GapMind for catabolism of small carbon sources

 

sucrose catabolism in Phaeobacter inhibens BS107

Best path

aglE, aglF, aglG, aglK, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE sucrose ABC transporter, substrate-binding component AglK PGA1_c07860
aglF sucrose ABC transporter, permease component 1 (AglF) PGA1_c07870 PGA1_c07410
aglG sucrose ABC transporter, permease component 2 (AglG) PGA1_c07880 PGA1_c19480
aglK sucrose ABC transporter, ATPase component AglK PGA1_c07900 PGA1_c16680
ams sucrose hydrolase (invertase) PGA1_c07890
scrK fructokinase PGA1_c28020
glk glucokinase PGA1_c05420 PGA1_262p00420
Alternative steps:
1pfk 1-phosphofructokinase
aglE' glucose ABC transporter, substrate-binding component (AglE) PGA1_c07860
aglF' glucose ABC transporter, permease component 1 (AglF) PGA1_c07870
aglG' glucose ABC transporter, permease component 2 (AglG) PGA1_c07880 PGA1_78p00180
aglK' glucose ABC transporter, ATPase component (AglK) PGA1_c07900 PGA1_c16680
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 PGA1_c02740 PGA1_c07900
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 PGA1_c28010 PGA1_c07350
edd phosphogluconate dehydratase PGA1_c28000 PGA1_c07380
fba fructose 1,6-bisphosphate aldolase PGA1_c23910 PGA1_c07220
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA PGA1_c28040 PGA1_c23060
frcB fructose ABC transporter, substrate-binding component FrcB PGA1_c28060
frcC fructose ABC transporter, permease component FrcC PGA1_c28050 PGA1_c23080
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 PGA1_c35960
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) PGA1_c23080 PGA1_c07310
fruG fructose ABC transporter, permease component 2 (FruG)
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components PGA1_c23500
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component PGA1_c35960
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 PGA1_c23060 PGA1_c03960
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase PGA1_c34480 PGA1_65p00220
gdh quinoprotein glucose dehydrogenase PGA1_c15880
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) PGA1_c02740 PGA1_c27320
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) PGA1_c19500 PGA1_78p00160
gtsB glucose ABC transporter, permease component 1 (GtsB) PGA1_c19490 PGA1_78p00170
gtsC glucose ABC transporter, permease component 2 (GtsC) PGA1_c19480 PGA1_78p00180
gtsD glucose ABC transporter, ATPase component (GtsD) PGA1_c19470 PGA1_c16680
kguD 2-keto-6-phosphogluconate reductase PGA1_c28260 PGA1_c24680
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
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) PGA1_262p00450 PGA1_c23060
mglB glucose ABC transporter, substrate-binding component PGA1_262p00430
mglC glucose ABC transporter, permease component (MglC) PGA1_262p00440 PGA1_c28050
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PGA1_c24340 PGA1_c06550
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
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) PGA1_c16700 PGA1_c07410
thuG sucrose ABC transporter, permease component 2 (ThuG) PGA1_c27350 PGA1_c16690
thuK sucrose ABC transporter, ATPase component ThuK PGA1_c13180 PGA1_c16680
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase PGA1_c20650 PGA1_c17530

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