GapMind for catabolism of small carbon sources

 

D-fructose catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

fruA, fruI, 1pfk, fba, tpi

Also see fitness data for the top candidates

Rules

Overview: Many bacteria take up fructose by a phosphotransferase (PTS) system that forms fructose 1-phosphate; this can be consumed via 1-phosphofructokinase and glycolysis (link). Alternatively, some PTS systems form fructose 6-phosphate, which is a central metabolic intermediate. Fructose can also be taken up directly and then phosphorylated to fructose 6-phosphate, a central metabolic intermediate. Another path is known in Aeromonas hydrophila -- phosphofructomutase converts fructose 1-phosphate (formed by a PTS system) to fructose 6-phosphate (PMID:9579084). This path is not included in GapMind because phosphofructomutase has not been linked to sequence. Also, in eukaryotes, fructose-1,6-bisphosphate aldolase is reported to cleave fructose 1-phosphate to glycerone phosphate and glyceraldehyde (link). This would make 1-phosphofructokinase unnececessary. It's not clear that this occurs in prokaryotes, so this is not listed.

37 steps (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components Pf1N1B4_1144
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components Pf1N1B4_1146 Pf1N1B4_833
1pfk 1-phosphofructokinase Pf1N1B4_1145 Pf1N1B4_6031
fba fructose 1,6-bisphosphate aldolase Pf1N1B4_2402
tpi triose-phosphate isomerase Pf1N1B4_1164 Pf1N1B4_2399
Alternative steps:
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
BT1758 fructose transporter
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
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
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
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP
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
scrK fructokinase Pf1N1B4_4844 Pf1N1B4_4765
Slc2a5 fructose:H+ symporter
STP6 sugar transport protein 6
THT2A fructose THT2A

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