GapMind for catabolism of small carbon sources

 

Definition of D-galactose catabolism

As rules and steps, or see full text

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.)

Steps

mglA: galactose ABC transporter, ATPase component MglA

mglB: galactose ABC transporter, substrate-binding component MglB

mglC: galactose ABC transporter, permease component MglC

ytfQ: galactose ABC transporter, substrate-binding component

ytfR: galactose ABC transporter, ATPase component

ytfT: galactose ABC transporter, permease component 1

yjtF: galactose ABC transporter, permease component 2

gguA: galactose ABC transporter, ATPase component GguA

gguB: galactose ABC transporter, permease component GguB

chvE: galactose ABC transporter, substrate-binding component ChvE

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)

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

PfGW456L13_1897: ABC transporter for D-Galactose and D-Glucose, ATPase component

BPHYT_RS16935: galactose ABC transporter, substrate-binding component

BPHYT_RS16930: galactose ABC transporter, ATPase component

BPHYT_RS16925: galactose ABC transporter, permease component

ptcA: galactose PTS system, EIIA component

ptcB: galactose PTS system, EIIB component

ptcEIIC: galactose PTS system, EIIC component

galP: galactose:H+ symporter GalP

HP1174: Na+-dependent galactose transporter

gal2: galactose transporter

SGLT1: sodium/galactose cotransporter

CeSWEET1: galactose transporter

sglS: sodium/galactose cotransporter

MST1: galactose:H+ symporter

lacP: galactose:H+ symporter

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)

gatY: D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY)

gatZ: D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)

tpi: triose-phosphate isomerase

galK: galactokinase (-1-phosphate forming)

galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase

galE: UDP-glucose 4-epimerase

pgmA: alpha-phosphoglucomutase

galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones)

galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone)

dgoD: D-galactonate dehydratase

dgoK: 2-dehydro-3-deoxygalactonokinase

dgoA: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase

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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