GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Phaeobacter inhibens BS107

Best path

galP, 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
galP galactose:H+ symporter GalP
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) PGA1_c07370 PGA1_c23480
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) PGA1_c07340
dgoD D-galactonate dehydratase PGA1_c07380 PGA1_c04540
dgoK 2-dehydro-3-deoxygalactonokinase PGA1_c07360
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase PGA1_c07350 PGA1_c28010
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component PGA1_c23080 PGA1_c23070
BPHYT_RS16930 galactose ABC transporter, ATPase component PGA1_c23060 PGA1_c28130
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 PGA1_c34470 PGA1_65p00240
galK galactokinase (-1-phosphate forming)
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) PGA1_c07220
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA PGA1_c23060 PGA1_c03960
gguB galactose ABC transporter, permease component GguB PGA1_262p00440
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) PGA1_c02740 PGA1_c27320
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit PGA1_c10730
lacB galactose-6-phosphate isomerase, lacB subunit PGA1_c10730
lacC D-tagatose-6-phosphate kinase
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA PGA1_c23060 PGA1_c26910
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC PGA1_c28050 PGA1_c23080
MST1 galactose:H+ symporter
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component PGA1_c19500 PGA1_78p00160
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 PGA1_c19490 PGA1_78p00170
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 PGA1_78p00180 PGA1_c19480
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component PGA1_c02740 PGA1_c19470
pgmA alpha-phosphoglucomutase PGA1_c24340 PGA1_c06550
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 PGA1_c20650 PGA1_c17530
yjtF galactose ABC transporter, permease component 2 PGA1_c23080 PGA1_c28050
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component PGA1_c23060 PGA1_c26910
ytfT galactose ABC transporter, permease component 1 PGA1_c28050

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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