GapMind for catabolism of small carbon sources

 

D-fructose catabolism in Oceanisphaera arctica V1-41

Best path

fruA, fruI, 1pfk, fba, tpi

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 UN63_RS01635
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components UN63_RS01625 UN63_RS04950
1pfk 1-phosphofructokinase UN63_RS01630
fba fructose 1,6-bisphosphate aldolase UN63_RS09780
tpi triose-phosphate isomerase UN63_RS15720 UN63_RS09785
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 UN63_RS12840 UN63_RS02300
BT1758 fructose transporter
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA UN63_RS08345 UN63_RS06410
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC UN63_RS08340
frt1 fructose:H+ symporter Frt1
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components UN63_RS01625
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) UN63_RS08340
fruG fructose ABC transporter, permease component 2 (FruG) UN63_RS08340
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component UN63_RS06425
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components UN63_RS01635
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component UN63_RS01635
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component UN63_RS01635
fruK fructose ABC transporter, ATPase component FruK UN63_RS08345
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 UN63_RS00805 UN63_RS08330
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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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