GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Pseudomonas fluorescens FW300-N1B4

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 (26 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 Pf1N1B4_596
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 Pf1N1B4_595
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 Pf1N1B4_594
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component Pf1N1B4_593 Pf1N1B4_4847
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Pf1N1B4_412 Pf1N1B4_512
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Pf1N1B4_4626 Pf1N1B4_413
dgoD D-galactonate dehydratase Pf1N1B4_398 Pf1N1B4_4621
dgoK 2-dehydro-3-deoxygalactonokinase Pf1N1B4_400 Pf1N1B4_5638
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Pf1N1B4_587 Pf1N1B4_399
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component Pf1N1B4_409 Pf1N1B4_4287
BPHYT_RS16930 galactose ABC transporter, ATPase component Pf1N1B4_410 Pf1N1B4_4286
BPHYT_RS16935 galactose ABC transporter, substrate-binding component Pf1N1B4_411
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE
gal2 galactose transporter
galE UDP-glucose 4-epimerase Pf1N1B4_2638 Pf1N1B4_3585
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) Pf1N1B4_2402
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA Pf1N1B4_4286 Pf1N1B4_6034
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) Pf1N1B4_594
glcV galactose ABC transporter, ATPase component (GlcV) Pf1N1B4_2538 Pf1N1B4_4352
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 Pf1N1B4_1145
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA Pf1N1B4_4286 Pf1N1B4_410
mglB galactose ABC transporter, substrate-binding component MglB Pf1N1B4_4386
mglC galactose ABC transporter, permease component MglC Pf1N1B4_4287 Pf1N1B4_409
MST1 galactose:H+ symporter
pgmA alpha-phosphoglucomutase Pf1N1B4_4886 Pf1N1B4_2122
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 Pf1N1B4_1164 Pf1N1B4_2399
yjtF galactose ABC transporter, permease component 2 Pf1N1B4_4287 Pf1N1B4_6033
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component Pf1N1B4_4286 Pf1N1B4_410
ytfT galactose ABC transporter, permease component 1 Pf1N1B4_4287 Pf1N1B4_6033

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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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