GapMind for catabolism of small carbon sources

 

sucrose catabolism in Klebsiella michiganensis M5al

Best path

ams, fruA, fruB, 1pfk, fba, tpi

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 (67 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) BWI76_RS07310 BWI76_RS23410
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components BWI76_RS19725 BWI76_RS24865
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components BWI76_RS19735
1pfk 1-phosphofructokinase BWI76_RS19730 BWI76_RS24860
fba fructose 1,6-bisphosphate aldolase BWI76_RS23975 BWI76_RS19370
tpi triose-phosphate isomerase BWI76_RS27465 BWI76_RS23980
Alternative steps:
aglE sucrose ABC transporter, substrate-binding component AglK
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF sucrose ABC transporter, permease component 1 (AglF) BWI76_RS03135
aglF' glucose ABC transporter, permease component 1 (AglF) BWI76_RS03135
aglG sucrose ABC transporter, permease component 2 (AglG) BWI76_RS17835 BWI76_RS06705
aglG' glucose ABC transporter, permease component 2 (AglG) BWI76_RS01820
aglK sucrose ABC transporter, ATPase component AglK BWI76_RS01840 BWI76_RS06690
aglK' glucose ABC transporter, ATPase component (AglK) BWI76_RS01840 BWI76_RS06690
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 BWI76_RS06035 BWI76_RS03270
bglF glucose PTS, enzyme II (BCA components, BglF) BWI76_RS19555 BWI76_RS07290
BT1758 fructose transporter
crr glucose PTS, enzyme IIA BWI76_RS20655 BWI76_RS08220
cscB sucrose:H+ symporter CscB BWI76_RS23415 BWI76_RS00610
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BWI76_RS18095 BWI76_RS27940
edd phosphogluconate dehydratase BWI76_RS18100 BWI76_RS00975
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA BWI76_RS14860 BWI76_RS00275
frcB fructose ABC transporter, substrate-binding component FrcB BWI76_RS14855 BWI76_RS07665
frcC fructose ABC transporter, permease component FrcC BWI76_RS14865 BWI76_RS00280
frt1 fructose:H+ symporter Frt1 BWI76_RS03110 BWI76_RS24055
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) BWI76_RS02805 BWI76_RS00280
fruG fructose ABC transporter, permease component 2 (FruG) BWI76_RS02810 BWI76_RS14865
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components BWI76_RS20650 BWI76_RS23270
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component BWI76_RS25275 BWI76_RS10675
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components BWI76_RS24865 BWI76_RS19725
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component BWI76_RS24865 BWI76_RS10665
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component BWI76_RS19725 BWI76_RS27570
fruK fructose ABC transporter, ATPase component FruK BWI76_RS02800 BWI76_RS07240
fruP fructose porter FruP BWI76_RS22920 BWI76_RS23685
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase BWI76_RS17270 BWI76_RS19105
gdh quinoprotein glucose dehydrogenase BWI76_RS04950 BWI76_RS13270
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP BWI76_RS21205 BWI76_RS10225
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) BWI76_RS09465 BWI76_RS06035
glk glucokinase BWI76_RS20510 BWI76_RS22415
gnl gluconolactonase BWI76_RS23720 BWI76_RS21470
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) BWI76_RS23380
gtsC glucose ABC transporter, permease component 2 (GtsC) BWI76_RS17835 BWI76_RS06705
gtsD glucose ABC transporter, ATPase component (GtsD) BWI76_RS03270 BWI76_RS06690
kguD 2-keto-6-phosphogluconate reductase BWI76_RS26960 BWI76_RS27925
kguK 2-ketogluconokinase BWI76_RS26950 BWI76_RS07325
kguT 2-ketogluconate transporter BWI76_RS26955 BWI76_RS06145
levD fructose PTS system (fructose 6-phosphate forming), EII-A component BWI76_RS17890
levDE fructose PTS system (fructose 6-phosphate forming), EII-AB component BWI76_RS17890
levE fructose PTS system (fructose 6-phosphate forming), EII-B component BWI76_RS17890 BWI76_RS01735
levF fructose PTS system (fructose 6-phosphate forming), EII-C component BWI76_RS17895 BWI76_RS01730
levG fructose PTS system (fructose 6-phosphate forming), EII-D component BWI76_RS17900 BWI76_RS01725
manX glucose PTS, enzyme EIIAB BWI76_RS17890 BWI76_RS01735
manY glucose PTS, enzyme EIIC BWI76_RS17895 BWI76_RS01730
manZ glucose PTS, enzyme EIID BWI76_RS17900 BWI76_RS01725
MFS-glucose glucose transporter, MFS superfamily BWI76_RS24055 BWI76_RS17580
mglA glucose ABC transporter, ATP-binding component (MglA) BWI76_RS19640 BWI76_RS07240
mglB glucose ABC transporter, substrate-binding component BWI76_RS19645 BWI76_RS27030
mglC glucose ABC transporter, permease component (MglC) BWI76_RS19635 BWI76_RS14865
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BWI76_RS08290 BWI76_RS25130
ptsG glucose PTS, enzyme IICB BWI76_RS11130 BWI76_RS08220
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BWI76_RS11130 BWI76_RS08220
ptsS sucrose phosphotransferase enzyme EII-BCA BWI76_RS07315 BWI76_RS19555
sacP sucrose phosphotransferase enzyme EII-BC BWI76_RS07315 BWI76_RS02965
scrB sucrose-6-phosphate hydrolase BWI76_RS07310 BWI76_RS23410
scrK fructokinase BWI76_RS07325 BWI76_RS14875
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter BWI76_RS24055 BWI76_RS17580
SLC45A2 sucrose transporter
SLC45A3 sucrose:H+ symporter
SLC45A4 sucrose:H+ symporter
SSS-glucose Sodium/glucose cotransporter
STP6 sugar transport protein 6 BWI76_RS24055 BWI76_RS03110
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) BWI76_RS17840 BWI76_RS23380
thuG sucrose ABC transporter, permease component 2 (ThuG) BWI76_RS03240 BWI76_RS17835
thuK sucrose ABC transporter, ATPase component ThuK BWI76_RS01840 BWI76_RS03270
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component

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