GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Pseudomonas fluorescens FW300-N2E3

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 (25 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 AO353_03395
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 AO353_03390
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 AO353_03385
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component AO353_03380 AO353_25895
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) AO353_01660 AO353_23170
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) AO353_23650
dgoD D-galactonate dehydratase AO353_03420
dgoK 2-dehydro-3-deoxygalactonokinase AO353_01270 AO353_21745
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase AO353_03350 AO353_01265
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component AO353_21390 AO353_20825
BPHYT_RS16930 galactose ABC transporter, ATPase component AO353_21385 AO353_20820
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 AO353_06770 AO353_21135
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) AO353_07930
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA AO353_21385 AO353_20820
gguB galactose ABC transporter, permease component GguB
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) AO353_07265 AO353_29310
HP1174 Na+-dependent galactose transporter AO353_25100
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase AO353_05480
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA AO353_21385 AO353_20820
mglB galactose ABC transporter, substrate-binding component MglB AO353_21380
mglC galactose ABC transporter, permease component MglC AO353_21390
MST1 galactose:H+ symporter
pgmA alpha-phosphoglucomutase AO353_24665 AO353_09235
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 AO353_05590 AO353_07945
yjtF galactose ABC transporter, permease component 2 AO353_21390 AO353_20825
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component AO353_21385 AO353_20820
ytfT galactose ABC transporter, permease component 1 AO353_21390 AO353_20825

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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