GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Lacinutrix algicola AKS293

Best path

sglS, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
sglS sodium/galactose cotransporter ASC41_RS12275
galK galactokinase (-1-phosphate forming) ASC41_RS12270
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase ASC41_RS12265
galE UDP-glucose 4-epimerase ASC41_RS12290 ASC41_RS05320
pgmA alpha-phosphoglucomutase ASC41_RS15750 ASC41_RS11255
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component ASC41_RS13450
BPHYT_RS16930 galactose ABC transporter, ATPase component ASC41_RS13455
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 ASC41_RS03320
dgoD D-galactonate dehydratase ASC41_RS01600
dgoK 2-dehydro-3-deoxygalactonokinase ASC41_RS03325
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone)
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) ASC41_RS13975 ASC41_RS03330
galP galactose:H+ symporter GalP
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY)
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA ASC41_RS13455
gguB galactose ABC transporter, permease component GguB ASC41_RS13450
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) ASC41_RS15790 ASC41_RS09735
HP1174 Na+-dependent galactose transporter ASC41_RS02945
lacA galactose-6-phosphate isomerase, lacA subunit ASC41_RS08300
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase ASC41_RS12995
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA ASC41_RS13455
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC ASC41_RS13450
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 ASC41_RS09735 ASC41_RS15790
ptcA galactose PTS system, EIIA component
ptcB galactose PTS system, EIIB component
ptcEIIC galactose PTS system, EIIC component
SGLT1 sodium/galactose cotransporter
tpi triose-phosphate isomerase ASC41_RS06475 ASC41_RS08425
yjtF galactose ABC transporter, permease component 2 ASC41_RS13450
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component ASC41_RS13455
ytfT galactose ABC transporter, permease component 1 ASC41_RS13450

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