GapMind for catabolism of small carbon sources

 

sucrose catabolism in Pseudomonas simiae WCS417

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 (55 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) PS417_23045 PS417_12800
gtsA glucose ABC transporter, substrate-binding component (GtsA) PS417_22145
gtsB glucose ABC transporter, permease component 1 (GtsB) PS417_22140
gtsC glucose ABC transporter, permease component 2 (GtsC) PS417_22135
gtsD glucose ABC transporter, ATPase component (GtsD) PS417_22130 PS417_12700
glk glucokinase PS417_22685
Alternative steps:
1pfk 1-phosphofructokinase PS417_03970 PS417_18385
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) PS417_16225 PS417_22135
aglG' glucose ABC transporter, permease component 2 (AglG) PS417_22135 PS417_16225
aglK sucrose ABC transporter, ATPase component AglK PS417_12700 PS417_22130
aglK' glucose ABC transporter, ATPase component (AglK) PS417_12700 PS417_22130
araS fructose ABC transporter, substrate-binding component AraS
araT fructose ABC transporter, permease component 2 (AraT)
araU fructose ABC transporter, permease component 1 (AraU) PS417_22135
araV fructose ABC transporter, ATPase component AraV PS417_12700 PS417_22130
bglF glucose PTS, enzyme II (BCA components, BglF) PS417_23050
BT1758 fructose transporter
crr glucose PTS, enzyme IIA PS417_23035 PS417_22995
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PS417_22100 PS417_00160
edd phosphogluconate dehydratase PS417_22690 PS417_26890
fba fructose 1,6-bisphosphate aldolase PS417_26415
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA PS417_13635 PS417_11890
frcB fructose ABC transporter, substrate-binding component FrcB PS417_13645 PS417_17735
frcC fructose ABC transporter, permease component FrcC PS417_13640 PS417_12060
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components PS417_03975
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components PS417_03965
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) PS417_13640 PS417_12060
fruG fructose ABC transporter, permease component 2 (FruG) PS417_17725 PS417_12060
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components PS417_03965 PS417_23035
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component PS417_04335
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components PS417_03975
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component PS417_03975
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component PS417_03975
fruK fructose ABC transporter, ATPase component FruK PS417_13635 PS417_11890
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit PS417_00265
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PS417_00270 PS417_10880
gadh3 gluconate 2-dehydrogenase subunit 3 PS417_00260
galU glucose 1-phosphate uridylyltransferase PS417_14065 PS417_01325
gdh quinoprotein glucose dehydrogenase PS417_05300 PS417_10960
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) PS417_27115 PS417_25760
gnl gluconolactonase PS417_15140 PS417_14855
kguD 2-keto-6-phosphogluconate reductase PS417_04730 PS417_12555
kguK 2-ketogluconokinase PS417_12565
kguT 2-ketogluconate transporter PS417_12560 PS417_10835
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 PS417_04925
mglA glucose ABC transporter, ATP-binding component (MglA) PS417_11890 PS417_13635
mglB glucose ABC transporter, substrate-binding component PS417_10940 PS417_11885
mglC glucose ABC transporter, permease component (MglC) PS417_10930 PS417_12060
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PS417_13395 PS417_27785
ptsG glucose PTS, enzyme IICB PS417_23000
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) PS417_23000
ptsS sucrose phosphotransferase enzyme EII-BCA PS417_23050
sacP sucrose phosphotransferase enzyme EII-BC PS417_23050
scrB sucrose-6-phosphate hydrolase
scrK fructokinase PS417_12685 PS417_12565
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) PS417_12710
thuG sucrose ABC transporter, permease component 2 (ThuG) PS417_12705 PS417_16225
thuK sucrose ABC transporter, ATPase component ThuK PS417_12700 PS417_22130
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase PS417_24000 PS417_26430

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, 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