GapMind for catabolism of small carbon sources

 

D-fructose catabolism in Klebsiella michiganensis M5al

Best path

fruA, fruB, 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 (28 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 BWI76_RS19725 BWI76_RS24865
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components BWI76_RS19735
1pfk 1-phosphofructokinase BWI76_RS19730 BWI76_RS24860
fba fructose 1,6-bisphosphate aldolase BWI76_RS23975 BWI76_RS19370
tpi triose-phosphate isomerase BWI76_RS27465 BWI76_RS23980
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 BWI76_RS06035 BWI76_RS03270
BT1758 fructose transporter
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA BWI76_RS14860 BWI76_RS00275
frcB fructose ABC transporter, substrate-binding component FrcB BWI76_RS14855 BWI76_RS07665
frcC fructose ABC transporter, permease component FrcC BWI76_RS14865 BWI76_RS00280
frt1 fructose:H+ symporter Frt1 BWI76_RS03110 BWI76_RS24055
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) BWI76_RS02805 BWI76_RS00280
fruG fructose ABC transporter, permease component 2 (FruG) BWI76_RS02810 BWI76_RS14865
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components BWI76_RS20650 BWI76_RS23270
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component BWI76_RS25275 BWI76_RS10675
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components BWI76_RS24865 BWI76_RS19725
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component BWI76_RS24865 BWI76_RS10665
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component BWI76_RS19725 BWI76_RS27570
fruK fructose ABC transporter, ATPase component FruK BWI76_RS02800 BWI76_RS07240
fruP fructose porter FruP BWI76_RS22920 BWI76_RS23685
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP BWI76_RS21205 BWI76_RS10225
levD fructose PTS system (fructose 6-phosphate forming), EII-A component BWI76_RS17890
levDE fructose PTS system (fructose 6-phosphate forming), EII-AB component BWI76_RS17890
levE fructose PTS system (fructose 6-phosphate forming), EII-B component BWI76_RS17890 BWI76_RS01735
levF fructose PTS system (fructose 6-phosphate forming), EII-C component BWI76_RS17895 BWI76_RS01730
levG fructose PTS system (fructose 6-phosphate forming), EII-D component BWI76_RS17900 BWI76_RS01725
scrK fructokinase BWI76_RS07325 BWI76_RS14875
Slc2a5 fructose:H+ symporter BWI76_RS24055 BWI76_RS17580
STP6 sugar transport protein 6 BWI76_RS24055 BWI76_RS03110
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.

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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