GapMind for catabolism of small carbon sources

 

sucrose catabolism in Rhodobacter viridis JA737

Best path

aglE, aglF, aglG, aglK, ams, scrK, glk

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE sucrose ABC transporter, substrate-binding component AglK C8J30_RS01970
aglF sucrose ABC transporter, permease component 1 (AglF) C8J30_RS01975
aglG sucrose ABC transporter, permease component 2 (AglG) C8J30_RS01980
aglK sucrose ABC transporter, ATPase component AglK C8J30_RS01990 C8J30_RS03245
ams sucrose hydrolase (invertase) C8J30_RS01985 C8J30_RS02110
scrK fructokinase C8J30_RS08890
glk glucokinase C8J30_RS01955 C8J30_RS04445
Alternative steps:
1pfk 1-phosphofructokinase C8J30_RS09075 C8J30_RS11270
aglE' glucose ABC transporter, substrate-binding component (AglE) C8J30_RS01970
aglF' glucose ABC transporter, permease component 1 (AglF) C8J30_RS01975
aglG' glucose ABC transporter, permease component 2 (AglG) C8J30_RS01980
aglK' glucose ABC transporter, ATPase component (AglK) C8J30_RS01990 C8J30_RS03245
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 C8J30_RS08100 C8J30_RS01990
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 C8J30_RS09810
edd phosphogluconate dehydratase C8J30_RS09805 C8J30_RS14975
fba fructose 1,6-bisphosphate aldolase C8J30_RS02175 C8J30_RS02965
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA C8J30_RS03205 C8J30_RS14105
frcB fructose ABC transporter, substrate-binding component FrcB C8J30_RS03215
frcC fructose ABC transporter, permease component FrcC C8J30_RS03210 C8J30_RS10880
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components C8J30_RS09070
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components C8J30_RS09080
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)
fruG fructose ABC transporter, permease component 2 (FruG) C8J30_RS10880
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components C8J30_RS09080 C8J30_RS06375
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components C8J30_RS09070
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component C8J30_RS09070
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component C8J30_RS09070
fruK fructose ABC transporter, ATPase component FruK C8J30_RS14105 C8J30_RS10885
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 C8J30_RS04030 C8J30_RS03860
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)
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) C8J30_RS08100 C8J30_RS09730
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) C8J30_RS01980
gtsD glucose ABC transporter, ATPase component (GtsD) C8J30_RS03245 C8J30_RS01990
kguD 2-keto-6-phosphogluconate reductase C8J30_RS11315 C8J30_RS06910
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) C8J30_RS04460 C8J30_RS14105
mglB glucose ABC transporter, substrate-binding component C8J30_RS04450 C8J30_RS14110
mglC glucose ABC transporter, permease component (MglC) C8J30_RS04455 C8J30_RS10880
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase C8J30_RS02140 C8J30_RS11560
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
thuE sucrose ABC transporter, substrate-binding component ThuE
thuF sucrose ABC transporter, permease component 1 (ThuF) C8J30_RS03235
thuG sucrose ABC transporter, permease component 2 (ThuG) C8J30_RS03240 C8J30_RS01980
thuK sucrose ABC transporter, ATPase component ThuK C8J30_RS03245 C8J30_RS01990
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase C8J30_RS01230 C8J30_RS02960

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