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  • Aliphatic amine: ammonia derivatives where at least one H has been replaced by alkyl substituents (e.g.: Arginine to putrescine, Putrescine to spermidine pathways)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

pubmed 27242734

Arginine to putrescine

pubmed 30183487

Putrescine to spermidine

pubmed 30183487

tma operon

pubmed 25873372

AAA reductive branch

pubmed 29168502

Caffeate respiration

pubmed 23315745

Gallic acid metabolism

pubmed 30054365

Indoleacetate to scatole

pubmed 30310076

P-cresol synthesis gene cluster

pubmed 11231288

Phenylacetate to toluene

pubmed 29556105

hydroxybenzoate to phenol

femsec 5042942

Carnitine caiTABCDE gene cluster

wiley 1994

Proline to 5-aminovalerate gene cluster

pubmed 20937090

Threonine to propionate

pubmed 9484901

Acetate to butyrate gene cluster

pubmed 17241242

Acetyl-CoA pathway

pubmed 27733845

Acrylate to propionate gene cluster

pubmed 24553467

Aminobutyrate to butyrate

pubmed 27994578

eut operon

pubmed 20234377

Fumarate to succinate

pubmed 28049145

Glutamate to butyrate gene cluster

pubmed 27994578

Glycine reductase

pubmed 11271425

Leucine reductive branch

pubmed 15654892

Lysine degradation gene cluster

pubmed 26620920

PFOR-II pathway

pubmed 32301184

Pyruvate to acetate-formate

pubmed 20622067

Succinate to propionate

pubmed 24553467

porA pathway

pubmed 31831639

Arginine to Hcarbonate

PMC5300872

Glycine cleavage

pubmed 8375392

Histidine to glutamate

PMC3429618

Hydroxy-L-proline to proline

pubmed 32180548

bai operon

nature 2020

sulfate to sulfide

pubmed 10792666

Phenylpyruvate to phenylacetylCoA

PMC9839529

Bilirubin to urobilinogen

nature 2023

r-butyrobetaine to TMA

pubmed 34949826

Anaerobic sulfite to H2S

pubmed 1704886

APS to sulfite + AMP

pubmed 19820092

sulfate to 3’-Phosphoadenosine-5’-Phosphosulfate (PAPS)

pubmed 39152482

PAPS to H2S

pubmed 39152482

Taurine to H2S

pubmed 8808933

Alkanesulfonate to H2S

pubmed 10506196

sulfoqunovose to sulphonate

pubmed 24463506

sulfoqunovose to 3-sulfolactaldehyde

pubmed 26195800

Uric acid to Xanthine

pubmed 10986234

Uric acid to SCFA

PMC10421625

2-oxoglutarate to succinyl-CoA

PMC9839529