GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Paraburkholderia phymatum STM815

Best path

ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA

Rules

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.)

48 steps (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ytfQ galactose ABC transporter, substrate-binding component BPHY_RS27605
ytfR galactose ABC transporter, ATPase component BPHY_RS27600 BPHY_RS02520
ytfT galactose ABC transporter, permease component 1 BPHY_RS27595 BPHY_RS02525
yjtF galactose ABC transporter, permease component 2 BPHY_RS27590 BPHY_RS02525
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BPHY_RS21215 BPHY_RS13250
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) BPHY_RS13245 BPHY_RS10650
dgoD D-galactonate dehydratase BPHY_RS02165 BPHY_RS17490
dgoK 2-dehydro-3-deoxygalactonokinase BPHY_RS13280 BPHY_RS04935
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase BPHY_RS13275 BPHY_RS13085
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component BPHY_RS13255 BPHY_RS21230
BPHYT_RS16930 galactose ABC transporter, ATPase component BPHY_RS13260 BPHY_RS21225
BPHYT_RS16935 galactose ABC transporter, substrate-binding component BPHY_RS13265 BPHY_RS21220
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE BPHY_RS11895
gal2 galactose transporter
galE UDP-glucose 4-epimerase BPHY_RS11550 BPHY_RS15345
galK galactokinase (-1-phosphate forming)
galP galactose:H+ symporter GalP
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) BPHY_RS02315
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA BPHY_RS11890 BPHY_RS31570
gguB galactose ABC transporter, permease component GguB BPHY_RS11885 BPHY_RS33915
glcS galactose ABC transporter, substrate-binding component GlcS
glcT galactose ABC transporter, permease component 1 (GlcT)
glcU galactose ABC transporter, permease component 2 (GlcU) BPHY_RS03155
glcV galactose ABC transporter, ATPase component (GlcV) BPHY_RS31680 BPHY_RS08285
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase BPHY_RS05570
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA BPHY_RS31570 BPHY_RS28025
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC BPHY_RS02525 BPHY_RS18165
MST1 galactose:H+ symporter
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component BPHY_RS03145 BPHY_RS31485
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 BPHY_RS03150 BPHY_RS27185
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 BPHY_RS03155 BPHY_RS27190
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component BPHY_RS03160 BPHY_RS33165
pgmA alpha-phosphoglucomutase BPHY_RS11530 BPHY_RS04465
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 BPHY_RS10260 BPHY_RS02305

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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