count": "2803", "protein_coding_gene_count": "2700", "non_coding_gene_count": "78", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-08-18", "dateModified": "2023-08-18", "datePublished": "2023-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Hathewaya limosa" ], "sample_taxid": [ "1536" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Cote d'Ivoire: Cote d Ivoire,Africa, Ebrie Laguna" ], "sample_host_location_id": [], "data_size": "0.826 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)": "3052708", "Number of Sequences": "55", "Longest Sequences (bp)": "305170", "N50 (bp)": "109619", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "27.4", "Number of CDSs": "2724", "Average Protein Length": "321.4", "Coding Ratio (%)": "86.0", "Number of rRNAs": "7", "Number of tRNAs": "65", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Hathewaya histolytica", "strain": "strain=NCTC503", "accession": "GCA_901482605.1", "taxid": 1498, "species_taxid": 1498, "relation_to_type": "type", "validated": true, "ani": 78.4612, "matched_fragments": 307, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hathewaya massiliensis", "strain": "strain=Marseille-P3545", "accession": "GCA_902143515.1", "taxid": 1964382, "species_taxid": 1964382, "relation_to_type": "type", "validated": true, "ani": 78.4051, "matched_fragments": 309, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium niameyense", "strain": "strain=MT5", "accession": "GCA_001243045.1", "taxid": 1622073, "species_taxid": 1622073, "relation_to_type": "type", "validated": true, "ani": 78.0225, "matched_fragments": 182, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium collagenovorans", "strain": "strain=DSM 3089", "accession": "GCA_900130005.1", "taxid": 29357, "species_taxid": 29357, "relation_to_type": "type", "validated": true, "ani": 77.3135, "matched_fragments": 190, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloimpatiens massiliensis", "strain": "strain=Mt13", "accession": "GCA_900184255.1", "taxid": 1658110, "species_taxid": 1658110, "relation_to_type": "type", "validated": true, "ani": 77.1023, "matched_fragments": 184, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium senegalense", "strain": "strain=type strain: JC122", "accession": "GCA_000285575.1", "taxid": 1465809, "species_taxid": 1465809, "relation_to_type": "type", "validated": true, "ani": 76.7958, "matched_fragments": 192, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium ihumii", "strain": "strain=AP5", "accession": "GCA_000612845.1", "taxid": 1470356, "species_taxid": 1470356, "relation_to_type": "type", "validated": true, "ani": 76.7661, "matched_fragments": 201, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium massiliodielmoense", "strain": "strain=MT26", "accession": "GCA_900176615.1", "taxid": 1776385, "species_taxid": 1776385, "relation_to_type": "type", "validated": true, "ani": 76.7299, "matched_fragments": 162, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium acetireducens", "strain": "strain=DSM 10703", "accession": "GCA_001758365.1", "taxid": 76489, "species_taxid": 76489, "relation_to_type": "type", "validated": true, "ani": 76.5301, "matched_fragments": 149, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium botulinum", "strain": "strain=ATCC 25763", "accession": "GCA_011017965.1", "taxid": 1491, "species_taxid": 1491, "relation_to_type": "type", "validated": true, "ani": 76.4114, "matched_fragments": 166, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium nigeriense", "strain": "strain=Marseille-P2414", "accession": "GCA_900086595.1", "taxid": 1805470, "species_taxid": 1805470, "relation_to_type": "type", "validated": true, "ani": 76.3916, "matched_fragments": 129, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium moniliforme", "strain": "strain=DSM 3984", "accession": "GCA_017873235.1", "taxid": 39489, "species_taxid": 39489, "relation_to_type": "type", "validated": true, "ani": 76.3805, "matched_fragments": 152, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium weizhouense", "strain": "strain=YB-6", "accession": "GCA_019431045.1", "taxid": 2859781, "species_taxid": 2859781, "relation_to_type": "type", "validated": true, "ani": 76.1973, "matched_fragments": 154, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium algidicarnis", "strain": "strain=DSM 15099", "accession": "GCA_002934235.1", "taxid": 37659, "species_taxid": 37659, "relation_to_type": "type", "validated": true, "ani": 76.1633, "matched_fragments": 115, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium saudiense", "strain": "strain=JCC", "accession": "GCA_000577815.1", "taxid": 1414720, "species_taxid": 1414720, "relation_to_type": "type", "validated": true, "ani": 76.0409, "matched_fragments": 137, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium ljungdahlii", "strain": "strain=DSM 13528", "accession": "GCA_000143685.1", "taxid": 1538, "species_taxid": 1538, "relation_to_type": "suspected-type", "validated": true, "ani": 76.0028, "matched_fragments": 113, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium prolinivorans", "strain": "strain=PYR-10", "accession": "GCA_004011155.1", "taxid": 2769420, "species_taxid": 2769420, "relation_to_type": "type", "validated": true, "ani": 75.8776, "matched_fragments": 150, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium kluyveri", "strain": "strain=DSM 555", "accession": "GCA_000016505.1", "taxid": 1534, "species_taxid": 1534, "relation_to_type": "type", "validated": true, "ani": 75.7487, "matched_fragments": 80, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium kluyveri", "strain": "strain=NBRC 12016", "accession": "GCA_000010265.1", "taxid": 1534, "species_taxid": 1534, "relation_to_type": "type", "validated": true, "ani": 75.7487, "matched_fragments": 80, "total_fragments": 995, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_003288255.1", "gtdb_species": "s__Hathewaya sp003288255", "ani": 98.2504, "matched_fragments": 873, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya", "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": "GCF_901482605.1", "gtdb_species": "s__Hathewaya histolytica", "ani": 78.4612, "matched_fragments": 307, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya", "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_902143515.1", "gtdb_species": "s__Hathewaya massiliensis", "ani": 78.4085, "matched_fragments": 308, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya", "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_900130005.1", "gtdb_species": "s__Clostridium_D collagenovorans", "ani": 77.284, "matched_fragments": 192, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_D", "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_003614235.1", "gtdb_species": "s__Clostridium_H haemolyticum", "ani": 77.1487, "matched_fragments": 160, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "97.38", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_900184255.1", "gtdb_species": "s__Haloimpatiens massiliensis", "ani": 77.1023, "matched_fragments": 184, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens", "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_000285575.1", "gtdb_species": "s__Clostridium_J senegalense", "ani": 76.7716, "matched_fragments": 194, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.19", "min_intra_species_ani": "95.52", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000612845.1", "gtdb_species": "s__Clostridium_J ihumii", "ani": 76.7547, "matched_fragments": 202, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900176615.1", "gtdb_species": "s__Clostridium_H massiliodielmoense", "ani": 76.7021, "matched_fragments": 164, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "96.44", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_017435645.1", "gtdb_species": "s__Clostridium sp017435645", "ani": 76.4786, "matched_fragments": 68, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_900086595.1", "gtdb_species": "s__Clostridium nigeriense", "ani": 76.3786, "matched_fragments": 130, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000789395.1", "gtdb_species": "s__Clostridium baratii", "ani": 76.2789, "matched_fragments": 120, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.53", "min_intra_species_ani": "95.37", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_018918285.1", "gtdb_species": "s__MSJ-11 sp018918285", "ani": 76.2515, "matched_fragments": 133, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11", "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_018917145.1", "gtdb_species": "s__Clostridium_AN bornimense_A", "ani": 76.2045, "matched_fragments": 115, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AN", "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_002934235.1", "gtdb_species": "s__Clostridium_L algidicarnis", "ani": 76.1633, "matched_fragments": 115, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.66", "min_intra_species_ani": "96.15", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCA_900539375.1", "gtdb_species": "s__Clostridium sp900539375", "ani": 76.0414, "matched_fragments": 137, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000577815.1", "gtdb_species": "s__Clostridium saudiense", "ani": 76.0409, "matched_fragments": 137, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "99.24", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_001675165.1", "gtdb_species": "s__Clostridium_B ragsdalei", "ani": 75.9677, "matched_fragments": 100, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.18", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902785295.1", "gtdb_species": "s__Clostridium sp902785295", "ani": 75.8973, "matched_fragments": 113, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_009928485.1", "gtdb_species": "s__Clostridium sp009928485", "ani": 75.8681, "matched_fragments": 141, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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_000686705.1", "gtdb_species": "s__Clostridium_Z hydrogeniformans", "ani": 75.8668, "matched_fragments": 154, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_Z", "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_900129265.1", "gtdb_species": "s__Caloramator_A proteoclasticus", "ani": 75.6701, "matched_fragments": 63, "total_fragments": 995, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "98.54", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": 0.23, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 2818024.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Hathewaya", "limosa" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }