GapMind for catabolism of small carbon sources

 

sucrose catabolism in Pseudomonas fluorescens FW300-N1B4

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 (49 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
thuE sucrose ABC transporter, substrate-binding component ThuE Pf1N1B4_5112
thuF sucrose ABC transporter, permease component 1 (ThuF) Pf1N1B4_5113 Pf1N1B4_4849
thuG sucrose ABC transporter, permease component 2 (ThuG) Pf1N1B4_5114 Pf1N1B4_4848
thuK sucrose ABC transporter, ATPase component ThuK Pf1N1B4_5115 Pf1N1B4_4847
ams sucrose hydrolase (invertase) Pf1N1B4_5116 Pf1N1B4_4677
scrK fructokinase Pf1N1B4_4844 Pf1N1B4_4765
glk glucokinase Pf1N1B4_600
Alternative steps:
1pfk 1-phosphofructokinase Pf1N1B4_1145 Pf1N1B4_6031
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) Pf1N1B4_5114 Pf1N1B4_594
aglG' glucose ABC transporter, permease component 2 (AglG) Pf1N1B4_4011 Pf1N1B4_594
aglK sucrose ABC transporter, ATPase component AglK Pf1N1B4_5115 Pf1N1B4_4847
aglK' glucose ABC transporter, ATPase component (AglK) Pf1N1B4_4847 Pf1N1B4_5115
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 Pf1N1B4_3974 Pf1N1B4_4847
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA Pf1N1B4_833
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf1N1B4_587 Pf1N1B4_399
edd phosphogluconate dehydratase Pf1N1B4_601 Pf1N1B4_2303
fba fructose 1,6-bisphosphate aldolase Pf1N1B4_2402
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA Pf1N1B4_4286 Pf1N1B4_410
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC Pf1N1B4_4287 Pf1N1B4_6033
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components Pf1N1B4_1144
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components Pf1N1B4_1146
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) Pf1N1B4_4287 Pf1N1B4_6033
fruG fructose ABC transporter, permease component 2 (FruG) Pf1N1B4_4287
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components Pf1N1B4_1146 Pf1N1B4_833
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component Pf1N1B4_1082
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components Pf1N1B4_1144
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component Pf1N1B4_1144
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component Pf1N1B4_1144
fruK fructose ABC transporter, ATPase component FruK Pf1N1B4_4286 Pf1N1B4_410
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase Pf1N1B4_5015 Pf1N1B4_5948
gdh quinoprotein glucose dehydrogenase Pf1N1B4_821 Pf1N1B4_5582
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP
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
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
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
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
ptsS sucrose phosphotransferase enzyme EII-BCA Pf1N1B4_836
sacP sucrose phosphotransferase enzyme EII-BC Pf1N1B4_836
scrB sucrose-6-phosphate hydrolase Pf1N1B4_5116
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter
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 Pf1N1B4_1164 Pf1N1B4_2399

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