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

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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