GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Maridesulfovibrio zosterae DSM 11974

Best path

galP, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
galP galactose:H+ symporter GalP H589_RS0105145
galK galactokinase (-1-phosphate forming)
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase H589_RS0116485
galE UDP-glucose 4-epimerase H589_RS0103695 H589_RS0111125
pgmA alpha-phosphoglucomutase H589_RS0107025 H589_RS0101995
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component
BPHYT_RS16930 galactose ABC transporter, ATPase component H589_RS0113340
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 H589_RS0102910 H589_RS0110565
dgoK 2-dehydro-3-deoxygalactonokinase
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone)
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) H589_RS0117160 H589_RS0116820
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) H589_RS0115820
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA H589_RS0113340
gguB galactose ABC transporter, permease component GguB
glcS galactose ABC transporter, substrate-binding component GlcS
glcT galactose ABC transporter, permease component 1 (GlcT) H589_RS0116455
glcU galactose ABC transporter, permease component 2 (GlcU) H589_RS0116450
glcV galactose ABC transporter, ATPase component (GlcV) H589_RS0116465 H589_RS0104095
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit H589_RS0103405
lacB galactose-6-phosphate isomerase, lacB subunit H589_RS0103405
lacC D-tagatose-6-phosphate kinase H589_RS0115580
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA H589_RS0113340
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 H589_RS0116455
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 H589_RS0116450
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component H589_RS0116465 H589_RS0104095
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 H589_RS0114465 H589_RS0114460
yjtF galactose ABC transporter, permease component 2
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component H589_RS0113340
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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