GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Bradyrhizobium sp. BTAi1

Best path

ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA

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
ytfQ galactose ABC transporter, substrate-binding component BBTA_RS09910
ytfR galactose ABC transporter, ATPase component BBTA_RS09915 BBTA_RS31430
ytfT galactose ABC transporter, permease component 1 BBTA_RS09920 BBTA_RS31435
yjtF galactose ABC transporter, permease component 2 BBTA_RS09925 BBTA_RS36615
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BBTA_RS09945 BBTA_RS07425
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) BBTA_RS09955 BBTA_RS29500
dgoD D-galactonate dehydratase BBTA_RS09935 BBTA_RS02575
dgoK 2-dehydro-3-deoxygalactonokinase BBTA_RS09625 BBTA_RS09900
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase BBTA_RS09630 BBTA_RS09905
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component BBTA_RS36615 BBTA_RS11385
BPHYT_RS16930 galactose ABC transporter, ATPase component BBTA_RS31430 BBTA_RS28795
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE BBTA_RS09960
gal2 galactose transporter
galE UDP-glucose 4-epimerase BBTA_RS26520 BBTA_RS07540
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) BBTA_RS02170 BBTA_RS32445
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA BBTA_RS09965 BBTA_RS28795
gguB galactose ABC transporter, permease component GguB BBTA_RS09970 BBTA_RS36615
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) BBTA_RS11860 BBTA_RS00545
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 BBTA_RS30360
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA BBTA_RS28795 BBTA_RS09965
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC BBTA_RS11385 BBTA_RS31435
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 BBTA_RS11850
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 BBTA_RS11855
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component BBTA_RS19305 BBTA_RS16625
pgmA alpha-phosphoglucomutase BBTA_RS10445 BBTA_RS34395
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 BBTA_RS20935 BBTA_RS02165

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 Apr 09 2024. 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:

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