The 1 gene cluster 'bins' that were sotred in the anvi'o pan database for 'Prevotella nigrescens homd HMT 693' under the collection name "DEFAULT", describe 4,070 gene clusters with 38,500 genes that were identified in 16 genomes.

Basics

Here are some of the details about the pan database, and genomes storage.
Pan DB for Prevotella nigrescens homd HMT 693 w/ 16 samples.
Key Value
Created on 2025-12-13 00:18:18
Version 16
Number of genes 38,500
Number of gene clusters 4,070
Partial genes excluded No
Minbit parameter 0.5
Gene cluster min occurrence parameter 1
MCL inflation parameter 10.0
NCBI blastp or DIAMOND? NCBI blastp
Additional parameters for sequence search
Number of genomes used 16
Items aditional data keys num_genomes_gene_cluster_has_hits, num_genes_in_gene_cluster, max_num_paralogs, SCG, functional_homogeneity_index, geometric_homogeneity_index, combined_homogeneity_index
Genomes storage
Key Value
Created on Storage DB knows nothing :(
Version 7
Number of genomes described 16
Functional annotation Available
Functional annotation sources KOfam, KEGG_Module, KEGG_Class, Pfam, COG20_CATEGORY, COG20_PATHWAY, CAZyme, KEGG_BRITE, COG20_FUNCTION
These are the list of genomes used in this pan database: Prevotella_nigrescens_str_ATCC_33563_id_GCA_000220235_1, Prevotella_nigrescens_str_CC14M_id_GCA_000507825_1, Prevotella_nigrescens_str_DSM_13386_id_GCA_031191185_1, Prevotella_nigrescens_str_ERR589362_bin_1_CONCOCT_v1_1_MAG_id_GCA_938028575_1, Prevotella_nigrescens_str_F0103_id_GCA_000336235_1, Prevotella_nigrescens_str_F0103_id_GCA_018127865_1, Prevotella_nigrescens_str_F0109_id_GCA_018127825_1, Prevotella_nigrescens_str_F0630_id_GCA_018127845_1, Prevotella_nigrescens_str_FDAARGOS_1486_id_GCA_019930605_1, Prevotella_nigrescens_str_JCVI_32_bin_50_id_GCA_015262115_1, Prevotella_nigrescens_str_KCOM_1102_id_GCA_002204475_1, Prevotella_nigrescens_str_MGYG_HGUT_04627_id_GCA_902497265_1, Prevotella_nigrescens_str_NCTC9336_id_GCA_900454985_1, Prevotella_nigrescens_str_SCHI0028_S_5_id_GCA_019375595_1, Prevotella_nigrescens_str_SRR1045097_bin_7_metaWRAP_v1_1_MAG_id_GCA_915063465_1, Prevotella_nigrescens_str_SRR9217449_mag_bin_15_id_GCA_905372985_1

Summary files for gene clusters

This was a full summary (i.e., the `--quick` flag has not been used), hence the gene clusters summary file is not succint by any means.

The summary file: Prevotella_nigrescens_homd_HMT_693_gene_clusters_summary.txt.gz

Misc Data

For layers

The directory misc data layers contains TAB-delimited files for additional data stored under the following data group names for each sample/layer found in the merged database: default.

The default data group, which often is added by anvi'o automatically and contains important information, contained these keys: total_length, gc_content, percent_completion, percent_redundancy, num_genes, avg_gene_length, num_genes_per_kb, singleton_gene_clusters, num_gene_clusters.

For items

The directory misc data items contains TAB-delimited files for additional data stored under the following data group names for each item found in the merged database: default.