This subsystem has been initially encoded by master:NeilJ_UCSD and master:MaryP_UCSD, whose contributions we gratefully acknowledge, as "Homofermentative_lactate_fermentation" and Heterofermentative_lactate_fermentation. It is currently curated by SelkovEE and SvetaG.
Three major types of lactate fermentations have been described: homofermentation, heterofermentation, and bifidum pathway (see attached diagrams). Homofermentation is associated with the Embden-Meyerhof glycolytic pathway (see the corresponding SS for details); heterofermentation uses the Pentose Phosphate pathway (see the corresponding SS). Theoretical ATP yield of homofermentation is 2 ATP molecules per glucose, the yield of heterofermentative pathway is 1 ATP per glucose. Bifidobacteria perform specific bifidum pathway with net gain of 2.5 ATP molecules per 1 glucose.
Although the presence of Xylulose-5-phosphate phosphoketolase is generally considered diagnostic for lactate heterofermentation pathway, in a few organisms containing XPK, no lactate dehydrogenase could be identified (variant code [9] - see below), hence apparently XPK activity is not necessarily associated with production of lactate.
The presence of Fructose-6-phosphate phosphoketolase enzymatic activity is characteristic for bifidum pathway. However, since no distinction between Fructose-6-phosphate phosphoketolase and Xylulose-5-phosphate phosphoketolase activities can be done currently based on protein sequence alone, and a single enzyme has been shown to catalyze both reactions in several species, all clear XPK/FPK homologs have been annotated as potentially capable of catalyzing both reactions - “Xylulose-5-phosphate phosphoketolase (EC 4.1.2.9); Fructose-6-phosphate phosphoketolase (EC 4.1.2.22)” probably leading to severe over-annotation. In an attempt to minimize the damage of it, the XPK/FPK homologs where FPK activity was experimentally demonstrated (in Bifidum species) or could be inferred from genome context (see below) were annotated “Xylulose-5-phosphate phosphoketolase (EC 4.1.2.9) / Fructose-6-phosphate phosphoketolase (EC 4.1.2.22)” with a slash “/”. Also, such organisms were assigned variant codes [_4]. In addition to Bifidobacteria these include Clostridium acetobutylicum and Streptococcus agalactiae where the absence of Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) and 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) may necessitate FPK activity in XPK/FPK homolog.
For more information, please check out the description and the additional notes tabs, below
This subsystem has been initially encoded by master:NeilJ_UCSD and master:MaryP_UCSD, whose contributions we gratefully acknowledge, as "Homofermentative_lactate_fermentation" and Heterofermentative_lactate_fermentation. It is currently curated by SelkovEE and SvetaG.
Three major types of lactate fermentations have been described: homofermentation, heterofermentation, and bifidum pathway (see attached diagrams). Homofermentation is associated with the Embden-Meyerhof glycolytic pathway (see the corresponding SS for details); heterofermentation uses the Pentose Phosphate pathway (see the corresponding SS). Theoretical ATP yield of homofermentation is 2 ATP molecules per glucose, the yield of heterofermentative pathway is 1 ATP per glucose. Bifidobacteria perform specific bifidum pathway with net gain of 2.5 ATP molecules per 1 glucose.
Although the presence of Xylulose-5-phosphate phosphoketolase is generally considered diagnostic for lactate heterofermentation pathway, in a few organisms containing XPK, no lactate dehydrogenase could be identified (variant code [9] - see below), hence apparently XPK activity is not necessarily associated with production of lactate.
The presence of Fructose-6-phosphate phosphoketolase enzymatic activity is characteristic for bifidum pathway. However, since no distinction between Fructose-6-phosphate phosphoketolase and Xylulose-5-phosphate phosphoketolase activities can be done currently based on protein sequence alone, and a single enzyme has been shown to catalyze both reactions in several species, all clear XPK/FPK homologs have been annotated as potentially capable of catalyzing both reactions - “Xylulose-5-phosphate phosphoketolase (EC 4.1.2.9); Fructose-6-phosphate phosphoketolase (EC 4.1.2.22)” probably leading to severe over-annotation. In an attempt to minimize the damage of it, the XPK/FPK homologs where FPK activity was experimentally demonstrated (in Bifidum species) or could be inferred from genome context (see below) were annotated “Xylulose-5-phosphate phosphoketolase (EC 4.1.2.9) / Fructose-6-phosphate phosphoketolase (EC 4.1.2.22)” with a slash “/”. Also, such organisms were assigned variant codes [_4]. In addition to Bifidobacteria these include Clostridium acetobutylicum and Streptococcus agalactiae where the absence of Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) and 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) may necessitate FPK activity in XPK/FPK homolog.
Note, that no protein sequence has yet been associated with functional role of Lactate racemase (EC 5.1.2.1)
The roles "Acetaldehyde dehydrogenase (EC 1.2.1.10)" and "Alcohol dehydrogenase (EC 1.1.1.1)", although essential for ethanol fermentation, are treated here as "auxiliary", because they are notoriously difficult to curate: multiple paralogs of undetermined specificity are present in most genomes. As an attempt at preliminary disambiguation process, several subfamilies of AADH, unrelated to ethanol fermentation, are included in this SS as "auxiliary" roles, along with protein families they are functionally coupled with (which point to their substrate specificity)
Variant codes:
-1 = no lactate fermentation can be asserted in an organism
1 = organism is potentially capable of homofermentation, yielding lactate: 1.10 = lactate fermentation leading to production of L-lactose 1.20 = lactate fermentation leading to production of D-lactose 1.30 = lactate fermentation potentially leading to production of both stereoisomers
2 = organism is potentially capable of heterofermentation yielding: 2.1 = organism is potentially capable of heterofermentation yielding lactate and ethanol 2.2 = organism is potentially capable of heterofermentation yielding lactate and acetate 2.3 = organism is potentially capable of heterofermentation yielding lactate, acetate, and ethanol
4 = bifidum pathway
8 = XPK/FPK homolog is present, but the fate of Ac~P unclear (no ACK or PTA in an organism)
9.6 = XPK/FPK homolog is present, but no lactate dehydrogenase(s). Although the presence of Xylulose-5-phosphate phosphoketolase is generally considered diagnostic for lactate heterofermentation pathway, in a few organisms containing XPK, no lactate dehydrogenase could be identified (see below), hence apparently XPK activity is not necessarily associated with production of lactate. 9.5 = same as above, but no PTA can be asserted in the organism (significance not clear)
