GapMind for catabolism of small carbon sources

 

D-galactose catabolism in Halomonas desiderata SP1

Best path

PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, 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 (27 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 BZY95_RS15410
PfGW456L13_1895 ABC transporter for D-Galactose and D-Glucose, permease component 1 BZY95_RS15415
PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 BZY95_RS15420
PfGW456L13_1897 ABC transporter for D-Galactose and D-Glucose, ATPase component BZY95_RS15425 BZY95_RS11680
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BZY95_RS16540 BZY95_RS16600
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) BZY95_RS16655 BZY95_RS16570
dgoD D-galactonate dehydratase BZY95_RS06130 BZY95_RS16565
dgoK 2-dehydro-3-deoxygalactonokinase BZY95_RS06125 BZY95_RS16175
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase BZY95_RS11410 BZY95_RS06120
Alternative steps:
BPHYT_RS16925 galactose ABC transporter, permease component BZY95_RS16560
BPHYT_RS16930 galactose ABC transporter, ATPase component BZY95_RS16555
BPHYT_RS16935 galactose ABC transporter, substrate-binding component BZY95_RS16550
CeSWEET1 galactose transporter
chvE galactose ABC transporter, substrate-binding component ChvE
gal2 galactose transporter
galE UDP-glucose 4-epimerase BZY95_RS05040 BZY95_RS18600
galK galactokinase (-1-phosphate forming)
galP galactose:H+ symporter GalP BZY95_RS16640
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) BZY95_RS21105
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA galactose ABC transporter, ATPase component GguA BZY95_RS16555
gguB galactose ABC transporter, permease component GguB BZY95_RS16560
glcS galactose ABC transporter, substrate-binding component GlcS
glcT galactose ABC transporter, permease component 1 (GlcT)
glcU galactose ABC transporter, permease component 2 (GlcU) BZY95_RS15420
glcV galactose ABC transporter, ATPase component (GlcV) BZY95_RS01120 BZY95_RS10495
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 BZY95_RS07795
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP galactose:H+ symporter
mglA galactose ABC transporter, ATPase component MglA BZY95_RS16555
mglB galactose ABC transporter, substrate-binding component MglB
mglC galactose ABC transporter, permease component MglC BZY95_RS16560
MST1 galactose:H+ symporter
pgmA alpha-phosphoglucomutase BZY95_RS05705 BZY95_RS13600
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 BZY95_RS13595 BZY95_RS21100
yjtF galactose ABC transporter, permease component 2 BZY95_RS16560
ytfQ galactose ABC transporter, substrate-binding component
ytfR galactose ABC transporter, ATPase component BZY95_RS16555 BZY95_RS19340
ytfT galactose ABC transporter, permease component 1 BZY95_RS16560

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