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  • Aliphatic amine: ammonia derivatives where at least one H has been replaced by alkyl substituents (e.g.: Arginine to putrescine, Putrescine to spermidine pathways)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 propionate
  • Other: 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:

Pathway Reference
pdu operon https://pubmed.ncbi.nlm.nih.gov/27242734/
Arginine to putrescine https://pubmed.ncbi.nlm.nih.gov/30183487/
Putrescine to spermidine https://pubmed.ncbi.nlm.nih.gov/30183487/
tma operon https://pubmed.ncbi.nlm.nih.gov/25873372/
AAA reductive branch https://pubmed.ncbi.nlm.nih.gov/29168502/
Caffeate respiration https://pubmed.ncbi.nlm.nih.gov/23315745/
Gallic acid metabolism https://pubmed.ncbi.nlm.nih.gov/30054365/
Indoleacetate to scatole https://pubmed.ncbi.nlm.nih.gov/30310076/
P-cresol synthesis gene cluster https://pubmed.ncbi.nlm.nih.gov/11231288/
Phenylacetate to toluene https://pubmed.ncbi.nlm.nih.gov/29556105/
hydroxybenzoate to phenol https://academic.oup.com/femsec/article/94/9/fiy125/5042942
Carnitine caiTABCDE gene cluster https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2958.1994.tb00470.x
Proline to 5-aminovalerate gene cluster https://pubmed.ncbi.nlm.nih.gov/20937090/
Threonine to propionate https://pubmed.ncbi.nlm.nih.gov/9484901/
Acetate to butyrate gene cluster https://pubmed.ncbi.nlm.nih.gov/17241242/
Acetyl-CoA pathway https://pubmed.ncbi.nlm.nih.gov/27733845/
Acrylate to propionate gene cluster https://pubmed.ncbi.nlm.nih.gov/24553467/
Aminobutyrate to butyrate https://pubmed.ncbi.nlm.nih.gov/27994578/
eut operon https://pubmed.ncbi.nlm.nih.gov/20234377/
Fumarate to succinate https://pubmed.ncbi.nlm.nih.gov/28049145/
Glutamate to butyrate gene cluster https://pubmed.ncbi.nlm.nih.gov/27994578/
Glycine reductase https://pubmed.ncbi.nlm.nih.gov/11271425/
Leucine reductive branch https://pubmed.ncbi.nlm.nih.gov/15654892/
Lysine degradation gene cluster https://pubmed.ncbi.nlm.nih.gov/26620920/
PFOR-II pathway https://pubmed.ncbi.nlm.nih.gov/32301184/
Pyruvate to acetate-formate https://pubmed.ncbi.nlm.nih.gov/20622067/
Succinate to propionate https://pubmed.ncbi.nlm.nih.gov/24553467/
porA pathway https://pubmed.ncbi.nlm.nih.gov/31831639/
Arginine to Hcarbonate https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5300872/
Glycine cleavage https://pubmed.ncbi.nlm.nih.gov/8375392/
Histidine to glutamate https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429618/
Hydroxy-L-proline to proline https://pubmed.ncbi.nlm.nih.gov/32180548/
bai operon https://www.nature.com/articles/s41586-020-2396-4
sulfate to sulfide https://pubmed.ncbi.nlm.nih.gov/10792666/

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/