GapMind for catabolism of small carbon sources

 

sucrose catabolism in Dinoroseobacter shibae DFL-12

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE sucrose ABC transporter, substrate-binding component AglK Dshi_1652
aglF sucrose ABC transporter, permease component 1 (AglF) Dshi_1651
aglG sucrose ABC transporter, permease component 2 (AglG) Dshi_1650 Dshi_0549
aglK sucrose ABC transporter, ATPase component AglK Dshi_1648 Dshi_1357
ams sucrose hydrolase (invertase) Dshi_1649 Dshi_3898
scrK fructokinase Dshi_2797 Dshi_1976
glk glucokinase Dshi_1655 Dshi_2001
Alternative steps:
1pfk 1-phosphofructokinase Dshi_1621 Dshi_1976
aglE' glucose ABC transporter, substrate-binding component (AglE) Dshi_1652
aglF' glucose ABC transporter, permease component 1 (AglF) Dshi_1651
aglG' glucose ABC transporter, permease component 2 (AglG) Dshi_1650 Dshi_0549
aglK' glucose ABC transporter, ATPase component (AglK) Dshi_1648 Dshi_1357
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 Dshi_2017 Dshi_3141
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 Dshi_1768 Dshi_1241
edd phosphogluconate dehydratase Dshi_1769 Dshi_0129
fba fructose 1,6-bisphosphate aldolase Dshi_2156 Dshi_1266
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA Dshi_0388 Dshi_2433
frcB fructose ABC transporter, substrate-binding component FrcB Dshi_0390
frcC fructose ABC transporter, permease component FrcC Dshi_0389 Dshi_2432
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
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) Dshi_0389
fruG fructose ABC transporter, permease component 2 (FruG) Dshi_0529
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components Dshi_2062
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component Dshi_3582
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 Dshi_2433 Dshi_0530
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit Dshi_3895
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Dshi_4060 Dshi_3784
gadh3 gluconate 2-dehydrogenase subunit 3 Dshi_3896
galU glucose 1-phosphate uridylyltransferase Dshi_3577 Dshi_4118
gdh quinoprotein glucose dehydrogenase Dshi_2294 Dshi_1523
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) Dshi_3141 Dshi_2017
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) Dshi_1246 Dshi_1650
gtsD glucose ABC transporter, ATPase component (GtsD) Dshi_1416 Dshi_1250
kguD 2-keto-6-phosphogluconate reductase Dshi_2970 Dshi_2643
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) Dshi_1998 Dshi_2433
mglB glucose ABC transporter, substrate-binding component Dshi_2000
mglC glucose ABC transporter, permease component (MglC) Dshi_1999 Dshi_2431
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Dshi_2020 Dshi_1900
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 Dshi_1824
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 Dshi_3906 Dshi_3904
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) Dshi_3143 Dshi_0548
thuG sucrose ABC transporter, permease component 2 (ThuG) Dshi_1415 Dshi_0549
thuK sucrose ABC transporter, ATPase component ThuK Dshi_0971 Dshi_1416
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase Dshi_2078 Dshi_2155

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