GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Polaromonas naphthalenivorans CJ2

Best path

PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component PNAP_RS18440 PNAP_RS02600
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 PNAP_RS18450
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 PNAP_RS18455
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component PNAP_RS18460 PNAP_RS01135
galK galactokinase (-1-phosphate forming)
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galE UDP-glucose 4-epimerase PNAP_RS13580 PNAP_RS05275
pgmA alpha-phosphoglucomutase PNAP_RS22340 PNAP_RS05550
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component
BPHYT_RS16930 galactose ABC transporter, ATPase component PNAP_RS20195 PNAP_RS05160
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 PNAP_RS14930
dgoD D-galactonate dehydratase PNAP_RS13320 PNAP_RS08485
dgoK 2-dehydro-3-deoxygalactonokinase PNAP_RS10375
gal2 galactose transporter
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) PNAP_RS07950 PNAP_RS00605
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) PNAP_RS06215 PNAP_RS11540
galP galactose:H+ symporter GalP
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) PNAP_RS19335 PNAP_RS09965
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA PNAP_RS05160 PNAP_RS20195
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) PNAP_RS18460 PNAP_RS14290
HP1174 Na+-dependent galactose transporter
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase PNAP_RS10440
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA PNAP_RS05160 PNAP_RS13010
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC PNAP_RS13005
MST1 galactose:H+ symporter
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 PNAP_RS07095 PNAP_RS09960
yjtF galactose ABC transporter, permease component 2
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component PNAP_RS05160 PNAP_RS20195
ytfT galactose ABC transporter, permease component 1 PNAP_RS13005

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