GapMind for catabolism of small carbon sources

 

sucrose catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

thuE, thuF, thuG, thuK, ams, scrK, glk

Also see fitness data for the top candidates

Rules

Overview: Sucrose utilization in GapMind is based on MetaCyc pathways sucrose degradation I via sucrose 6-phosphate hydrolase (link), pathway II via sucrose synthase (link), pathway III via invertase (link), and pathway IV via sucrose phosphorylase (link). Pathway V is similar to pathway III and is not reported in prokaryotes, so it is not included. There is no pathway VI. Pathway VII (via sucrose 3-dehydrogenase, link) is too poorly understood to include in GapMind.

101 steps (56 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
thuE sucrose ABC transporter, substrate-binding component ThuE AO353_25115
thuF sucrose ABC transporter, permease component 1 (ThuF) AO353_25120 AO353_25885
thuG sucrose ABC transporter, permease component 2 (ThuG) AO353_25125 AO353_25890
thuK sucrose ABC transporter, ATPase component ThuK AO353_25130 AO353_25895
ams sucrose hydrolase (invertase) AO353_25135 AO353_04255
scrK fructokinase AO353_25910 AO353_25105
glk glucokinase AO353_03415
Alternative steps:
1pfk 1-phosphofructokinase AO353_05480
aglE sucrose ABC transporter, substrate-binding component AglK
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF sucrose ABC transporter, permease component 1 (AglF)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG sucrose ABC transporter, permease component 2 (AglG) AO353_25125 AO353_03385
aglG' glucose ABC transporter, permease component 2 (AglG) AO353_03385
aglK sucrose ABC transporter, ATPase component AglK AO353_25895 AO353_25130
aglK' glucose ABC transporter, ATPase component (AglK) AO353_25895 AO353_25130
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 AO353_25895 AO353_25130
bglF glucose PTS, enzyme II (BCA components, BglF) AO353_15980
BT1758 fructose transporter
crr glucose PTS, enzyme IIA AO353_15995 AO353_04460
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO353_03350 AO353_01265
edd phosphogluconate dehydratase AO353_03420 AO353_08345
fba fructose 1,6-bisphosphate aldolase AO353_07930
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA AO353_21385 AO353_20820
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC AO353_21390 AO353_20825
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components AO353_05475
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components AO353_05485
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) AO353_21390 AO353_20825
fruG fructose ABC transporter, permease component 2 (FruG) AO353_21390 AO353_20825
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components AO353_05485 AO353_15995
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component AO353_05190
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components AO353_05475
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component AO353_05475
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component AO353_05475
fruK fructose ABC transporter, ATPase component FruK AO353_21385 AO353_20820
fruP fructose porter FruP AO353_25100
gadh1 gluconate 2-dehydrogenase flavoprotein subunit AO353_10795
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AO353_10800 AO353_27065
gadh3 gluconate 2-dehydrogenase subunit 3 AO353_10790
galU glucose 1-phosphate uridylyltransferase AO353_26975 AO353_11880
gdh quinoprotein glucose dehydrogenase AO353_16045
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU)
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) AO353_07265 AO353_29310
gnl gluconolactonase AO353_23650
gtsA glucose ABC transporter, substrate-binding component (GtsA) AO353_03395
gtsB glucose ABC transporter, permease component 1 (GtsB) AO353_03390
gtsC glucose ABC transporter, permease component 2 (GtsC) AO353_03385 AO353_25125
gtsD glucose ABC transporter, ATPase component (GtsD) AO353_03380 AO353_25130
kguD 2-keto-6-phosphogluconate reductase AO353_04850 AO353_26885
kguK 2-ketogluconokinase AO353_26875
kguT 2-ketogluconate transporter AO353_26880 AO353_26910
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
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily AO353_25100
mglA glucose ABC transporter, ATP-binding component (MglA) AO353_21385 AO353_20820
mglB glucose ABC transporter, substrate-binding component AO353_21380
mglC glucose ABC transporter, permease component (MglC) AO353_21390 AO353_20825
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase AO353_24665 AO353_09235
ptsG glucose PTS, enzyme IICB AO353_04465
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AO353_04465
ptsS sucrose phosphotransferase enzyme EII-BCA AO353_15980
sacP sucrose phosphotransferase enzyme EII-BC AO353_15980
scrB sucrose-6-phosphate hydrolase AO353_25135
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter
SLC45A2 sucrose transporter
SLC45A3 sucrose:H+ symporter
SLC45A4 sucrose:H+ symporter
SSS-glucose Sodium/glucose cotransporter
STP6 sugar transport protein 6
SUS sucrose synthase
sut sucrose:proton symporter SUT/SUC
sut1 alpha-glucoside permease Sut1
SWEET1 bidirectional sugar transporter SWEET1
THT2A fructose THT2A
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase AO353_05590 AO353_07945

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.

Links

Downloads

Related tools

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 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