GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Pseudomonas simiae WCS417

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 (29 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 PS417_22145
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 PS417_22140
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 PS417_22135
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component PS417_22130 PS417_12700
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) PS417_21340 PS417_11045
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) PS417_15140 PS417_17365
dgoD D-galactonate dehydratase PS417_00165 PS417_11000
dgoK 2-dehydro-3-deoxygalactonokinase PS417_00155 PS417_12130
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase PS417_22100 PS417_00160
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component PS417_11035 PS417_21325
BPHYT_RS16930 galactose ABC transporter, ATPase component PS417_11030 PS417_21330
BPHYT_RS16935 galactose ABC transporter, substrate-binding component PS417_11025 PS417_21335
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE PS417_10940
gal2 galactose transporter
galE UDP-glucose 4-epimerase PS417_02315 PS417_01385
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) PS417_26415
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA PS417_10935 PS417_11890
gguB galactose ABC transporter, permease component GguB PS417_10930 PS417_12060
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) PS417_27115 PS417_25760
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit PS417_12070
lacB galactose-6-phosphate isomerase, lacB subunit PS417_12070
lacC D-tagatose-6-phosphate kinase PS417_03970
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA PS417_11890 PS417_21330
mglB galactose ABC transporter, substrate-binding component MglB PS417_11885
mglC galactose ABC transporter, permease component MglC PS417_11895 PS417_13640
MST1 galactose:H+ symporter
pgmA alpha-phosphoglucomutase PS417_13395 PS417_27785
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 PS417_24000 PS417_26430
yjtF galactose ABC transporter, permease component 2 PS417_12060 PS417_17725
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component PS417_17730 PS417_13635
ytfT galactose ABC transporter, permease component 1 PS417_17725 PS417_12060

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