GapMind for catabolism of small carbon sources

 

sucrose catabolism in Sinorhizobium meliloti 1021

Best path

thuE, thuF, thuG, thuK, 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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
thuE sucrose ABC transporter, substrate-binding component ThuE SM_b20325 SM_b21461
thuF sucrose ABC transporter, permease component 1 (ThuF) SM_b20326 SM_b21459
thuG sucrose ABC transporter, permease component 2 (ThuG) SM_b20327 SM_b21458
thuK sucrose ABC transporter, ATPase component ThuK SM_b20328 SMc02869
ams sucrose hydrolase (invertase) SMc03064 SMc01532
scrK fructokinase SMc02164 SMc03109
glk glucokinase SMc02835 SMc03109
Alternative steps:
1pfk 1-phosphofructokinase SMc01103
aglE sucrose ABC transporter, substrate-binding component AglK SMc03061
aglE' glucose ABC transporter, substrate-binding component (AglE) SMc03061
aglF sucrose ABC transporter, permease component 1 (AglF) SMc03062 SM_b20232
aglF' glucose ABC transporter, permease component 1 (AglF) SMc03062 SM_b20232
aglG sucrose ABC transporter, permease component 2 (AglG) SMc03063 SMc04257
aglG' glucose ABC transporter, permease component 2 (AglG) SMc03063 SMc04257
aglK sucrose ABC transporter, ATPase component AglK SMc03065 SMc04140
aglK' glucose ABC transporter, ATPase component (AglK) SMc03065 SM_b21605
araS fructose ABC transporter, substrate-binding component AraS
araT fructose ABC transporter, permease component 2 (AraT)
araU fructose ABC transporter, permease component 1 (AraU) SM_b20632
araV fructose ABC transporter, ATPase component AraV SM_b20235 SMc03065
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 SMc03153 SMc02043
edd phosphogluconate dehydratase SMc03068 SMc04045
fba fructose 1,6-bisphosphate aldolase SM_b20199 SM_b21192
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA SMc02169 SM_b20673
frcB fructose ABC transporter, substrate-binding component FrcB SMc02171
frcC fructose ABC transporter, permease component FrcC SMc02170 SMc02031
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 SM_b21345 SM_b21587
fruF fructose ABC transporter, permease component 1 (FruF) SM_b21589 SM_b21343
fruG fructose ABC transporter, permease component 2 (FruG) SM_b21590 SMc02772
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components SMc02437
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component SMc01141
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 SM_b21588 SM_b21344
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit SM_b20402 SMc00086
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase SMc04023 SM_b20960
gdh quinoprotein glucose dehydrogenase SMc00110 SMa0564
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) SM_b20419 SMc01608
gnl gluconolactonase SMa0196 SM_b20453
gtsA glucose ABC transporter, substrate-binding component (GtsA) SMc04396 SMc04259
gtsB glucose ABC transporter, permease component 1 (GtsB) SMc04395 SMc04258
gtsC glucose ABC transporter, permease component 2 (GtsC) SMc04394 SMc04257
gtsD glucose ABC transporter, ATPase component (GtsD) SM_b20661 SMc04393
kguD 2-keto-6-phosphogluconate reductase SMc01943 SMa2137
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) SM_b20894 SM_b20904
mglB glucose ABC transporter, substrate-binding component SM_b20895 SM_b20902
mglC glucose ABC transporter, permease component (MglC) SM_b20893 SM_b20903
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase SMc03925 SM_b21081
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
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase SMc01023 SMc01614

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