GapMind for catabolism of small carbon sources

 

sucrose catabolism in Pseudomonas fluorescens GW456-L13

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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) PfGW456L13_3254
gtsA glucose ABC transporter, substrate-binding component (GtsA) PfGW456L13_1894
gtsB glucose ABC transporter, permease component 1 (GtsB) PfGW456L13_1895
gtsC glucose ABC transporter, permease component 2 (GtsC) PfGW456L13_1896
gtsD glucose ABC transporter, ATPase component (GtsD) PfGW456L13_1897 PfGW456L13_3039
glk glucokinase PfGW456L13_1890
Alternative steps:
1pfk 1-phosphofructokinase PfGW456L13_5074 PfGW456L13_3908
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) PfGW456L13_1896 PfGW456L13_2615
aglG' glucose ABC transporter, permease component 2 (AglG) PfGW456L13_1896 PfGW456L13_2615
aglK sucrose ABC transporter, ATPase component AglK PfGW456L13_3039 PfGW456L13_1897
aglK' glucose ABC transporter, ATPase component (AglK) PfGW456L13_3039 PfGW456L13_1897
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 PfGW456L13_3039 PfGW456L13_1897
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA PfGW456L13_4832
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PfGW456L13_1903 PfGW456L13_2127
edd phosphogluconate dehydratase PfGW456L13_1889 PfGW456L13_3725
fba fructose 1,6-bisphosphate aldolase PfGW456L13_1069
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA PfGW456L13_2121 PfGW456L13_3911
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC PfGW456L13_3910 PfGW456L13_2122
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components PfGW456L13_5073
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components PfGW456L13_5075
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) PfGW456L13_3910
fruG fructose ABC transporter, permease component 2 (FruG)
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components PfGW456L13_5075 PfGW456L13_4832
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component PfGW456L13_5016
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components PfGW456L13_5073
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component PfGW456L13_5073
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component PfGW456L13_5073
fruK fructose ABC transporter, ATPase component FruK PfGW456L13_2121 PfGW456L13_3911
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PfGW456L13_3925
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase PfGW456L13_2923 PfGW456L13_4006
gdh quinoprotein glucose dehydrogenase PfGW456L13_4805 PfGW456L13_1173
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) PfGW456L13_4204 PfGW456L13_1210
gnl gluconolactonase PfGW456L13_3314
kguD 2-keto-6-phosphogluconate reductase PfGW456L13_4945 PfGW456L13_2948
kguK 2-ketogluconokinase PfGW456L13_2950
kguT 2-ketogluconate transporter PfGW456L13_2949 PfGW456L13_2939
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) PfGW456L13_2121 PfGW456L13_3911
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) PfGW456L13_2122 PfGW456L13_3910
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PfGW456L13_3066 PfGW456L13_794
ptsG glucose PTS, enzyme IICB PfGW456L13_4833
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) PfGW456L13_4833
ptsS sucrose phosphotransferase enzyme EII-BCA
sacP sucrose phosphotransferase enzyme EII-BC
scrB sucrose-6-phosphate hydrolase
scrK fructokinase PfGW456L13_3036 PfGW456L13_2950
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) PfGW456L13_3041
thuG sucrose ABC transporter, permease component 2 (ThuG) PfGW456L13_3040 PfGW456L13_2615
thuK sucrose ABC transporter, ATPase component ThuK PfGW456L13_3039 PfGW456L13_1897
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase PfGW456L13_5091 PfGW456L13_1066

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