GapMind for catabolism of small carbon sources

 

D-fructose catabolism in Pseudomonas simiae WCS417

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 (19 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 PS417_03975
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components PS417_03965 PS417_23035
1pfk 1-phosphofructokinase PS417_03970 PS417_18385
fba fructose 1,6-bisphosphate aldolase PS417_26415
tpi triose-phosphate isomerase PS417_24000 PS417_26430
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) PS417_22135
araV fructose ABC transporter, ATPase component AraV PS417_12700 PS417_22130
BT1758 fructose transporter
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA PS417_13635 PS417_11890
frcB fructose ABC transporter, substrate-binding component FrcB PS417_13645 PS417_17735
frcC fructose ABC transporter, permease component FrcC PS417_13640 PS417_12060
frt1 fructose:H+ symporter Frt1
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components PS417_03965
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) PS417_13640 PS417_12060
fruG fructose ABC transporter, permease component 2 (FruG) PS417_17725 PS417_12060
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component PS417_04335
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components PS417_03975
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component PS417_03975
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component PS417_03975
fruK fructose ABC transporter, ATPase component FruK PS417_13635 PS417_11890
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 PS417_12685 PS417_12565
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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