GapMind for catabolism of small carbon sources

 

D-fructose catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

frcA, frcB, frcC, 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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
frcA fructose ABC transporter, ATPase component FrcA H281DRAFT_03224 H281DRAFT_00426
frcB fructose ABC transporter, substrate-binding component FrcB H281DRAFT_03226 H281DRAFT_04150
frcC fructose ABC transporter, permease component FrcC H281DRAFT_03225 H281DRAFT_04148
scrK fructokinase H281DRAFT_02118 H281DRAFT_00856
Alternative steps:
1pfk 1-phosphofructokinase
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 H281DRAFT_01260 H281DRAFT_02040
BT1758 fructose transporter
fba fructose 1,6-bisphosphate aldolase H281DRAFT_04188 H281DRAFT_01311
ffz fructose facilitator (uniporter)
frt1 fructose:H+ symporter Frt1
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 H281DRAFT_01929
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) H281DRAFT_05271 H281DRAFT_04148
fruG fructose ABC transporter, permease component 2 (FruG) H281DRAFT_05272 H281DRAFT_00427
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components H281DRAFT_01852 H281DRAFT_01977
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component H281DRAFT_01929
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 H281DRAFT_05270 H281DRAFT_02174
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
Slc2a5 fructose:H+ symporter
STP6 sugar transport protein 6
THT2A fructose THT2A
tpi triose-phosphate isomerase H281DRAFT_04564 H281DRAFT_04190

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