GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Gallaecimonas xiamenensis 3-C-1

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ytfQ galactose ABC transporter, substrate-binding component B3C1_RS10875
ytfR galactose ABC transporter, ATPase component B3C1_RS10870
ytfT galactose ABC transporter, permease component 1 B3C1_RS10865 B3C1_RS10860
yjtF galactose ABC transporter, permease component 2 B3C1_RS10860 B3C1_RS10865
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) B3C1_RS10890 B3C1_RS09380
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) B3C1_RS10855
dgoD D-galactonate dehydratase B3C1_RS10895
dgoK 2-dehydro-3-deoxygalactonokinase B3C1_RS16155
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase B3C1_RS03510 B3C1_RS16160
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component B3C1_RS10865
BPHYT_RS16930 galactose ABC transporter, ATPase component B3C1_RS10870
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE
gal2 galactose transporter
galE UDP-glucose 4-epimerase B3C1_RS06810 B3C1_RS06805
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) B3C1_RS18205
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) B3C1_RS01950
gguA galactose ABC transporter, ATPase component GguA B3C1_RS10870
gguB galactose ABC transporter, permease component GguB B3C1_RS10860 B3C1_RS10865
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) B3C1_RS03280 B3C1_RS04305
HP1174 Na+-dependent galactose transporter B3C1_RS00390 B3C1_RS00395
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA B3C1_RS10870
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC
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 B3C1_RS03280 B3C1_RS04305
pgmA alpha-phosphoglucomutase B3C1_RS00785 B3C1_RS09430
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 B3C1_RS13285 B3C1_RS18200

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.

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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