GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Streptacidiphilus oryzae TH49

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
galP galactose:H+ symporter GalP BS73_RS29790 BS73_RS21860
galK galactokinase (-1-phosphate forming) BS73_RS17230
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BS73_RS17240
galE UDP-glucose 4-epimerase BS73_RS17235 BS73_RS22190
pgmA alpha-phosphoglucomutase BS73_RS30025 BS73_RS09785
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component BS73_RS01760 BS73_RS15630
BPHYT_RS16930 galactose ABC transporter, ATPase component BS73_RS01755 BS73_RS32735
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE BS73_RS12685
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase BS73_RS13710 BS73_RS31540
dgoD D-galactonate dehydratase BS73_RS07155 BS73_RS01920
dgoK 2-dehydro-3-deoxygalactonokinase BS73_RS31555 BS73_RS13700
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) BS73_RS30860
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BS73_RS04585 BS73_RS10320
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) BS73_RS17935 BS73_RS16635
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) BS73_RS16655
gguA galactose ABC transporter, ATPase component GguA BS73_RS01755 BS73_RS32735
gguB galactose ABC transporter, permease component GguB BS73_RS12675 BS73_RS01760
glcS galactose ABC transporter, substrate-binding component GlcS
glcT galactose ABC transporter, permease component 1 (GlcT)
glcU galactose ABC transporter, permease component 2 (GlcU) BS73_RS15830 BS73_RS17900
glcV galactose ABC transporter, ATPase component (GlcV) BS73_RS18100 BS73_RS12870
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit BS73_RS25720
lacB galactose-6-phosphate isomerase, lacB subunit BS73_RS25720 BS73_RS16520
lacC D-tagatose-6-phosphate kinase BS73_RS04905 BS73_RS09750
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA BS73_RS01755 BS73_RS32735
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC BS73_RS01760 BS73_RS32740
MST1 galactose:H+ symporter BS73_RS03880
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component BS73_RS21840
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 BS73_RS30650
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component BS73_RS18100 BS73_RS07930
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 BS73_RS12430 BS73_RS16890
yjtF galactose ABC transporter, permease component 2 BS73_RS13065 BS73_RS01760
ytfQ galactose ABC transporter, substrate-binding component BS73_RS13050
ytfR galactose ABC transporter, ATPase component BS73_RS13055 BS73_RS01755
ytfT galactose ABC transporter, permease component 1 BS73_RS13060 BS73_RS01760

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