GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Sphingomonas koreensis DSMZ 15582

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HP1174 Na+-dependent galactose transporter Ga0059261_0767 Ga0059261_2650
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Ga0059261_1621 Ga0059261_1894
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Ga0059261_1893
dgoD D-galactonate dehydratase Ga0059261_2649 Ga0059261_4216
dgoK 2-dehydro-3-deoxygalactonokinase Ga0059261_2965 Ga0059261_1624
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Ga0059261_1625 Ga0059261_0356
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component
BPHYT_RS16930 galactose ABC transporter, ATPase component Ga0059261_2250
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 Ga0059261_1305 Ga0059261_3099
galK galactokinase (-1-phosphate forming)
galP galactose:H+ symporter GalP Ga0059261_1891 Ga0059261_1777
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
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
gguB galactose ABC transporter, permease component GguB
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) Ga0059261_3874 Ga0059261_1321
lacA galactose-6-phosphate isomerase, lacA subunit Ga0059261_1987
lacB galactose-6-phosphate isomerase, lacB subunit Ga0059261_1987
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
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC
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 Ga0059261_0562
pgmA alpha-phosphoglucomutase Ga0059261_2456 Ga0059261_1954
ptcA galactose PTS system, EIIA component
ptcB galactose PTS system, EIIB component
ptcEIIC galactose PTS system, EIIC component
sglS sodium/galactose cotransporter Ga0059261_1623
SGLT1 sodium/galactose cotransporter Ga0059261_1623
tpi triose-phosphate isomerase Ga0059261_0254 Ga0059261_0728
yjtF galactose ABC transporter, permease component 2
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component
ytfT galactose ABC transporter, permease component 1

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