Glossary¶
Gene Cluster Classes¶
The anaerobic metabolic pathways that gutSMASH predicts can be divided into different gene cluster classes based on their product:
Aliphatic amine
: ammonia derivatives where at least one H has been replaced by alkyl substituents (e.g.: Arginine to putrescine, Putrescine to spermidine pathways)npAA
: non-proteinogenic amino acids (e.g.: Proline to 5-aminovalerate)Aromatic
: derivatives of benzene (e.g.: P-cresol pathway, Caffeate respiration)SCFA
: fatty acids with 5 carbon atoms maximum (e.g.: Acetate to butyrate pathway, Threonine to propionate)SCFA-other
: a SCFA is produced in combination with another molecule. For instance, the pdu operon, releases propanol and propionateOther
: pathways that don’t fit in any other categories are classified in here (e.g.: bai operon)E-MGC
: related to energy-capturing mechanisms (e.g.: Ech complex, Rnf complex)Putative
: gene clusters of unknown function
Gene Cluster Types¶
gutSMASH uses some abbreviations internally to refer to the different types of primary metabolic clusters:
Energy-capturing-related gene clusters (E-MGCs):
Pathway | Reference |
---|---|
Rnf complex | https://pubmed.ncbi.nlm.nih.gov/23269825/ |
Tetrathionate to thiosulfate | https://pubmed.ncbi.nlm.nih.gov/10231485/ |
DMSO/TMAO reductase | https://pubmed.ncbi.nlm.nih.gov/1917829/ |
Nitrate reductase | https://pubmed.ncbi.nlm.nih.gov/2674654/ |
Ech complex | https://pubmed.ncbi.nlm.nih.gov/30850546/ |
Formate dehydrogenase | https://pubmed.ncbi.nlm.nih.gov/26443736/ |
Glycerol-3-P dehydrogenase | https://pubmed.ncbi.nlm.nih.gov/26443736/ |
NADH dehydrogenase I | https://pubmed.ncbi.nlm.nih.gov/26443736/ |