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 (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