GapMind for catabolism of small carbon sources

 

trehalose catabolism in Pseudomonas fluorescens GW456-L13

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase PfGW456L13_3254
gtsA glucose ABC transporter, substrate-binding component (GtsA) PfGW456L13_1894
gtsB glucose ABC transporter, permease component 1 (GtsB) PfGW456L13_1895
gtsC glucose ABC transporter, permease component 2 (GtsC) PfGW456L13_1896
gtsD glucose ABC transporter, ATPase component (GtsD) PfGW456L13_1897 PfGW456L13_3039
glk glucokinase PfGW456L13_1890
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) PfGW456L13_1896 PfGW456L13_2615
aglG' glucose ABC transporter, permease component 2 (AglG) PfGW456L13_1896 PfGW456L13_2615
aglK trehalose ABC trehalose, ATPase component AglK PfGW456L13_3039 PfGW456L13_1897
aglK' glucose ABC transporter, ATPase component (AglK) PfGW456L13_3039 PfGW456L13_1897
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA PfGW456L13_4832
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PfGW456L13_1903 PfGW456L13_2127
edd phosphogluconate dehydratase PfGW456L13_1889 PfGW456L13_3725
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PfGW456L13_3925
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase PfGW456L13_4805 PfGW456L13_1173
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) PfGW456L13_4204 PfGW456L13_1210
gnl gluconolactonase PfGW456L13_3314
kguD 2-keto-6-phosphogluconate reductase PfGW456L13_4945 PfGW456L13_2948
kguK 2-ketogluconokinase PfGW456L13_2950
kguT 2-ketogluconate transporter PfGW456L13_2949 PfGW456L13_2939
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) PfGW456L13_3720
lacC periplasmic trehalose 3-dehydrogenase, LacC subunit
lpqY trehalose ABC transporter, substrate-binding lipoprotein component LpqY
malE2 trehalose ABC transporter, substrate-binding component MalE2
malF trehalose ABC transporter, permease component 1 (MalF)
malF1 trehalose ABC transporter, permease component 1
malG trehalose ABC transporter, permease component 2 (MalG)
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK PfGW456L13_3039 PfGW456L13_1897
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) PfGW456L13_2121 PfGW456L13_3911
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) PfGW456L13_2122 PfGW456L13_3910
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PfGW456L13_3066 PfGW456L13_794
pgmB beta-phosphoglucomutase PfGW456L13_4130
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB PfGW456L13_4833
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) PfGW456L13_4833
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) PfGW456L13_3041 PfGW456L13_2614
thuG trehalose ABC transporter, permease component 2 (ThuG) PfGW456L13_3040 PfGW456L13_2615
thuK trehalose ABC transporter, ATPase component ThuK PfGW456L13_1897 PfGW456L13_3039
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase PfGW456L13_3254
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) PfGW456L13_4832 PfGW456L13_5075
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)
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV PfGW456L13_1897 PfGW456L13_3039

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, 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