GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Ruegeria conchae TW15

Best path

PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component G7G_RS0103670 G7G_RS0117185
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 G7G_RS0103675 G7G_RS0117190
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 G7G_RS0103680 G7G_RS0117195
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component G7G_RS0103685 G7G_RS0121175
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) G7G_RS0111310 G7G_RS0103500
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) G7G_RS0100425 G7G_RS0111325
dgoD D-galactonate dehydratase G7G_RS0111305 G7G_RS0100630
dgoK 2-dehydro-3-deoxygalactonokinase G7G_RS0100465 G7G_RS0117160
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase G7G_RS0111320 G7G_RS0100470
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component G7G_RS0100410 G7G_RS22595
BPHYT_RS16930 galactose ABC transporter, ATPase component G7G_RS0100435 G7G_RS0100415
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 G7G_RS0114775 G7G_RS0118490
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) G7G_RS0103280
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA G7G_RS0100435 G7G_RS0100415
gguB galactose ABC transporter, permease component GguB G7G_RS0115590 G7G_RS0100410
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) G7G_RS0114935 G7G_RS0115525
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
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA G7G_RS0100415 G7G_RS0100435
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC G7G_RS0100410 G7G_RS0115755
MST1 galactose:H+ symporter
pgmA alpha-phosphoglucomutase G7G_RS0112845 G7G_RS0105430
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 G7G_RS0106540 G7G_RS0114345
yjtF galactose ABC transporter, permease component 2 G7G_RS0115755 G7G_RS0100410
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component G7G_RS0100415 G7G_RS0100435
ytfT galactose ABC transporter, permease component 1 G7G_RS0100410 G7G_RS22595

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