GapMind for catabolism of small carbon sources

 

sucrose catabolism in Pseudomonas fluorescens FW300-N2E2

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 (50 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
thuE sucrose ABC transporter, substrate-binding component ThuE Pf6N2E2_1646
thuF sucrose ABC transporter, permease component 1 (ThuF) Pf6N2E2_1647 Pf6N2E2_809
thuG sucrose ABC transporter, permease component 2 (ThuG) Pf6N2E2_1648 Pf6N2E2_808
thuK sucrose ABC transporter, ATPase component ThuK Pf6N2E2_1649 Pf6N2E2_807
ams sucrose hydrolase (invertase) Pf6N2E2_1650 Pf6N2E2_4966
scrK fructokinase Pf6N2E2_1965 Pf6N2E2_804
glk glucokinase Pf6N2E2_2897
Alternative steps:
1pfk 1-phosphofructokinase Pf6N2E2_3338 Pf6N2E2_165
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) Pf6N2E2_1648 Pf6N2E2_2890
aglG' glucose ABC transporter, permease component 2 (AglG) Pf6N2E2_2890 Pf6N2E2_106
aglK sucrose ABC transporter, ATPase component AglK Pf6N2E2_1960 Pf6N2E2_1649
aglK' glucose ABC transporter, ATPase component (AglK) Pf6N2E2_807 Pf6N2E2_1960
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 Pf6N2E2_1960 Pf6N2E2_807
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf6N2E2_2883 Pf6N2E2_5976
edd phosphogluconate dehydratase Pf6N2E2_2898 Pf6N2E2_1668
fba fructose 1,6-bisphosphate aldolase Pf6N2E2_4660
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA Pf6N2E2_523 Pf6N2E2_5969
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC Pf6N2E2_524 Pf6N2E2_163
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components Pf6N2E2_3337
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components Pf6N2E2_3339
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) Pf6N2E2_163 Pf6N2E2_524
fruG fructose ABC transporter, permease component 2 (FruG) Pf6N2E2_524 Pf6N2E2_163
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components Pf6N2E2_3339 Pf6N2E2_3942
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component Pf6N2E2_3269
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components Pf6N2E2_3337
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component Pf6N2E2_3337
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component Pf6N2E2_3337
fruK fructose ABC transporter, ATPase component FruK Pf6N2E2_523 Pf6N2E2_5969
fruP fructose porter FruP Pf6N2E2_1003
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Pf6N2E2_1903 Pf6N2E2_4408
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase Pf6N2E2_445 Pf6N2E2_4810
gdh quinoprotein glucose dehydrogenase Pf6N2E2_5442 Pf6N2E2_1939
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP Pf6N2E2_883
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
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
kguD 2-keto-6-phosphogluconate reductase Pf6N2E2_5310 Pf6N2E2_627
kguK 2-ketogluconokinase Pf6N2E2_629
kguT 2-ketogluconate transporter Pf6N2E2_628 Pf6N2E2_1312
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 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
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
ptsS sucrose phosphotransferase enzyme EII-BCA
sacP sucrose phosphotransferase enzyme EII-BC
scrB sucrose-6-phosphate hydrolase Pf6N2E2_1650
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter Pf6N2E2_883
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 Pf6N2E2_3356 Pf6N2E2_4657

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