GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

HP1174, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HP1174 Na+-dependent galactose transporter Echvi_3909 Echvi_0508
galK galactokinase (-1-phosphate forming) Echvi_0696
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase Echvi_0695
galE UDP-glucose 4-epimerase Echvi_1472 Echvi_4409
pgmA alpha-phosphoglucomutase Echvi_2982 Echvi_1178
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component Echvi_1280
BPHYT_RS16930 galactose ABC transporter, ATPase component Echvi_1282 Echvi_0300
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 Echvi_3630 Echvi_3770
dgoD D-galactonate dehydratase Echvi_3769 Echvi_2055
dgoK 2-dehydro-3-deoxygalactonokinase Echvi_3631
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Echvi_3728
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Echvi_2940 Echvi_4610
galP galactose:H+ symporter GalP Echvi_2805 Echvi_2810
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) Echvi_0155
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA Echvi_1282
gguB galactose ABC transporter, permease component GguB Echvi_1280
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) Echvi_1022 Echvi_2123
lacA galactose-6-phosphate isomerase, lacA subunit Echvi_1186
lacB galactose-6-phosphate isomerase, lacB subunit Echvi_2860 Echvi_1186
lacC D-tagatose-6-phosphate kinase Echvi_2325 Echvi_2380
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA Echvi_1282
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC Echvi_1280
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 Echvi_1022 Echvi_2123
ptcA galactose PTS system, EIIA component
ptcB galactose PTS system, EIIB component
ptcEIIC galactose PTS system, EIIC component
sglS sodium/galactose cotransporter Echvi_1871 Echvi_1880
SGLT1 sodium/galactose cotransporter Echvi_1880 Echvi_1871
tpi triose-phosphate isomerase Echvi_1196 Echvi_0337
yjtF galactose ABC transporter, permease component 2 Echvi_1280
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component Echvi_1282
ytfT galactose ABC transporter, permease component 1 Echvi_1280

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:

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