eggNOG-Roary
Summary of eggNOG-Roary results from project: [mq_saccharopolyspora]
Description
This report summarizes the functional annotation of Roary results using the eggNOG mapper. The eggNOG mapper provides functional annotation to genes based on the eggNOG database, which includes information on orthologous groups, functional descriptions, and additional metabolic and pathway data.
Annotation Table
| locus_tag | seed_ortholog | evalue | score | max_annot_lvl | COG_category | Description | Preferred_name | EC | KEGG_ko | KEGG_Pathway | KEGG_Module | KEGG_Reaction | KEGG_rclass | BRITE | KEGG_TC | CAZy | BiGG_Reaction | PFAMs |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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COG Category Distribution
Core Pangene
Accessory Pangene
Rare Pangene
COG Categories
A: RNA processing and modification | B: Chromatin structure and dynamics | C: Energy production and conversion | D: Cell cycle control, cell division, chromosome partitioning | E: Amino acid transport and metabolism | F: Nucleotide transport and metabolism | G: Carbohydrate transport and metabolism | H: Coenzyme transport and metabolism | I: Lipid transport and metabolism | J: Translation, ribosomal structure and biogenesis | K: Transcription | L: Replication, recombination and repair | M: Cell wall/membrane/envelope biogenesis | N: Cell motility | O: Post-translational modification, protein turnover, and chaperones | P: Inorganic ion transport and metabolism | Q: Secondary metabolites biosynthesis, transport, and catabolism | R: General function prediction only | S: Function unknown | T: Signal transduction mechanisms | U: Intracellular trafficking, secretion, and vesicular transport | V: Defense mechanisms | W: Extracellular structures | X: Mobilome: prophages, transposons | Y: Nuclear structure | Z: Cytoskeleton | -: Not found in COG |
References
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Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, 'Roary: Rapid large-scale prokaryote pan genome analysis', Bioinformatics, 2015;31(22):3691-3693 doi:10.1093/bioinformatics/btv421
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eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021. Molecular Biology and Evolution, msab293
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eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085