GapMind for catabolism of small carbon sources

 

D-fructose catabolism in Dyella japonica UNC79MFTsu3.2

Best path

fruP, scrK

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fruP fructose porter FruP N515DRAFT_1918 N515DRAFT_1222
scrK fructokinase N515DRAFT_1919 N515DRAFT_2221
Alternative steps:
1pfk 1-phosphofructokinase N515DRAFT_0917 N515DRAFT_0916
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 N515DRAFT_4212 N515DRAFT_1562
BT1758 fructose transporter
fba fructose 1,6-bisphosphate aldolase N515DRAFT_4284 N515DRAFT_0914
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA N515DRAFT_2413 N515DRAFT_3232
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC N515DRAFT_2414 N515DRAFT_2415
frt1 fructose:H+ symporter Frt1 N515DRAFT_1228
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
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) N515DRAFT_2414
fruG fructose ABC transporter, permease component 2 (FruG) N515DRAFT_2415
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components N515DRAFT_3957
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
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
fruK fructose ABC transporter, ATPase component FruK N515DRAFT_2413 N515DRAFT_3232
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP N515DRAFT_0382 N515DRAFT_1228
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
Slc2a5 fructose:H+ symporter N515DRAFT_1228 N515DRAFT_0382
STP6 sugar transport protein 6 N515DRAFT_1228 N515DRAFT_0382
THT2A fructose THT2A
tpi triose-phosphate isomerase N515DRAFT_1376 N515DRAFT_4291

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, the preprint on GapMind for carbon sources, 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