GapMind for catabolism of small carbon sources

 

sucrose catabolism in Lactobacillus delbrueckii ZN7a-9

Best path

ams, fruII-ABC, 1pfk, fba, tpi

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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) B506_RS04435 B506_RS02050
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components B506_RS06100
1pfk 1-phosphofructokinase B506_RS06105
fba fructose 1,6-bisphosphate aldolase B506_RS06860
tpi triose-phosphate isomerase B506_RS07310 B506_RS07305
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)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG sucrose ABC transporter, permease component 2 (AglG) B506_RS02095
aglG' glucose ABC transporter, permease component 2 (AglG) B506_RS02095
aglK sucrose ABC transporter, ATPase component AglK B506_RS02080 B506_RS07355
aglK' glucose ABC transporter, ATPase component (AglK) B506_RS02080 B506_RS07355
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 B506_RS02080 B506_RS07355
bglF glucose PTS, enzyme II (BCA components, BglF) B506_RS07030 B506_RS04430
BT1758 fructose transporter
crr glucose PTS, enzyme IIA B506_RS01025 B506_RS04430
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase
edd phosphogluconate dehydratase
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA B506_RS03305 B506_RS05665
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components B506_RS06100
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 B506_RS06100
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF)
fruG fructose ABC transporter, permease component 2 (FruG)
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components B506_RS02315
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component B506_RS06100
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component B506_RS06100
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component B506_RS06100
fruK fructose ABC transporter, ATPase component FruK B506_RS03305
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase B506_RS02390
gdh quinoprotein glucose dehydrogenase
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) B506_RS02095
glcU' Glucose uptake protein GlcU B506_RS00850
glcV glucose ABC transporter, ATPase component (GclV) B506_RS07355 B506_RS06405
glk glucokinase B506_RS01780 B506_RS08595
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) B506_RS02080 B506_RS06405
kguD 2-keto-6-phosphogluconate reductase B506_RS05055 B506_RS03600
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
levD fructose PTS system (fructose 6-phosphate forming), EII-A component B506_RS07695
levDE fructose PTS system (fructose 6-phosphate forming), EII-AB component B506_RS07695
levE fructose PTS system (fructose 6-phosphate forming), EII-B component B506_RS07695
levF fructose PTS system (fructose 6-phosphate forming), EII-C component B506_RS07700
levG fructose PTS system (fructose 6-phosphate forming), EII-D component B506_RS07705
manX glucose PTS, enzyme EIIAB B506_RS07695
manY glucose PTS, enzyme EIIC B506_RS07700
manZ glucose PTS, enzyme EIID B506_RS07705
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) B506_RS03305 B506_RS05665
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase B506_RS04420 B506_RS07815
ptsG glucose PTS, enzyme IICB B506_RS01010
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) B506_RS01010
ptsS sucrose phosphotransferase enzyme EII-BCA B506_RS04430 B506_RS07030
sacP sucrose phosphotransferase enzyme EII-BC B506_RS04430 B506_RS07030
scrB sucrose-6-phosphate hydrolase B506_RS04435
scrK fructokinase B506_RS08595 B506_RS02520
scrP sucrose phosphorylase B506_RS04490
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)
thuG sucrose ABC transporter, permease component 2 (ThuG) B506_RS06395 B506_RS02095
thuK sucrose ABC transporter, ATPase component ThuK B506_RS02080 B506_RS06405
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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