GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Escherichia coli BW25113

Best path

ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA

Also see fitness data for the top candidates

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ytfQ galactose ABC transporter, substrate-binding component b4227 b3751
ytfR galactose ABC transporter, ATPase component b4485 b3749
ytfT galactose ABC transporter, permease component 1 b4230 b3750
yjtF galactose ABC transporter, permease component 2 b4231 b3750
galK galactokinase (-1-phosphate forming) b0757
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase b0758
galE UDP-glucose 4-epimerase b0759 b2041
pgmA alpha-phosphoglucomutase b0688 b2048
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component b4460 b3750
BPHYT_RS16930 galactose ABC transporter, ATPase component b1900 b3749
BPHYT_RS16935 galactose ABC transporter, substrate-binding component b1901
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE b3566
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase b1850 b4477
dgoD D-galactonate dehydratase b4478 b4297
dgoK 2-dehydro-3-deoxygalactonokinase b3693 b3526
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) b3379
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) b2426 b2842
galP galactose:H+ symporter GalP b2841 b2943
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) b3137 b2096
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) b3132 b2095
gguA galactose ABC transporter, ATPase component GguA b3567 b3749
gguB galactose ABC transporter, permease component GguB b3568 b3750
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) b0262 b4035
HP1174 Na+-dependent galactose transporter b2801
lacA galactose-6-phosphate isomerase, lacA subunit b4090
lacB galactose-6-phosphate isomerase, lacB subunit b4090
lacC D-tagatose-6-phosphate kinase b3916 b1723
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA b2149 b3749
mglB galactose ABC transporter, substrate-binding component MglB b2150
mglC galactose ABC transporter, permease component MglC b2148 b3750
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 b3450 b4035
ptcA galactose PTS system, EIIA component b1736
ptcB galactose PTS system, EIIB component
ptcEIIC galactose PTS system, EIIC component b1737
sglS sodium/galactose cotransporter b3679
SGLT1 sodium/galactose cotransporter
tpi triose-phosphate isomerase b3919 b2926

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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