GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Caulobacter crescentus NA1000

Best path

HP1174, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HP1174 Na+-dependent galactose transporter CCNA_01159
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) CCNA_01018 CCNA_00864
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) CCNA_00863 CCNA_01882
dgoD D-galactonate dehydratase CCNA_01488 CCNA_00862
dgoK 2-dehydro-3-deoxygalactonokinase CCNA_00826 CCNA_01563
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase CCNA_00825 CCNA_01562
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component CCNA_00904
BPHYT_RS16930 galactose ABC transporter, ATPase component CCNA_00903
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE
gal2 galactose transporter
galE UDP-glucose 4-epimerase CCNA_00233 CCNA_02466
galK galactokinase (-1-phosphate forming)
galP galactose:H+ symporter GalP CCNA_00857
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) CCNA_03360
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA CCNA_00903
gguB galactose ABC transporter, permease component GguB CCNA_00904
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) CCNA_03235 CCNA_01670
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 CCNA_00903
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC CCNA_00904
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 CCNA_03235 CCNA_01670
pgmA alpha-phosphoglucomutase CCNA_00083 CCNA_02347
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 CCNA_01970 CCNA_03359
yjtF galactose ABC transporter, permease component 2 CCNA_00904
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component CCNA_00903
ytfT galactose ABC transporter, permease component 1 CCNA_00904

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 (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 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