GapMind for catabolism of small carbon sources

 

Definition of lactose catabolism

As rules and steps, or see full text

Rules

Overview: Lactose utilization in GapMind is based on MetaCyc pathway lactose degradation II via 3'-ketolactose (link), pathway III via beta-galactosidase (link), or uptake by a PTS system followed by hydrolysis of lactose 6'-phosphate. (There is no pathway I.)

Steps

lacE: lactose ABC transporter, substrate-binding component

lacF: lactose ABC transporter, permease component 1

lacG: lactose ABC transporter, permease component 2

lacK: lactose ABC transporter, ATPase component

lacIIA: lactose PTS system, EIIA component

lacIIB: lactose PTS system, EIIB component

lacIIC: lactose PTS system, EIIC component

lacIICB: lactose PTS system, fused EIIC and EIIB components

lacP: lactose permease LacP

lacS: lactose permease LacS

lacY: lactose:proton symporter LacY

pbgal: phospho-beta-galactosidase

tpi: triose-phosphate isomerase

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)

lacA: galactose-6-phosphate isomerase, lacA subunit

lacB: galactose-6-phosphate isomerase, lacB subunit

lacC: D-tagatose-6-phosphate kinase

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

lacA': periplasmic lactose 3-dehydrogenase, LacA subunit

lacC': periplasmic lactose 3-dehydrogenase, LacC subunit

lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)

klh: periplasmic 3'-ketolactose hydrolase

MFS-glucose: glucose transporter, MFS superfamily

SSS-glucose: Sodium/glucose cotransporter

glcU': Glucose uptake protein GlcU

PAST-A: proton-associated sugar transporter A

SemiSWEET: Sugar transporter SemiSWEET

SWEET1: bidirectional sugar transporter SWEET1

mglA: glucose ABC transporter, ATP-binding component (MglA)

mglB: glucose ABC transporter, substrate-binding component

mglC: glucose ABC transporter, permease component (MglC)

gtsA: glucose ABC transporter, substrate-binding component (GtsA)

gtsB: glucose ABC transporter, permease component 1 (GtsB)

gtsC: glucose ABC transporter, permease component 2 (GtsC)

gtsD: glucose ABC transporter, ATPase component (GtsD)

glcS: glucose ABC transporter, substrate-binding component (GlcS)

glcT: glucose ABC transporter, permease component 1 (GlcT)

glcU: glucose ABC transporter, permease component 2 (GlcU)

glcV: glucose ABC transporter, ATPase component (GclV)

aglE': glucose ABC transporter, substrate-binding component (AglE)

aglF': glucose ABC transporter, permease component 1 (AglF)

aglG': glucose ABC transporter, permease component 2 (AglG)

aglK': glucose ABC transporter, ATPase component (AglK)

ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)

bglF: glucose PTS, enzyme II (BCA components, BglF)

ptsG: glucose PTS, enzyme IICB

crr: glucose PTS, enzyme IIA

manX: glucose PTS, enzyme EIIAB

manY: glucose PTS, enzyme EIIC

manZ: glucose PTS, enzyme EIID

gdh: quinoprotein glucose dehydrogenase

gnl: gluconolactonase

gadh1: gluconate 2-dehydrogenase flavoprotein subunit

gadh2: gluconate 2-dehydrogenase cytochrome c subunit

gadh3: gluconate 2-dehydrogenase subunit 3

kguT: 2-ketogluconate transporter

kguK: 2-ketogluconokinase

kguD: 2-keto-6-phosphogluconate reductase

edd: phosphogluconate dehydratase

eda: 2-keto-3-deoxygluconate 6-phosphate aldolase

glk: glucokinase

lacL: heteromeric lactase, large subunit

lacM: heteromeric lactase, small subunit

lacZ: lactase (homomeric)

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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