GapMind for catabolism of small carbon sources

 

trehalose catabolism in Pseudomonas fluorescens FW300-N2E2

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase Pf6N2E2_1643 Pf6N2E2_6094
gtsA glucose ABC transporter, substrate-binding component (GtsA) Pf6N2E2_2892
gtsB glucose ABC transporter, permease component 1 (GtsB) Pf6N2E2_2891
gtsC glucose ABC transporter, permease component 2 (GtsC) Pf6N2E2_2890 Pf6N2E2_1648
gtsD glucose ABC transporter, ATPase component (GtsD) Pf6N2E2_2889 Pf6N2E2_807
glk glucokinase Pf6N2E2_2897
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) Pf6N2E2_1648 Pf6N2E2_2890
aglG' glucose ABC transporter, permease component 2 (AglG) Pf6N2E2_2890 Pf6N2E2_106
aglK trehalose ABC trehalose, ATPase component AglK Pf6N2E2_1960 Pf6N2E2_1649
aglK' glucose ABC transporter, ATPase component (AglK) Pf6N2E2_807 Pf6N2E2_1960
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 Pf6N2E2_2883 Pf6N2E2_5976
edd phosphogluconate dehydratase Pf6N2E2_2898 Pf6N2E2_1668
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Pf6N2E2_1903 Pf6N2E2_4408
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Pf6N2E2_5442 Pf6N2E2_1939
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) Pf6N2E2_4815 Pf6N2E2_4515
gnl gluconolactonase Pf6N2E2_614 Pf6N2E2_318
kguD 2-keto-6-phosphogluconate reductase Pf6N2E2_5310 Pf6N2E2_627
kguK 2-ketogluconokinase Pf6N2E2_629
kguT 2-ketogluconate transporter Pf6N2E2_628 Pf6N2E2_1312
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) Pf6N2E2_704
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) Pf6N2E2_1648
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK Pf6N2E2_807 Pf6N2E2_1960
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 Pf6N2E2_883 Pf6N2E2_1003
mglA glucose ABC transporter, ATP-binding component (MglA) Pf6N2E2_523 Pf6N2E2_1456
mglB glucose ABC transporter, substrate-binding component Pf6N2E2_1455 Pf6N2E2_1015
mglC glucose ABC transporter, permease component (MglC) Pf6N2E2_524 Pf6N2E2_1457
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Pf6N2E2_1059 Pf6N2E2_4374
pgmB beta-phosphoglucomutase Pf6N2E2_6049
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 Pf6N2E2_1646
thuF trehalose ABC transporter, permease component 1 (ThuF) Pf6N2E2_1647 Pf6N2E2_809
thuG trehalose ABC transporter, permease component 2 (ThuG) Pf6N2E2_1648 Pf6N2E2_808
thuK trehalose ABC transporter, ATPase component ThuK Pf6N2E2_2889 Pf6N2E2_1960
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase Pf6N2E2_2118
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) Pf6N2E2_3339 Pf6N2E2_3942
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 Pf6N2E2_807 Pf6N2E2_1960

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