GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Cereibacter sphaeroides ATCC 17029

Best path

galP, 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 (23 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) RSPH17029_RS00190 RSPH17029_RS04240
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) RSPH17029_RS19585
dgoD D-galactonate dehydratase RSPH17029_RS18320 RSPH17029_RS09155
dgoK 2-dehydro-3-deoxygalactonokinase RSPH17029_RS18270 RSPH17029_RS00195
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase RSPH17029_RS18275 RSPH17029_RS20365
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component RSPH17029_RS17250 RSPH17029_RS14660
BPHYT_RS16930 galactose ABC transporter, ATPase component RSPH17029_RS14655 RSPH17029_RS05240
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE RSPH17029_RS14330 RSPH17029_RS17310
gal2 galactose transporter
galE UDP-glucose 4-epimerase RSPH17029_RS09070 RSPH17029_RS11635
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) RSPH17029_RS20210 RSPH17029_RS14840
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA RSPH17029_RS14655 RSPH17029_RS17460
gguB galactose ABC transporter, permease component GguB RSPH17029_RS14325 RSPH17029_RS17320
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) RSPH17029_RS08750 RSPH17029_RS00495
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 RSPH17029_RS05145 RSPH17029_RS02210
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA RSPH17029_RS14655 RSPH17029_RS17460
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC RSPH17029_RS14660 RSPH17029_RS13365
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 RSPH17029_RS07675
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component RSPH17029_RS17190 RSPH17029_RS20290
pgmA alpha-phosphoglucomutase RSPH17029_RS07735 RSPH17029_RS12575
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 RSPH17029_RS03035 RSPH17029_RS05860
yjtF galactose ABC transporter, permease component 2 RSPH17029_RS17250 RSPH17029_RS14660
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component RSPH17029_RS05240 RSPH17029_RS17460
ytfT galactose ABC transporter, permease component 1 RSPH17029_RS17250 RSPH17029_RS14660

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 10 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