GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Sinorhizobium meliloti 1021

Best path

ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ytfQ galactose ABC transporter, substrate-binding component SM_b21587 SM_b21345
ytfR galactose ABC transporter, ATPase component SM_b21588 SM_b21344
ytfT galactose ABC transporter, permease component 1 SM_b21589 SM_b21343
yjtF galactose ABC transporter, permease component 2 SM_b21590 SMc02031
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) SMc00588 SMc00880
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) SMc00883 SMa0717
dgoD D-galactonate dehydratase SM_b20510 SM_b20890
dgoK 2-dehydro-3-deoxygalactonokinase SMc00881 SMc01531
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase SMc00882 SMc02043
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component SM_b20506 SM_b21375
BPHYT_RS16930 galactose ABC transporter, ATPase component SM_b20507 SM_b20713
BPHYT_RS16935 galactose ABC transporter, substrate-binding component SM_b20508
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE SM_b20895
gal2 galactose transporter
galE UDP-glucose 4-epimerase SMc02252 SM_b20942
galK galactokinase (-1-phosphate forming)
galP galactose:H+ symporter GalP
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) SM_b21192 SM_b20199
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) SM_b21373
gguA galactose ABC transporter, ATPase component GguA SM_b20894 SM_b20713
gguB galactose ABC transporter, permease component GguB SM_b20893 SMc02031
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) SM_b20419 SMc01608
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit SMc01613 SM_b20371
lacB galactose-6-phosphate isomerase, lacB subunit SM_b20371 SMc01613
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 SM_b20713 SM_b20673
mglB galactose ABC transporter, substrate-binding component MglB SM_b20712
mglC galactose ABC transporter, permease component MglC SM_b20714 SMc03000
MST1 galactose:H+ symporter
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component SMc04396 SMc04259
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 SMc04395 SMc04258
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 SMc04394 SMc04257
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component SMc04393 SM_b20661
pgmA alpha-phosphoglucomutase SMc03925 SM_b21081
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 SMc01023 SMc01614

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