GapMind for catabolism of small carbon sources

 

trehalose catabolism in Pseudomonas fluorescens FW300-N2C3

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase AO356_24205 AO356_21075
gtsA glucose ABC transporter, substrate-binding component (GtsA) AO356_05195
gtsB glucose ABC transporter, permease component 1 (GtsB) AO356_05190
gtsC glucose ABC transporter, permease component 2 (GtsC) AO356_05185 AO356_28580
gtsD glucose ABC transporter, ATPase component (GtsD) AO356_05180 AO356_28585
glk glucokinase AO356_05215
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) AO356_28580 AO356_21625
aglG' glucose ABC transporter, permease component 2 (AglG) AO356_05185 AO356_21625
aglK trehalose ABC trehalose, ATPase component AglK AO356_00010 AO356_27685
aglK' glucose ABC transporter, ATPase component (AglK) AO356_27685 AO356_00010
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA AO356_17540
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO356_05150 AO356_20285
edd phosphogluconate dehydratase AO356_05220 AO356_28760
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AO356_30205
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase AO356_17600 AO356_30385
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) AO356_14385 AO356_13165
gnl gluconolactonase AO356_24610 AO356_23060
kguD 2-keto-6-phosphogluconate reductase AO356_16925 AO356_24675
kguK 2-ketogluconokinase AO356_24685
kguT 2-ketogluconate transporter AO356_24680 AO356_22860
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) AO356_25070
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) AO356_28580
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK AO356_27685 AO356_28585
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 AO356_27270
mglA glucose ABC transporter, ATP-binding component (MglA) AO356_23205 AO356_28510
mglB glucose ABC transporter, substrate-binding component AO356_28505 AO356_23200
mglC glucose ABC transporter, permease component (MglC) AO356_23210 AO356_28515
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase AO356_27065 AO356_12530
pgmB beta-phosphoglucomutase AO356_20805
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB AO356_17535
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AO356_17535
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
thuE trehalose ABC transporter, substrate-binding component ThuE AO356_28570
thuF trehalose ABC transporter, permease component 1 (ThuF) AO356_28575 AO356_27675
thuG trehalose ABC transporter, permease component 2 (ThuG) AO356_28580 AO356_27680
thuK trehalose ABC transporter, ATPase component ThuK AO356_05180 AO356_00010
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase AO356_01250
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) AO356_17540 AO356_07335
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 AO356_27685 AO356_00010

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