GapMind for catabolism of small carbon sources

 

sucrose catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) H281DRAFT_02777 H281DRAFT_06049
gtsA glucose ABC transporter, substrate-binding component (GtsA) H281DRAFT_00166 H281DRAFT_01454
gtsB glucose ABC transporter, permease component 1 (GtsB) H281DRAFT_00167 H281DRAFT_01453
gtsC glucose ABC transporter, permease component 2 (GtsC) H281DRAFT_00168 H281DRAFT_01452
gtsD glucose ABC transporter, ATPase component (GtsD) H281DRAFT_00169 H281DRAFT_03749
glk glucokinase H281DRAFT_00163
Alternative steps:
1pfk 1-phosphofructokinase
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) H281DRAFT_03232 H281DRAFT_02632
aglG' glucose ABC transporter, permease component 2 (AglG) H281DRAFT_00168 H281DRAFT_03232
aglK sucrose ABC transporter, ATPase component AglK H281DRAFT_04155 H281DRAFT_03228
aglK' glucose ABC transporter, ATPase component (AglK) H281DRAFT_04155 H281DRAFT_03228
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 H281DRAFT_01260 H281DRAFT_02040
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA H281DRAFT_01852 H281DRAFT_01977
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase H281DRAFT_04277 H281DRAFT_06295
edd phosphogluconate dehydratase H281DRAFT_04278 H281DRAFT_00127
fba fructose 1,6-bisphosphate aldolase H281DRAFT_04188 H281DRAFT_01311
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA H281DRAFT_03224 H281DRAFT_00426
frcB fructose ABC transporter, substrate-binding component FrcB H281DRAFT_03226 H281DRAFT_04150
frcC fructose ABC transporter, permease component FrcC H281DRAFT_03225 H281DRAFT_04148
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 H281DRAFT_01929
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) H281DRAFT_05271 H281DRAFT_04148
fruG fructose ABC transporter, permease component 2 (FruG) H281DRAFT_05272 H281DRAFT_00427
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components H281DRAFT_01852 H281DRAFT_01977
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component H281DRAFT_01929
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 H281DRAFT_05270 H281DRAFT_02174
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit H281DRAFT_04220 H281DRAFT_05401
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase H281DRAFT_04467 H281DRAFT_00962
gdh quinoprotein glucose dehydrogenase H281DRAFT_03298 H281DRAFT_00328
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) H281DRAFT_01452 H281DRAFT_00168
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) H281DRAFT_05887 H281DRAFT_05405
gnl gluconolactonase H281DRAFT_00300 H281DRAFT_05949
kguD 2-keto-6-phosphogluconate reductase H281DRAFT_05213 H281DRAFT_04333
kguK 2-ketogluconokinase H281DRAFT_05211
kguT 2-ketogluconate transporter H281DRAFT_05212 H281DRAFT_00211
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) H281DRAFT_02712 H281DRAFT_00426
mglB glucose ABC transporter, substrate-binding component H281DRAFT_03877 H281DRAFT_02713
mglC glucose ABC transporter, permease component (MglC) H281DRAFT_02714 H281DRAFT_04148
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase H281DRAFT_00078 H281DRAFT_04410
ptsG glucose PTS, enzyme IICB H281DRAFT_01853 H281DRAFT_01976
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) H281DRAFT_01853 H281DRAFT_01976
ptsS sucrose phosphotransferase enzyme EII-BCA
sacP sucrose phosphotransferase enzyme EII-BC
scrB sucrose-6-phosphate hydrolase
scrK fructokinase H281DRAFT_02118 H281DRAFT_00856
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) H281DRAFT_05891 H281DRAFT_03746
thuG sucrose ABC transporter, permease component 2 (ThuG) H281DRAFT_03745 H281DRAFT_05890
thuK sucrose ABC transporter, ATPase component ThuK H281DRAFT_04155 H281DRAFT_03228
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase H281DRAFT_04564 H281DRAFT_04190

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