GapMind for catabolism of small carbon sources

 

sucrose catabolism in Dyella japonica UNC79MFTsu3.2

Best path

ams, MFS-glucose, 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) N515DRAFT_3393 N515DRAFT_3391
MFS-glucose glucose transporter, MFS superfamily N515DRAFT_1228 N515DRAFT_0382
glk glucokinase N515DRAFT_4210 N515DRAFT_0393
Alternative steps:
1pfk 1-phosphofructokinase N515DRAFT_0917 N515DRAFT_0916
aglE sucrose ABC transporter, substrate-binding component AglK
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF sucrose ABC transporter, permease component 1 (AglF) N515DRAFT_3134
aglF' glucose ABC transporter, permease component 1 (AglF) N515DRAFT_3134
aglG sucrose ABC transporter, permease component 2 (AglG) N515DRAFT_3133
aglG' glucose ABC transporter, permease component 2 (AglG) N515DRAFT_3133
aglK sucrose ABC transporter, ATPase component AglK N515DRAFT_4212 N515DRAFT_1562
aglK' glucose ABC transporter, ATPase component (AglK) N515DRAFT_4212 N515DRAFT_1562
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 N515DRAFT_4212 N515DRAFT_1562
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 N515DRAFT_3178 N515DRAFT_1232
edd phosphogluconate dehydratase N515DRAFT_3177
fba fructose 1,6-bisphosphate aldolase N515DRAFT_4284 N515DRAFT_0914
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA N515DRAFT_2413 N515DRAFT_3232
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC N515DRAFT_2414 N515DRAFT_2415
frt1 fructose:H+ symporter Frt1 N515DRAFT_1228
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) N515DRAFT_2414
fruG fructose ABC transporter, permease component 2 (FruG) N515DRAFT_2415
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components N515DRAFT_3957
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component
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 N515DRAFT_2413 N515DRAFT_3232
fruP fructose porter FruP N515DRAFT_1918 N515DRAFT_1222
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit N515DRAFT_0703 N515DRAFT_2297
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase N515DRAFT_2700 N515DRAFT_4302
gdh quinoprotein glucose dehydrogenase N515DRAFT_0461
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP N515DRAFT_0382 N515DRAFT_1228
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) N515DRAFT_4212 N515DRAFT_1562
gnl gluconolactonase N515DRAFT_1229
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) N515DRAFT_3133
gtsD glucose ABC transporter, ATPase component (GtsD) N515DRAFT_4212 N515DRAFT_1562
kguD 2-keto-6-phosphogluconate reductase N515DRAFT_0108 N515DRAFT_3581
kguK 2-ketogluconokinase N515DRAFT_0916
kguT 2-ketogluconate transporter N515DRAFT_2085
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
mglA glucose ABC transporter, ATP-binding component (MglA) N515DRAFT_3232 N515DRAFT_2413
mglB glucose ABC transporter, substrate-binding component N515DRAFT_3231
mglC glucose ABC transporter, permease component (MglC) N515DRAFT_3233 N515DRAFT_2415
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase N515DRAFT_2990 N515DRAFT_1372
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 N515DRAFT_1919 N515DRAFT_2221
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter N515DRAFT_1228 N515DRAFT_0382
SLC45A2 sucrose transporter
SLC45A3 sucrose:H+ symporter
SLC45A4 sucrose:H+ symporter
SSS-glucose Sodium/glucose cotransporter
STP6 sugar transport protein 6 N515DRAFT_1228 N515DRAFT_0382
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) N515DRAFT_3134
thuG sucrose ABC transporter, permease component 2 (ThuG) N515DRAFT_3133
thuK sucrose ABC transporter, ATPase component ThuK N515DRAFT_4212 N515DRAFT_1562
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase N515DRAFT_1376 N515DRAFT_4291

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