GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ytfQ galactose ABC transporter, substrate-binding component H281DRAFT_05269 H281DRAFT_02173
ytfR galactose ABC transporter, ATPase component H281DRAFT_05270 H281DRAFT_02174
ytfT galactose ABC transporter, permease component 1 H281DRAFT_05271 H281DRAFT_02175
yjtF galactose ABC transporter, permease component 2 H281DRAFT_05272 H281DRAFT_02703
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) H281DRAFT_06300 H281DRAFT_06296
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) H281DRAFT_06301 H281DRAFT_00300
dgoD D-galactonate dehydratase H281DRAFT_04215 H281DRAFT_02329
dgoK 2-dehydro-3-deoxygalactonokinase H281DRAFT_06294 H281DRAFT_00856
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase H281DRAFT_06295 H281DRAFT_04277
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component H281DRAFT_06299 H281DRAFT_02330
BPHYT_RS16930 galactose ABC transporter, ATPase component H281DRAFT_06298 H281DRAFT_02331
BPHYT_RS16935 galactose ABC transporter, substrate-binding component H281DRAFT_06297 H281DRAFT_02332
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE H281DRAFT_03877
gal2 galactose transporter
galE UDP-glucose 4-epimerase H281DRAFT_00074 H281DRAFT_04849
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) H281DRAFT_04188 H281DRAFT_01311
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA H281DRAFT_03878 H281DRAFT_03380
gguB galactose ABC transporter, permease component GguB H281DRAFT_03879 H281DRAFT_00427
glcS galactose ABC transporter, substrate-binding component GlcS
glcT galactose ABC transporter, permease component 1 (GlcT)
glcU galactose ABC transporter, permease component 2 (GlcU) H281DRAFT_01452 H281DRAFT_00168
glcV galactose ABC transporter, ATPase component (GlcV) H281DRAFT_05887 H281DRAFT_05405
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
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA H281DRAFT_00426 H281DRAFT_03380
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC H281DRAFT_04148 H281DRAFT_02703
MST1 galactose:H+ symporter
PfGW456L13_1894 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component H281DRAFT_00166 H281DRAFT_01454
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 H281DRAFT_00167 H281DRAFT_01453
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 H281DRAFT_00168 H281DRAFT_01452
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component H281DRAFT_00169 H281DRAFT_03749
pgmA alpha-phosphoglucomutase H281DRAFT_00078 H281DRAFT_04410
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 H281DRAFT_04564 H281DRAFT_04190

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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