GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

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

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
ytfQ galactose ABC transporter, substrate-binding component CEV31_RS02615 CEV31_RS20760
ytfR galactose ABC transporter, ATPase component CEV31_RS02620 CEV31_RS17255
ytfT galactose ABC transporter, permease component 1 CEV31_RS02625 CEV31_RS19245
yjtF galactose ABC transporter, permease component 2 CEV31_RS02630 CEV31_RS20785
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) CEV31_RS02605 CEV31_RS03445
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) CEV31_RS05370
dgoD D-galactonate dehydratase CEV31_RS20170 CEV31_RS02600
dgoK 2-dehydro-3-deoxygalactonokinase CEV31_RS02595 CEV31_RS18540
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase CEV31_RS02590 CEV31_RS20745
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component CEV31_RS19245 CEV31_RS09010
BPHYT_RS16930 galactose ABC transporter, ATPase component CEV31_RS17255 CEV31_RS17305
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE CEV31_RS02585 CEV31_RS17260
gal2 galactose transporter
galE UDP-glucose 4-epimerase CEV31_RS11660 CEV31_RS08270
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) CEV31_RS08915
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) CEV31_RS16790
gguA galactose ABC transporter, ATPase component GguA CEV31_RS02580 CEV31_RS17255
gguB galactose ABC transporter, permease component GguB CEV31_RS02575 CEV31_RS17250
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) CEV31_RS14655 CEV31_RS17415
HP1174 Na+-dependent galactose transporter CEV31_RS19855
lacA galactose-6-phosphate isomerase, lacA subunit CEV31_RS08920
lacB galactose-6-phosphate isomerase, lacB subunit CEV31_RS08920
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 CEV31_RS17255 CEV31_RS19250
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC CEV31_RS08970 CEV31_RS19245
MST1 galactose:H+ symporter
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component CEV31_RS09330
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 CEV31_RS09335 CEV31_RS14435
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 CEV31_RS09340
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component CEV31_RS09345 CEV31_RS17415
pgmA alpha-phosphoglucomutase CEV31_RS05910 CEV31_RS03255
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 CEV31_RS12005 CEV31_RS08925

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