GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Azospirillum brasilense Sp245

Best path

ytfQ, ytfR, ytfT, yjtF, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ytfQ galactose ABC transporter, substrate-binding component AZOBR_RS31215
ytfR galactose ABC transporter, ATPase component AZOBR_RS31210 AZOBR_RS31245
ytfT galactose ABC transporter, permease component 1 AZOBR_RS31205 AZOBR_RS27940
yjtF galactose ABC transporter, permease component 2 AZOBR_RS31200 AZOBR_RS27940
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) AZOBR_RS31255 AZOBR_RS29790
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) AZOBR_RS22710 AZOBR_RS31230
dgoD D-galactonate dehydratase AZOBR_RS31260 AZOBR_RS04900
dgoK 2-dehydro-3-deoxygalactonokinase AZOBR_RS29860
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase AZOBR_RS22730 AZOBR_RS29850
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component AZOBR_RS27940 AZOBR_RS31200
BPHYT_RS16930 galactose ABC transporter, ATPase component AZOBR_RS31210 AZOBR_RS31245
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE AZOBR_RS31240
gal2 galactose transporter
galE UDP-glucose 4-epimerase AZOBR_RS22395 AZOBR_RS33705
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)
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA AZOBR_RS31245 AZOBR_RS31210
gguB galactose ABC transporter, permease component GguB AZOBR_RS31250
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) AZOBR_RS30790 AZOBR_RS15495
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit AZOBR_RS10010
lacC D-tagatose-6-phosphate kinase AZOBR_RS06155 AZOBR_RS30840
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA AZOBR_RS31245 AZOBR_RS31210
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC AZOBR_RS27940
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 AZOBR_RS00060 AZOBR_RS27980
pgmA alpha-phosphoglucomutase AZOBR_RS02670 AZOBR_RS33725
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 AZOBR_RS03885 AZOBR_RS30960

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