GapMind for catabolism of small carbon sources

 

trehalose catabolism in Escherichia coli BW25113

Best path

treF, mglA, mglB, mglC, glk

Also see fitness data for the top candidates

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).

74 steps (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase b1197 b3519
mglA glucose ABC transporter, ATP-binding component (MglA) b2149 b3567
mglB glucose ABC transporter, substrate-binding component b2150 b3566
mglC glucose ABC transporter, permease component (MglC) b2148 b3750
glk glucokinase b2388 b0394
Alternative steps:
aglE trehalose ABC transporter, substrate-binding component AglE
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF trehalose ABC transporter, permease component 1 (AglF)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG trehalose ABC transporter, permease component 2 (AglG) b4032
aglG' glucose ABC transporter, permease component 2 (AglG) b4032
aglK trehalose ABC trehalose, ATPase component AglK b4035 b3450
aglK' glucose ABC transporter, ATPase component (AglK) b4035 b3450
bglF glucose PTS, enzyme II (BCA components, BglF) b3722 b2715
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA b2417 b0679
eda 2-keto-3-deoxygluconate 6-phosphate aldolase b1850 b4477
edd phosphogluconate dehydratase b1851 b3771
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase b0124 b0837
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU)
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) b0262 b4035
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) b1312 b4032
gtsD glucose ABC transporter, ATPase component (GtsD) b4035 b3450
kguD 2-keto-6-phosphogluconate reductase b3553 b2913
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB)
lacC periplasmic trehalose 3-dehydrogenase, LacC subunit
lpqY trehalose ABC transporter, substrate-binding lipoprotein component LpqY
malE2 trehalose ABC transporter, substrate-binding component MalE2 b4034
malF trehalose ABC transporter, permease component 1 (MalF) b4033
malF1 trehalose ABC transporter, permease component 1 b4033
malG trehalose ABC transporter, permease component 2 (MalG) b1312 b4032
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK b3450 b4035
malX trehalose ABC transporter, substrate-binding component MalX
manX glucose PTS, enzyme EIIAB b1817
manY glucose PTS, enzyme EIIC b1818
manZ glucose PTS, enzyme EIID b1819 b3140
MFS-glucose glucose transporter, MFS superfamily b2943 b2841
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase b0688 b2048
pgmB beta-phosphoglucomutase b1317 b2690
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB b1101 b0679
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) b0679 b1101
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter b3679
SWEET1 bidirectional sugar transporter SWEET1
thuE trehalose ABC transporter, substrate-binding component ThuE
thuF trehalose ABC transporter, permease component 1 (ThuF) b1311 b4033
thuG trehalose ABC transporter, permease component 2 (ThuG) b1312 b4032
thuK trehalose ABC transporter, ATPase component ThuK b3450 b4035
treB trehalose PTS system, EII-BC components TreB b4240 b3722
treC trehalose-6-phosphate hydrolase b4239
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) b2417 b0679
treP trehalose phosphorylase, inverting b1316
trePP trehalose-6-phosphate phosphorylase
treS trehalose ABC transporter, substrate-binding comopnent TreS
treT trehalose ABC transporter, permease component 1 (TreT) b3452
TRET1 facilitated trehalose transporter Tret1 b2943 b2841
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV b4035 b3450

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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, 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