GapMind for catabolism of small carbon sources

 

sucrose catabolism in Escherichia coli BW25113

Best path

ams, fruA, fruB, 1pfk, fba, tpi

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 (63 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) b4239
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components b2167 b0731
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components b2169
1pfk 1-phosphofructokinase b2168 b1723
fba fructose 1,6-bisphosphate aldolase b2925 b2097
tpi triose-phosphate isomerase b3919 b2926
Alternative steps:
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) b4032
aglG' glucose ABC transporter, permease component 2 (AglG) b4032
aglK sucrose ABC transporter, ATPase component AglK b4035 b3450
aglK' glucose ABC transporter, ATPase component (AglK) b4035 b3450
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 b0262 b3450
bglF glucose PTS, enzyme II (BCA components, BglF) b3722 b2715
BT1758 fructose transporter
crr glucose PTS, enzyme IIA b2417 b0679
cscB sucrose:H+ symporter CscB b0343
eda 2-keto-3-deoxygluconate 6-phosphate aldolase b1850 b4477
edd phosphogluconate dehydratase b1851 b3771
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA b3749 b1900
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC b3750 b2148
frt1 fructose:H+ symporter Frt1 b2943 b2841
fruD fructose-specific PTS system (fructose 1-phosphate forming), EII-A component b0731
fruE fructose ABC transporter, substrate-binding component FruE b4227
fruF fructose ABC transporter, permease component 1 (FruF) b4230 b3750
fruG fructose ABC transporter, permease component 2 (FruG) b4231 b3750
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components b2416 b2829
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component b3204 b3947
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components b2167 b0731
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component b3950 b2167
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component b2167 b3949
fruK fructose ABC transporter, ATPase component FruK b4485 b3749
fruP fructose porter FruP b2801
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase b1236 b2042
gdh quinoprotein glucose dehydrogenase b0124 b0837
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP b4031 b2943
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) b0262 b4035
glk glucokinase b2388 b0394
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) b1312 b4032
gtsD glucose ABC transporter, ATPase component (GtsD) b4035 b3450
kguD 2-keto-6-phosphogluconate reductase b3553 b2913
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
levD fructose PTS system (fructose 6-phosphate forming), EII-A component b1817
levDE fructose PTS system (fructose 6-phosphate forming), EII-AB component b1817
levE fructose PTS system (fructose 6-phosphate forming), EII-B component b1817 b3133
levF fructose PTS system (fructose 6-phosphate forming), EII-C component b1818
levG fructose PTS system (fructose 6-phosphate forming), EII-D component b1819 b3140
manX glucose PTS, enzyme EIIAB b1817
manY glucose PTS, enzyme EIIC b1818
manZ glucose PTS, enzyme EIID b1819 b3140
MFS-glucose glucose transporter, MFS superfamily b2943 b2841
mglA glucose ABC transporter, ATP-binding component (MglA) b2149 b3567
mglB glucose ABC transporter, substrate-binding component b2150 b3566
mglC glucose ABC transporter, permease component (MglC) b2148 b3750
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase b0688 b2048
ptsG glucose PTS, enzyme IICB b1101 b0679
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) b0679 b1101
ptsS sucrose phosphotransferase enzyme EII-BCA b3722 b4240
sacP sucrose phosphotransferase enzyme EII-BC b4240 b3722
scrB sucrose-6-phosphate hydrolase
scrK fructokinase b0394 b1119
scrP sucrose phosphorylase b1309
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter b2943 b2841
SLC45A2 sucrose transporter
SLC45A3 sucrose:H+ symporter
SLC45A4 sucrose:H+ symporter
SSS-glucose Sodium/glucose cotransporter b3679
STP6 sugar transport protein 6 b2943
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) b1311 b3452
thuG sucrose ABC transporter, permease component 2 (ThuG) b1312 b4032
thuK sucrose ABC transporter, ATPase component ThuK b4035 b3450
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component

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