GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Klebsiella michiganensis M5al

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ytfQ galactose ABC transporter, substrate-binding component BWI76_RS02795
ytfR galactose ABC transporter, ATPase component BWI76_RS02800 BWI76_RS07240
ytfT galactose ABC transporter, permease component 1 BWI76_RS02805 BWI76_RS14865
yjtF galactose ABC transporter, permease component 2 BWI76_RS02810 BWI76_RS00280
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BWI76_RS07640 BWI76_RS13720
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) BWI76_RS21760 BWI76_RS14780
dgoD D-galactonate dehydratase BWI76_RS27935 BWI76_RS15895
dgoK 2-dehydro-3-deoxygalactonokinase BWI76_RS27945 BWI76_RS03905
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase BWI76_RS18095 BWI76_RS27940
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component BWI76_RS18240 BWI76_RS14865
BPHYT_RS16930 galactose ABC transporter, ATPase component BWI76_RS18245 BWI76_RS07240
BPHYT_RS16935 galactose ABC transporter, substrate-binding component BWI76_RS18250
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE BWI76_RS27030
gal2 galactose transporter
galE UDP-glucose 4-epimerase BWI76_RS18995 BWI76_RS19065
galK galactokinase (-1-phosphate forming) BWI76_RS08615
galP galactose:H+ symporter GalP BWI76_RS23425 BWI76_RS24055
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BWI76_RS08620
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) BWI76_RS24855 BWI76_RS11550
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) BWI76_RS24875
gguA galactose ABC transporter, ATPase component GguA BWI76_RS27035 BWI76_RS07240
gguB galactose ABC transporter, permease component GguB BWI76_RS27040 BWI76_RS14865
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) BWI76_RS09465 BWI76_RS06035
HP1174 Na+-dependent galactose transporter BWI76_RS22920 BWI76_RS23685
lacA galactose-6-phosphate isomerase, lacA subunit BWI76_RS02175
lacB galactose-6-phosphate isomerase, lacB subunit BWI76_RS02175
lacC D-tagatose-6-phosphate kinase BWI76_RS00735 BWI76_RS17175
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA BWI76_RS19640 BWI76_RS07240
mglB galactose ABC transporter, substrate-binding component MglB BWI76_RS19645 BWI76_RS07235
mglC galactose ABC transporter, permease component MglC BWI76_RS19635 BWI76_RS07245
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 BWI76_RS06705
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component BWI76_RS17830 BWI76_RS26290
pgmA alpha-phosphoglucomutase BWI76_RS08290 BWI76_RS25130
ptcA galactose PTS system, EIIA component BWI76_RS22410 BWI76_RS11735
ptcB galactose PTS system, EIIB component BWI76_RS01520 BWI76_RS02945
ptcEIIC galactose PTS system, EIIC component BWI76_RS22395
sglS sodium/galactose cotransporter
SGLT1 sodium/galactose cotransporter
tpi triose-phosphate isomerase BWI76_RS27465 BWI76_RS23980

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, the preprint on GapMind for carbon sources, 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