GapMind for catabolism of small carbon sources

 

trehalose catabolism in Pseudomonas stutzeri RCH2

Best path

treF, gtsA, gtsB, gtsC, gtsD, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase Psest_0358 Psest_0870
gtsA glucose ABC transporter, substrate-binding component (GtsA) Psest_1896
gtsB glucose ABC transporter, permease component 1 (GtsB) Psest_1897
gtsC glucose ABC transporter, permease component 2 (GtsC) Psest_1898
gtsD glucose ABC transporter, ATPase component (GtsD) Psest_1899 Psest_0871
glk glucokinase Psest_0850 Psest_1893
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) Psest_1898 Psest_0865
aglG' glucose ABC transporter, permease component 2 (AglG) Psest_1898 Psest_0865
aglK trehalose ABC trehalose, ATPase component AglK Psest_0871 Psest_1899
aglK' glucose ABC transporter, ATPase component (AglK) Psest_0871 Psest_1899
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Psest_0854 Psest_1998
edd phosphogluconate dehydratase Psest_1892 Psest_0849
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Psest_2914 Psest_2915
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) Psest_3658 Psest_0871
gnl gluconolactonase Psest_4141 Psest_0364
kguD 2-keto-6-phosphogluconate reductase Psest_0378 Psest_0431
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) Psest_0819
lacC periplasmic trehalose 3-dehydrogenase, LacC subunit
lpqY trehalose ABC transporter, substrate-binding lipoprotein component LpqY
malE2 trehalose ABC transporter, substrate-binding component MalE2 Psest_0863
malF trehalose ABC transporter, permease component 1 (MalF) Psest_0864
malF1 trehalose ABC transporter, permease component 1 Psest_0864
malG trehalose ABC transporter, permease component 2 (MalG) Psest_0865
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK Psest_0871 Psest_1899
malX trehalose ABC transporter, substrate-binding component MalX
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) Psest_1392 Psest_1309
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Psest_0039 Psest_3806
pgmB beta-phosphoglucomutase
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
thuE trehalose ABC transporter, substrate-binding component ThuE
thuF trehalose ABC transporter, permease component 1 (ThuF) Psest_0864
thuG trehalose ABC transporter, permease component 2 (ThuG) Psest_0865 Psest_3655
thuK trehalose ABC transporter, ATPase component ThuK Psest_1899 Psest_0871
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase Psest_3785 Psest_0870
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) Psest_3355 Psest_3862
treP trehalose phosphorylase, inverting
trePP trehalose-6-phosphate phosphorylase
treS trehalose ABC transporter, substrate-binding comopnent TreS
treT trehalose ABC transporter, permease component 1 (TreT) Psest_0864
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV Psest_1899 Psest_0871

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.

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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, 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