GapMind for catabolism of small carbon sources

 

sucrose catabolism in Burkholderia phytofirmans PsJN

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 (47 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) BPHYT_RS33775
gtsA glucose ABC transporter, substrate-binding component (GtsA) BPHYT_RS00415 BPHYT_RS05025
gtsB glucose ABC transporter, permease component 1 (GtsB) BPHYT_RS05030 BPHYT_RS29185
gtsC glucose ABC transporter, permease component 2 (GtsC) BPHYT_RS05035 BPHYT_RS29180
gtsD glucose ABC transporter, ATPase component (GtsD) BPHYT_RS05040 BPHYT_RS35680
glk glucokinase BPHYT_RS05010
Alternative steps:
1pfk 1-phosphofructokinase BPHYT_RS20695
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) BPHYT_RS22780 BPHYT_RS05035
aglG' glucose ABC transporter, permease component 2 (AglG) BPHYT_RS05035 BPHYT_RS22780
aglK sucrose ABC transporter, ATPase component AglK BPHYT_RS16095 BPHYT_RS22760
aglK' glucose ABC transporter, ATPase component (AglK) BPHYT_RS16095 BPHYT_RS22760
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 BPHYT_RS32360 BPHYT_RS09400
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA BPHYT_RS02740
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BPHYT_RS16730 BPHYT_RS16945
edd phosphogluconate dehydratase BPHYT_RS16735 BPHYT_RS04815
fba fructose 1,6-bisphosphate aldolase BPHYT_RS16260 BPHYT_RS10545
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA BPHYT_RS22735 BPHYT_RS20740
frcB fructose ABC transporter, substrate-binding component FrcB BPHYT_RS22745 BPHYT_RS16065
frcC fructose ABC transporter, permease component FrcC BPHYT_RS22740 BPHYT_RS16055
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 BPHYT_RS02895
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) BPHYT_RS23880 BPHYT_RS16055
fruG fructose ABC transporter, permease component 2 (FruG) BPHYT_RS23885 BPHYT_RS16055
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components BPHYT_RS02740 BPHYT_RS02575
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component BPHYT_RS02895
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 BPHYT_RS23875 BPHYT_RS01820
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit BPHYT_RS23025 BPHYT_RS30780
gadh2 gluconate 2-dehydrogenase cytochrome c subunit BPHYT_RS23020 BPHYT_RS01060
gadh3 gluconate 2-dehydrogenase subunit 3 BPHYT_RS23030 BPHYT_RS01070
galU glucose 1-phosphate uridylyltransferase BPHYT_RS13860 BPHYT_RS31105
gdh quinoprotein glucose dehydrogenase BPHYT_RS08325
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) BPHYT_RS05035
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) BPHYT_RS24660 BPHYT_RS08805
gnl gluconolactonase BPHYT_RS06110 BPHYT_RS21245
kguD 2-keto-6-phosphogluconate reductase BPHYT_RS11290 BPHYT_RS14520
kguK 2-ketogluconokinase BPHYT_RS11300
kguT 2-ketogluconate transporter BPHYT_RS11295 BPHYT_RS10985
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) BPHYT_RS27185 BPHYT_RS20740
mglB glucose ABC transporter, substrate-binding component BPHYT_RS32820
mglC glucose ABC transporter, permease component (MglC) BPHYT_RS16055 BPHYT_RS27190
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BPHYT_RS04470 BPHYT_RS14155
ptsG glucose PTS, enzyme IICB BPHYT_RS02745
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BPHYT_RS02745
ptsS sucrose phosphotransferase enzyme EII-BCA
sacP sucrose phosphotransferase enzyme EII-BC
scrB sucrose-6-phosphate hydrolase
scrK fructokinase BPHYT_RS02045 BPHYT_RS09175
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) BPHYT_RS27975 BPHYT_RS35665
thuG sucrose ABC transporter, permease component 2 (ThuG) BPHYT_RS35660 BPHYT_RS16105
thuK sucrose ABC transporter, ATPase component ThuK BPHYT_RS16095 BPHYT_RS35680
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase BPHYT_RS06610 BPHYT_RS16270

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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