Overview: Galactose utilization in GapMind is based on MetaCyc pathways lactose and galactose degradation I via tagatose 6-phosphate (link), the Leloir pathway via UDP-galactose (link), and the oxidative pathway via D-galactonate (link). Pathway IV via galactitol (link) is not reported in prokaryotes and is not included. (There is no pathway III.)
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| galP | galactose:H+ symporter GalP | ||
| galK | galactokinase (-1-phosphate forming) | ||
| galT | UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | ||
| galE | UDP-glucose 4-epimerase | HMPREF9453_RS01825 | HMPREF9453_RS01120 |
| pgmA | alpha-phosphoglucomutase | HMPREF9453_RS01905 | HMPREF9453_RS04265 |
| Alternative steps: | |||
| BPHYT_RS16925 | galactose ABC transporter, permease component | HMPREF9453_RS04235 | |
| BPHYT_RS16930 | galactose ABC transporter, ATPase component | HMPREF9453_RS04240 | |
| BPHYT_RS16935 | galactose ABC transporter, substrate-binding component | ||
| CeSWEET1 | galactose transporter | ||
| chvE | galactose ABC transporter, substrate-binding component ChvE | ||
| dgoA | 2-dehydro-3-deoxy-6-phosphogalactonate aldolase | ||
| dgoD | D-galactonate dehydratase | ||
| dgoK | 2-dehydro-3-deoxygalactonokinase | ||
| gal2 | galactose transporter | ||
| galactonolactonase | galactonolactonase (either 1,4- or 1,5-lactone) | ||
| galdh | D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | HMPREF9453_RS01660 | HMPREF9453_RS08875 |
| gatY | D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) | HMPREF9453_RS02305 | |
| gatZ | D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) | ||
| gguA | galactose ABC transporter, ATPase component GguA | HMPREF9453_RS04240 | |
| gguB | galactose ABC transporter, permease component GguB | HMPREF9453_RS04235 | |
| glcS | galactose ABC transporter, substrate-binding component GlcS | ||
| glcT | galactose ABC transporter, permease component 1 (GlcT) | ||
| glcU | galactose ABC transporter, permease component 2 (GlcU) | ||
| glcV | galactose ABC transporter, ATPase component (GlcV) | HMPREF9453_RS10515 | HMPREF9453_RS05740 |
| HP1174 | Na+-dependent galactose transporter | ||
| lacA | galactose-6-phosphate isomerase, lacA subunit | HMPREF9453_RS02400 | |
| lacB | galactose-6-phosphate isomerase, lacB subunit | HMPREF9453_RS02400 | |
| lacC | D-tagatose-6-phosphate kinase | HMPREF9453_RS05465 | |
| lacD | D-tagatose-1,6-bisphosphate aldolase (monomeric) | ||
| lacP | galactose:H+ symporter | ||
| mglA | galactose ABC transporter, ATPase component MglA | HMPREF9453_RS04240 | |
| mglB | galactose ABC transporter, substrate-binding component MglB | ||
| mglC | galactose ABC transporter, permease component MglC | HMPREF9453_RS04235 | |
| MST1 | galactose:H+ symporter | ||
| PfGW456L13_1894 | ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component | ||
| PfGW456L13_1895 | ABC transporter for D-Galactose and D-Glucose, permease component 1 | ||
| PfGW456L13_1896 | ABC transporter for D-Galactose and D-Glucose, permease component 2 | ||
| PfGW456L13_1897 | ABC transporter for D-Galactose and D-Glucose, ATPase component | HMPREF9453_RS05740 | HMPREF9453_RS10515 |
| ptcA | galactose PTS system, EIIA component | ||
| ptcB | galactose PTS system, EIIB component | ||
| ptcEIIC | galactose PTS system, EIIC component | ||
| sglS | sodium/galactose cotransporter | ||
| SGLT1 | sodium/galactose cotransporter | ||
| tpi | triose-phosphate isomerase | HMPREF9453_RS11440 | HMPREF9453_RS11445 |
| yjtF | galactose ABC transporter, permease component 2 | HMPREF9453_RS04235 | |
| ytfQ | galactose ABC transporter, substrate-binding component | ||
| ytfR | galactose ABC transporter, ATPase component | HMPREF9453_RS04240 | |
| ytfT | galactose ABC transporter, permease component 1 | HMPREF9453_RS04235 | |
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory