GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Pseudomonas fluorescens FW300-N2E2

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 (30 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 Pf6N2E2_2892
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 Pf6N2E2_2891
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 Pf6N2E2_2890
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component Pf6N2E2_2889 Pf6N2E2_807
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Pf6N2E2_5967 Pf6N2E2_1441
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Pf6N2E2_614 Pf6N2E2_5966
dgoD D-galactonate dehydratase Pf6N2E2_5977 Pf6N2E2_609
dgoK 2-dehydro-3-deoxygalactonokinase Pf6N2E2_5975 Pf6N2E2_2046
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Pf6N2E2_2883 Pf6N2E2_5976
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component Pf6N2E2_5970 Pf6N2E2_524
BPHYT_RS16930 galactose ABC transporter, ATPase component Pf6N2E2_5969 Pf6N2E2_162
BPHYT_RS16935 galactose ABC transporter, substrate-binding component Pf6N2E2_5968
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE Pf6N2E2_1455
gal2 galactose transporter
galE UDP-glucose 4-epimerase Pf6N2E2_4908 Pf6N2E2_2512
galK galactokinase (-1-phosphate forming)
galP galactose:H+ symporter GalP Pf6N2E2_883
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) Pf6N2E2_4660
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA Pf6N2E2_1456 Pf6N2E2_523
gguB galactose ABC transporter, permease component GguB Pf6N2E2_1457
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) Pf6N2E2_4815 Pf6N2E2_4515
HP1174 Na+-dependent galactose transporter Pf6N2E2_1003
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase Pf6N2E2_3338
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA Pf6N2E2_523 Pf6N2E2_5969
mglB galactose ABC transporter, substrate-binding component MglB Pf6N2E2_1015
mglC galactose ABC transporter, permease component MglC Pf6N2E2_524 Pf6N2E2_5970
MST1 galactose:H+ symporter
pgmA alpha-phosphoglucomutase Pf6N2E2_1059 Pf6N2E2_4374
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 Pf6N2E2_3356 Pf6N2E2_4657
yjtF galactose ABC transporter, permease component 2 Pf6N2E2_524 Pf6N2E2_163
ytfQ galactose ABC transporter, substrate-binding component Pf6N2E2_1005
ytfR galactose ABC transporter, ATPase component Pf6N2E2_523 Pf6N2E2_5969
ytfT galactose ABC transporter, permease component 1 Pf6N2E2_524

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, 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