GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Dinoroseobacter shibae DFL-12

Best path

SGLT1, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SGLT1 sodium/galactose cotransporter Dshi_3906 Dshi_3904
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Dshi_1243 Dshi_3712
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Dshi_1240
dgoD D-galactonate dehydratase Dshi_1244 Dshi_0129
dgoK 2-dehydro-3-deoxygalactonokinase Dshi_1242
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Dshi_1241 Dshi_1768
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component Dshi_2432 Dshi_2431
BPHYT_RS16930 galactose ABC transporter, ATPase component Dshi_2433 Dshi_0519
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 Dshi_3868 Dshi_4115
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) Dshi_1266
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA Dshi_2433 Dshi_0530
gguB galactose ABC transporter, permease component GguB Dshi_1999
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) Dshi_3141 Dshi_2017
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 Dshi_1621
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA Dshi_2433 Dshi_0530
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC Dshi_2432 Dshi_0389
MST1 galactose:H+ symporter
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 Dshi_1246 Dshi_1650
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component Dshi_2017 Dshi_1357
pgmA alpha-phosphoglucomutase Dshi_2020 Dshi_1900
ptcA galactose PTS system, EIIA component
ptcB galactose PTS system, EIIB component
ptcEIIC galactose PTS system, EIIC component
sglS sodium/galactose cotransporter Dshi_3906 Dshi_3904
tpi triose-phosphate isomerase Dshi_2078 Dshi_2155
yjtF galactose ABC transporter, permease component 2 Dshi_2432 Dshi_2431
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component Dshi_2433 Dshi_0530
ytfT galactose ABC transporter, permease component 1 Dshi_2432 Dshi_0389

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