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 (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