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  • Aliphatic amine: ammonia derivatives where at least one H has been replaced by alkyl substituents (e.g.: Arginine to putrescine, Putrescine to spermidine pathways)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
Arginine to putrescine
Putrescine to spermidine
tma operon
AAA reductive branch
Caffeate respiration
Gallic acid metabolism
Indoleacetate to scatole
P-cresol synthesis gene cluster
Phenylacetate to toluene
hydroxybenzoate to phenol
Carnitine caiTABCDE gene cluster
Proline to 5-aminovalerate gene cluster
Threonine to propionate
Acetate to butyrate gene cluster
Acetyl-CoA pathway
Acrylate to propionate gene cluster
Aminobutyrate to butyrate
eut operon
Fumarate to succinate
Glutamate to butyrate gene cluster
Glycine reductase
Leucine reductive branch
Lysine degradation gene cluster
PFOR-II pathway
Pyruvate to acetate-formate
Succinate to propionate
porA pathway
Arginine to Hcarbonate
Glycine cleavage
Histidine to glutamate
Hydroxy-L-proline to proline
bai operon
sulfate to sulfide

Energy-capturing-related gene clusters (E-MGCs):

Pathway Reference
Rnf complex
Tetrathionate to thiosulfate
DMSO/TMAO reductase
Nitrate reductase
Ech complex
Formate dehydrogenase
Glycerol-3-P dehydrogenase
NADH dehydrogenase I