GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Kocuria turfanensis HO-9042

Best path

gguA, gguB, chvE, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gguA galactose ABC transporter, ATPase component GguA AYX06_RS12005 AYX06_RS15290
gguB galactose ABC transporter, permease component GguB AYX06_RS12010
chvE galactose ABC transporter, substrate-binding component ChvE AYX06_RS12000
galK galactokinase (-1-phosphate forming) AYX06_RS06420
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase AYX06_RS06425
galE UDP-glucose 4-epimerase AYX06_RS05100 AYX06_RS01450
pgmA alpha-phosphoglucomutase AYX06_RS14105 AYX06_RS07460
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component AYX06_RS12010
BPHYT_RS16930 galactose ABC transporter, ATPase component AYX06_RS12005 AYX06_RS15290
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase AYX06_RS11340
dgoD D-galactonate dehydratase AYX06_RS11335 AYX06_RS12820
dgoK 2-dehydro-3-deoxygalactonokinase AYX06_RS11345
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) AYX06_RS13455
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) AYX06_RS06860 AYX06_RS08805
galP galactose:H+ symporter GalP AYX06_RS10665 AYX06_RS14980
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) AYX06_RS10015
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
glcS galactose ABC transporter, substrate-binding component GlcS
glcT galactose ABC transporter, permease component 1 (GlcT)
glcU galactose ABC transporter, permease component 2 (GlcU) AYX06_RS12400
glcV galactose ABC transporter, ATPase component (GlcV) AYX06_RS14745 AYX06_RS12545
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 AYX06_RS05905 AYX06_RS14810
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA AYX06_RS12005 AYX06_RS15290
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC AYX06_RS12010
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 AYX06_RS05175 AYX06_RS06445
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component AYX06_RS14745 AYX06_RS12545
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 AYX06_RS01015 AYX06_RS01010
yjtF galactose ABC transporter, permease component 2
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component AYX06_RS12005 AYX06_RS15290
ytfT galactose ABC transporter, permease component 1 AYX06_RS12010

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.

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