GapMind for catabolism of small carbon sources

 

sucrose catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

thuE, thuF, thuG, thuK, ams, scrK, glk

Also see fitness data for the top candidates

Rules

Overview: Sucrose utilization in GapMind is based on MetaCyc pathways sucrose degradation I via sucrose 6-phosphate hydrolase (link), pathway II via sucrose synthase (link), pathway III via invertase (link), and pathway IV via sucrose phosphorylase (link). Pathway V is similar to pathway III and is not reported in prokaryotes, so it is not included. There is no pathway VI. Pathway VII (via sucrose 3-dehydrogenase, link) is too poorly understood to include in GapMind.

101 steps (52 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
thuE sucrose ABC transporter, substrate-binding component ThuE AO356_28570
thuF sucrose ABC transporter, permease component 1 (ThuF) AO356_28575 AO356_27675
thuG sucrose ABC transporter, permease component 2 (ThuG) AO356_28580 AO356_27680
thuK sucrose ABC transporter, ATPase component ThuK AO356_28585 AO356_27685
ams sucrose hydrolase (invertase) AO356_28590 AO356_15155
scrK fructokinase AO356_00035 AO356_27700
glk glucokinase AO356_05215
Alternative steps:
1pfk 1-phosphofructokinase AO356_07330 AO356_00950
aglE sucrose ABC transporter, substrate-binding component AglK
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF sucrose ABC transporter, permease component 1 (AglF)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG sucrose ABC transporter, permease component 2 (AglG) AO356_28580 AO356_21625
aglG' glucose ABC transporter, permease component 2 (AglG) AO356_05185 AO356_21625
aglK sucrose ABC transporter, ATPase component AglK AO356_00010 AO356_27685
aglK' glucose ABC transporter, ATPase component (AglK) AO356_27685 AO356_00010
araS fructose ABC transporter, substrate-binding component AraS
araT fructose ABC transporter, permease component 2 (AraT)
araU fructose ABC transporter, permease component 1 (AraU)
araV fructose ABC transporter, ATPase component AraV AO356_00010 AO356_01640
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA AO356_17540
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO356_05150 AO356_20285
edd phosphogluconate dehydratase AO356_05220 AO356_28760
fba fructose 1,6-bisphosphate aldolase AO356_13705
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA AO356_23205 AO356_20250
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC AO356_23210 AO356_00960
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components AO356_07325
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components AO356_07335
fruD fructose-specific PTS system (fructose 1-phosphate forming), EII-A component
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) AO356_00960 AO356_23210
fruG fructose ABC transporter, permease component 2 (FruG) AO356_23210 AO356_00960
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components AO356_07335 AO356_17540
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component AO356_07045
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components AO356_07325
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component AO356_07325
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component AO356_07325
fruK fructose ABC transporter, ATPase component FruK AO356_23205 AO356_20250
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AO356_30205
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase AO356_22795 AO356_14360
gdh quinoprotein glucose dehydrogenase AO356_17600 AO356_30385
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP AO356_27270
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
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
kguD 2-keto-6-phosphogluconate reductase AO356_16925 AO356_24675
kguK 2-ketogluconokinase AO356_24685
kguT 2-ketogluconate transporter AO356_24680 AO356_22860
levD fructose PTS system (fructose 6-phosphate forming), EII-A component
levDE fructose PTS system (fructose 6-phosphate forming), EII-AB component
levE fructose PTS system (fructose 6-phosphate forming), EII-B component
levF fructose PTS system (fructose 6-phosphate forming), EII-C component
levG fructose PTS system (fructose 6-phosphate forming), EII-D component
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
ptsG glucose PTS, enzyme IICB AO356_17535
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AO356_17535
ptsS sucrose phosphotransferase enzyme EII-BCA
sacP sucrose phosphotransferase enzyme EII-BC
scrB sucrose-6-phosphate hydrolase AO356_28590
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter AO356_27270
SLC45A2 sucrose transporter
SLC45A3 sucrose:H+ symporter
SLC45A4 sucrose:H+ symporter
SSS-glucose Sodium/glucose cotransporter
STP6 sugar transport protein 6
SUS sucrose synthase
sut sucrose:proton symporter SUT/SUC
sut1 alpha-glucoside permease Sut1
SWEET1 bidirectional sugar transporter SWEET1
THT2A fructose THT2A
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase AO356_07440 AO356_13690

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