GapMind for catabolism of small carbon sources

 

Definition of D-fructose catabolism

As rules and steps, or see full text

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.

Steps

fruA: fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components

fruB: fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components

fruI: fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components

fruD: fructose-specific PTS system (fructose 1-phosphate forming), EII-A component

fruII-A: fructose-specific PTS system (fructose 1-phosphate forming), EII-A component

fruII-B: fructose-specific PTS system (fructose 1-phosphate forming), EII-B component

fruII-C: fructose-specific PTS system (fructose 1-phosphate forming), EII-C component

fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components

levD: fructose PTS system (fructose 6-phosphate forming), EII-A component

levE: fructose PTS system (fructose 6-phosphate forming), EII-B component

levDE: fructose PTS system (fructose 6-phosphate forming), EII-AB component

levF: fructose PTS system (fructose 6-phosphate forming), EII-C component

levG: fructose PTS system (fructose 6-phosphate forming), EII-D component

araV: fructose ABC transporter, ATPase component AraV

araU: fructose ABC transporter, permease component 1 (AraU)

araT: fructose ABC transporter, permease component 2 (AraT)

araS: fructose ABC transporter, substrate-binding component AraS

fruE: fructose ABC transporter, substrate-binding component FruE

fruF: fructose ABC transporter, permease component 1 (FruF)

fruG: fructose ABC transporter, permease component 2 (FruG)

fruK: fructose ABC transporter, ATPase component FruK

frcA: fructose ABC transporter, ATPase component FrcA

frcB: fructose ABC transporter, substrate-binding component FrcB

frcC: fructose ABC transporter, permease component FrcC

Slc2a5: fructose:H+ symporter

ffz: fructose facilitator (uniporter)

glcP: fructose:H+ symporter GlcP

ght6: high-affinity fructose transporter ght6

STP6: sugar transport protein 6

THT2A: fructose THT2A

frt1: fructose:H+ symporter Frt1

fruP: fructose porter FruP

BT1758: fructose transporter

scrK: fructokinase

1pfk: 1-phosphofructokinase

fba: fructose 1,6-bisphosphate aldolase

tpi: triose-phosphate isomerase

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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