Table 2.
Comprehensive genomic features of C. funkei isolate RVMD1.
| Category | Feature | Value | Source(s) |
|---|---|---|---|
| Genome Assembly | Contigs | 857 | MiGA, BV-BRC, NCBI PGAP |
| Total length | 4,264,015 bp | MiGA, BV-BRC, NCBI PGAP | |
| N50 | 9,300 bp | MiGA, BV-BRC | |
| Longest sequence | 36,920 bp | MiGA | |
| G + C content | 74.59% | MiGA, BV-BRC, GTDB Tk-KBase, NCBI PGAP | |
| G-C skew | 0.14% | MiGA | |
| A-T skew | 0.15% | MiGA | |
| Genome Quality | Completeness | 98.55% | CheckM –Kbase |
| Contamination | 0.87% | CheckM –Kbase | |
| Coarse Consistency | 98.4 | BV-BRC | |
| Fine Consistency | 94.3 | BV-BRC | |
| Genome Quality Assessment | Good | BV-BRC | |
| Gene Prediction | Predicted proteins | 4,449 | MiGA |
| Average protein length | 288.3805 aa | MiGA | |
| Coding density | 90.27% | MiGA | |
| CDS | 4,511 | BV-BRC | |
| tRNA | 52 | BV-BRC, MiGA | |
| rRNA | 3 | BV-BRC | |
| Genes (total) | 4,350 | NCBI PGAP | |
| Genes (coding) | 4,232 | NCBI PGAP | |
| Genes (RNA) | 57 | NCBI PGAP | |
| Pseudo Genes (total) | 61 | NCBI PGAP | |
| Essential Genes | Essential genes found | 103/106 | MiGA |
| Multiple Copies | L28, Era, L32 (2 each) | MiGA | |
| Missing Genes | glyQ, valS, lysidine_TilS_N | MiGA | |
| UBCG* Recovery | 92.39% (85/92) | EzBiome Genome-ID | |
| Functional Analysis | Number of transporters | 144 | GTDB Tk-KBase, Protologger |
| Number of secretion genes | 14 | GTDB Tk-KBase, Protologger | |
| Number of unique enzymes | 643 | GTDB Tk-KBase, Protologger |
Data were compiled from multiple sources: The Microbial Genomes Atlas (MiGA) webserver, Bacterial Bioinformatics Resource Center (BV-BRC) PATRIC, NCBI Prokaryotic Genome Annotation Pipeline (PGAP), functional analysis via the GTDB-Tk in the KBase platform and Galaxy Protologger.
*
UBCG, Universal Bacterial Core Gene.