GapMind for catabolism of small carbon sources

 

Definition of trehalose catabolism

As rules and steps, or see full text

Rules

Overview: Trehalose degradation is based on MetaCyc pathways I via trehalose-6-phosphate hydrolase (link), II via cytoplasmic trehalase (link), III via trehalose-6-phosphate phosphorylase (link), IV via inverting trehalose phosphorylase (link), V via trehalose phosphorylase (link), VI via periplasmic trehalase (link), as well as trehalose degradation via 3-ketotrehalose (PMID:33657378).

Steps

treB: trehalose PTS system, EII-BC components TreB

treEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP)

thuE: trehalose ABC transporter, substrate-binding component ThuE

thuF: trehalose ABC transporter, permease component 1 (ThuF)

thuG: trehalose ABC transporter, permease component 2 (ThuG)

thuK: trehalose ABC transporter, ATPase component ThuK

lpqY: trehalose ABC transporter, substrate-binding lipoprotein component LpqY

malE2: trehalose ABC transporter, substrate-binding component MalE2

malF1: trehalose ABC transporter, permease component 1

malG1: trehalose ABC transporter, permease component 2 (MalG1/MalG2)

malF: trehalose ABC transporter, permease component 1 (MalF)

malG: trehalose ABC transporter, permease component 2 (MalG)

malK: trehalose ABC transporter, ATPase component MalK

malX: trehalose ABC transporter, substrate-binding component MalX

treS: trehalose ABC transporter, substrate-binding comopnent TreS

treT: trehalose ABC transporter, permease component 1 (TreT)

treU: trehalose ABC transporter, permease component 2 (TreU)

treV: trehalose ABC transporter, ATPase component TreV

aglE: trehalose ABC transporter, substrate-binding component AglE

aglF: trehalose ABC transporter, permease component 1 (AglF)

aglG: trehalose ABC transporter, permease component 2 (AglG)

aglK: trehalose ABC trehalose, ATPase component AglK

TRET1: facilitated trehalose transporter Tret1

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

BT2158: periplasmic trehalose 3-dehydrogenase (BT2158)

lacA: periplasmic trehalose 3-dehydrogenase, LacA subunit

lacC: periplasmic trehalose 3-dehydrogenase, LacC subunit

lacB: periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB)

klh: 3-ketotrehalose hydrolase

treF: trehalase

treC: trehalose-6-phosphate hydrolase

trePP: trehalose-6-phosphate phosphorylase

pgmB: beta-phosphoglucomutase

treP: trehalose phosphorylase, inverting

PsTP: trehalose phosphorylase

pgmA: alpha-phosphoglucomutase

Links

Downloads

Related tools

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