GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Shewanella sp. ANA-3

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ytfQ galactose ABC transporter, substrate-binding component Shewana3_2073
ytfR galactose ABC transporter, ATPase component Shewana3_2074
ytfT galactose ABC transporter, permease component 1 Shewana3_2075 Shewana3_2076
yjtF galactose ABC transporter, permease component 2 Shewana3_2076
galK galactokinase (-1-phosphate forming) Shewana3_3578
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galE UDP-glucose 4-epimerase Shewana3_2783 Shewana3_1302
pgmA alpha-phosphoglucomutase Shewana3_2134 Shewana3_2707
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component
BPHYT_RS16930 galactose ABC transporter, ATPase component Shewana3_2074
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 Shewana3_2148
dgoD D-galactonate dehydratase Shewana3_2070 Shewana3_2149
dgoK 2-dehydro-3-deoxygalactonokinase
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Shewana3_2088
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Shewana3_2071 Shewana3_2690
galP galactose:H+ symporter GalP
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) Shewana3_3350
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) Shewana3_2700
gguA galactose ABC transporter, ATPase component GguA Shewana3_2074
gguB galactose ABC transporter, permease component GguB Shewana3_2076
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) Shewana3_3192 Shewana3_3096
HP1174 Na+-dependent galactose transporter Shewana3_2310 Shewana3_3110
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA Shewana3_2074
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC Shewana3_2076
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 Shewana3_3096 Shewana3_3192
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 Shewana3_1026 Shewana3_3351

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