GapMind for catabolism of small carbon sources

 

sucrose catabolism in Pseudomonas putida KT2440

Best path

ams, gtsA, gtsB, gtsC, gtsD, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) PP_4059
gtsA glucose ABC transporter, substrate-binding component (GtsA) PP_1015
gtsB glucose ABC transporter, permease component 1 (GtsB) PP_1016
gtsC glucose ABC transporter, permease component 2 (GtsC) PP_1017
gtsD glucose ABC transporter, ATPase component (GtsD) PP_1018 PP_0411
glk glucokinase PP_1011
Alternative steps:
1pfk 1-phosphofructokinase PP_0794
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) PP_2263 PP_1017
aglG' glucose ABC transporter, permease component 2 (AglG) PP_1017 PP_2263
aglK sucrose ABC transporter, ATPase component AglK PP_1018 PP_0411
aglK' glucose ABC transporter, ATPase component (AglK) PP_1018 PP_5179
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 PP_1018 PP_1484
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PP_1024
edd phosphogluconate dehydratase PP_1010 PP_5128
fba fructose 1,6-bisphosphate aldolase PP_4960
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA PP_2455 PP_2759
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC PP_2456 PP_2761
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components PP_0795
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components PP_0793
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) PP_2456
fruG fructose ABC transporter, permease component 2 (FruG)
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components PP_0793 PP_5145
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component PP_0950
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components PP_0795
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component PP_0795
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component PP_0795
fruK fructose ABC transporter, ATPase component FruK PP_2759 PP_2455
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit PP_3383
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PP_3382 PP_3623
gadh3 gluconate 2-dehydrogenase subunit 3 PP_3384
galU glucose 1-phosphate uridylyltransferase PP_3821 PP_0406
gdh quinoprotein glucose dehydrogenase PP_1444 PP_3569
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) PP_0411 PP_5179
gnl gluconolactonase PP_2021 PP_3180
kguD 2-keto-6-phosphogluconate reductase PP_3376 PP_1261
kguK 2-ketogluconokinase PP_3378
kguT 2-ketogluconate transporter PP_3377 PP_3176
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
mglA glucose ABC transporter, ATP-binding component (MglA) PP_2759 PP_2455
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) PP_2761 PP_2456
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PP_3578 PP_5288
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
ptsS sucrose phosphotransferase enzyme EII-BCA
sacP sucrose phosphotransferase enzyme EII-BC
scrB sucrose-6-phosphate hydrolase
scrK fructokinase PP_3378
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
thuE sucrose ABC transporter, substrate-binding component ThuE
thuF sucrose ABC transporter, permease component 1 (ThuF) PP_5195
thuG sucrose ABC transporter, permease component 2 (ThuG) PP_2263 PP_5170
thuK sucrose ABC transporter, ATPase component ThuK PP_1018 PP_0411
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase PP_4715 PP_4963

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 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