GapMind for catabolism of small carbon sources

 

trehalose catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

treEIIA, treB, treC, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) Pf1N1B4_833 Pf1N1B4_1146
treB trehalose PTS system, EII-BC components TreB Pf1N1B4_836
treC trehalose-6-phosphate hydrolase Pf1N1B4_835 Pf1N1B4_4677
glk glucokinase Pf1N1B4_600
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) Pf1N1B4_5114 Pf1N1B4_594
aglG' glucose ABC transporter, permease component 2 (AglG) Pf1N1B4_4011 Pf1N1B4_594
aglK trehalose ABC trehalose, ATPase component AglK Pf1N1B4_5115 Pf1N1B4_4847
aglK' glucose ABC transporter, ATPase component (AglK) Pf1N1B4_4847 Pf1N1B4_5115
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA Pf1N1B4_833
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf1N1B4_587 Pf1N1B4_399
edd phosphogluconate dehydratase Pf1N1B4_601 Pf1N1B4_2303
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Pf1N1B4_821 Pf1N1B4_5582
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) Pf1N1B4_594
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) Pf1N1B4_2538 Pf1N1B4_4352
gnl gluconolactonase Pf1N1B4_4626 Pf1N1B4_4510
gtsA glucose ABC transporter, substrate-binding component (GtsA) Pf1N1B4_596
gtsB glucose ABC transporter, permease component 1 (GtsB) Pf1N1B4_595
gtsC glucose ABC transporter, permease component 2 (GtsC) Pf1N1B4_594 Pf1N1B4_5114
gtsD glucose ABC transporter, ATPase component (GtsD) Pf1N1B4_593 Pf1N1B4_5115
kguD 2-keto-6-phosphogluconate reductase Pf1N1B4_1004 Pf1N1B4_4763
kguK 2-ketogluconokinase Pf1N1B4_4765
kguT 2-ketogluconate transporter Pf1N1B4_4764 Pf1N1B4_5000
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) Pf1N1B4_5765
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) Pf1N1B4_5114
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK Pf1N1B4_5115 Pf1N1B4_593
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) Pf1N1B4_4286 Pf1N1B4_410
mglB glucose ABC transporter, substrate-binding component Pf1N1B4_4386
mglC glucose ABC transporter, permease component (MglC) Pf1N1B4_4287 Pf1N1B4_409
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Pf1N1B4_4886 Pf1N1B4_2122
pgmB beta-phosphoglucomutase Pf1N1B4_3808
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 Pf1N1B4_5112
thuF trehalose ABC transporter, permease component 1 (ThuF) Pf1N1B4_5113 Pf1N1B4_4849
thuG trehalose ABC transporter, permease component 2 (ThuG) Pf1N1B4_5114 Pf1N1B4_4848
thuK trehalose ABC transporter, ATPase component ThuK Pf1N1B4_593 Pf1N1B4_4847
treF trehalase Pf1N1B4_153 Pf1N1B4_835
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 Pf1N1B4_593 Pf1N1B4_4847

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 Aug 02 2021. The underlying query database was built on Aug 02 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