GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Pontibacter ramchanderi LP43

Best path

HP1174, galK, galT, galE, pgmA

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HP1174 Na+-dependent galactose transporter BD749_RS03265 BD749_RS16300
galK galactokinase (-1-phosphate forming) BD749_RS16430
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BD749_RS16425
galE UDP-glucose 4-epimerase BD749_RS10905 BD749_RS17655
pgmA alpha-phosphoglucomutase BD749_RS13885 BD749_RS18370
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component
BPHYT_RS16930 galactose ABC transporter, ATPase component BD749_RS17540
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
dgoD D-galactonate dehydratase BD749_RS13355
dgoK 2-dehydro-3-deoxygalactonokinase
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) BD749_RS18885
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BD749_RS14605 BD749_RS04795
galP galactose:H+ symporter GalP
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY)
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA
gguB galactose ABC transporter, permease component GguB
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) BD749_RS07915 BD749_RS06110
lacA galactose-6-phosphate isomerase, lacA subunit BD749_RS11805
lacB galactose-6-phosphate isomerase, lacB subunit BD749_RS11805
lacC D-tagatose-6-phosphate kinase BD749_RS03065 BD749_RS14010
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC
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
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component BD749_RS06110 BD749_RS07915
ptcA galactose PTS system, EIIA component
ptcB galactose PTS system, EIIB component
ptcEIIC galactose PTS system, EIIC component
sglS sodium/galactose cotransporter BD749_RS16420
SGLT1 sodium/galactose cotransporter BD749_RS16420
tpi triose-phosphate isomerase BD749_RS18150 BD749_RS06020
yjtF galactose ABC transporter, permease component 2
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component
ytfT galactose ABC transporter, permease component 1

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 24 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:

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