GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Sinorhizobium fredii NGR234

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 NGR_RS07415 NGR_RS19935
ytfR galactose ABC transporter, ATPase component NGR_RS07420 NGR_RS09875
ytfT galactose ABC transporter, permease component 1 NGR_RS07425 NGR_RS14580
yjtF galactose ABC transporter, permease component 2 NGR_RS07430 NGR_RS14580
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) NGR_RS15815 NGR_RS13555
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) NGR_RS13540 NGR_RS10650
dgoD D-galactonate dehydratase NGR_RS23200 NGR_RS13535
dgoK 2-dehydro-3-deoxygalactonokinase NGR_RS13550 NGR_RS23025
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase NGR_RS13545 NGR_RS25805
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component NGR_RS00530 NGR_RS14580
BPHYT_RS16930 galactose ABC transporter, ATPase component NGR_RS09420 NGR_RS09875
BPHYT_RS16935 galactose ABC transporter, substrate-binding component
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE NGR_RS23225
gal2 galactose transporter
galE UDP-glucose 4-epimerase NGR_RS12315 NGR_RS06395
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) NGR_RS06555 NGR_RS14610
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) NGR_RS00570
gguA galactose ABC transporter, ATPase component GguA NGR_RS23220 NGR_RS00525
gguB galactose ABC transporter, permease component GguB NGR_RS23215 NGR_RS00530
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) NGR_RS09940 NGR_RS01050
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit NGR_RS08350 NGR_RS14625
lacB galactose-6-phosphate isomerase, lacB subunit NGR_RS08350 NGR_RS14625
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 NGR_RS09420 NGR_RS09875
mglB galactose ABC transporter, substrate-binding component MglB NGR_RS09870 NGR_RS11320
mglC galactose ABC transporter, permease component MglC NGR_RS09555 NGR_RS00535
MST1 galactose:H+ symporter
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component NGR_RS27655 NGR_RS07700
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 NGR_RS27660 NGR_RS07695
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 NGR_RS07690 NGR_RS27665
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component NGR_RS07685 NGR_RS09720
pgmA alpha-phosphoglucomutase NGR_RS25635 NGR_RS06645
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 NGR_RS17645 NGR_RS14620

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 Apr 09 2024. 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