GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA

Also see fitness data for the top candidates

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 (27 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 AO356_05195
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 AO356_05190
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 AO356_05185
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component AO356_05180 AO356_27685
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) AO356_20240 AO356_28440
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) AO356_24610 AO356_20235
dgoD D-galactonate dehydratase AO356_20290 AO356_24585
dgoK 2-dehydro-3-deoxygalactonokinase AO356_20280 AO356_28555
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase AO356_05150 AO356_20285
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component AO356_20255 AO356_23210
BPHYT_RS16930 galactose ABC transporter, ATPase component AO356_20250 AO356_00965
BPHYT_RS16935 galactose ABC transporter, substrate-binding component AO356_20245
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE AO356_28505
gal2 galactose transporter
galE UDP-glucose 4-epimerase AO356_14875 AO356_10040
galK galactokinase (-1-phosphate forming)
galP galactose:H+ symporter GalP AO356_27270
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) AO356_13705
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA AO356_28510 AO356_23205
gguB galactose ABC transporter, permease component GguB AO356_28515
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) AO356_14385 AO356_13165
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 AO356_07330
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA AO356_23205 AO356_20250
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC AO356_23210 AO356_20255
MST1 galactose:H+ symporter
pgmA alpha-phosphoglucomutase AO356_27065 AO356_12530
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 AO356_07440 AO356_13690
yjtF galactose ABC transporter, permease component 2 AO356_23210 AO356_00960
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component AO356_23205 AO356_20250
ytfT galactose ABC transporter, permease component 1 AO356_23210

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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