GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Bacteroides fluxus YIT 12057

Best path

HP1174, 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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HP1174 Na+-dependent galactose transporter HMPREF9446_RS01995 HMPREF9446_RS05575
galK galactokinase (-1-phosphate forming) HMPREF9446_RS03120
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galE UDP-glucose 4-epimerase HMPREF9446_RS05080 HMPREF9446_RS02105
pgmA alpha-phosphoglucomutase HMPREF9446_RS16585 HMPREF9446_RS00850
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component
BPHYT_RS16930 galactose ABC transporter, ATPase component
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 HMPREF9446_RS00140 HMPREF9446_RS04360
dgoD D-galactonate dehydratase
dgoK 2-dehydro-3-deoxygalactonokinase HMPREF9446_RS04365
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) HMPREF9446_RS07190
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) HMPREF9446_RS05935 HMPREF9446_RS06920
galP galactose:H+ symporter GalP HMPREF9446_RS10365
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) HMPREF9446_RS00040
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) HMPREF9446_RS13805 HMPREF9446_RS02185
lacA galactose-6-phosphate isomerase, lacA subunit HMPREF9446_RS03135
lacB galactose-6-phosphate isomerase, lacB subunit HMPREF9446_RS03135
lacC D-tagatose-6-phosphate kinase HMPREF9446_RS05270 HMPREF9446_RS13905
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 HMPREF9446_RS13805 HMPREF9446_RS16200
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 HMPREF9446_RS10880 HMPREF9446_RS04015
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 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