GapMind for catabolism of small carbon sources

 

sucrose catabolism in Cereibacter sphaeroides ATCC 17029

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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE sucrose ABC transporter, substrate-binding component AglK RSPH17029_RS07685
aglF sucrose ABC transporter, permease component 1 (AglF) RSPH17029_RS07680
aglG sucrose ABC transporter, permease component 2 (AglG) RSPH17029_RS07675 RSPH17029_RS06705
aglK sucrose ABC transporter, ATPase component AglK RSPH17029_RS07670 RSPH17029_RS20290
ams sucrose hydrolase (invertase) RSPH17029_RS00200 RSPH17029_RS13100
scrK fructokinase RSPH17029_RS04740 RSPH17029_RS00375
glk glucokinase RSPH17029_RS07695 RSPH17029_RS00375
Alternative steps:
1pfk 1-phosphofructokinase RSPH17029_RS02210 RSPH17029_RS05145
aglE' glucose ABC transporter, substrate-binding component (AglE) RSPH17029_RS07685
aglF' glucose ABC transporter, permease component 1 (AglF) RSPH17029_RS07680
aglG' glucose ABC transporter, permease component 2 (AglG) RSPH17029_RS07675 RSPH17029_RS06705
aglK' glucose ABC transporter, ATPase component (AglK) RSPH17029_RS07670 RSPH17029_RS00495
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 RSPH17029_RS10060 RSPH17029_RS17190
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 RSPH17029_RS06600 RSPH17029_RS20365
edd phosphogluconate dehydratase RSPH17029_RS06605 RSPH17029_RS18285
fba fructose 1,6-bisphosphate aldolase RSPH17029_RS20210 RSPH17029_RS14840
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA RSPH17029_RS13360 RSPH17029_RS14655
frcB fructose ABC transporter, substrate-binding component FrcB RSPH17029_RS13370 RSPH17029_RS17240
frcC fructose ABC transporter, permease component FrcC RSPH17029_RS13365 RSPH17029_RS17250
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components RSPH17029_RS02215
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 RSPH17029_RS14215
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) RSPH17029_RS17250 RSPH17029_RS13365
fruG fructose ABC transporter, permease component 2 (FruG) RSPH17029_RS14660 RSPH17029_RS17250
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components RSPH17029_RS02205 RSPH17029_RS02530
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component RSPH17029_RS14215
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components RSPH17029_RS02215
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component RSPH17029_RS02215
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component RSPH17029_RS02215
fruK fructose ABC transporter, ATPase component FruK RSPH17029_RS17460 RSPH17029_RS14655
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit RSPH17029_RS07210
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase RSPH17029_RS14220 RSPH17029_RS06210
gdh quinoprotein glucose dehydrogenase RSPH17029_RS06740 RSPH17029_RS17905
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) RSPH17029_RS08750 RSPH17029_RS00495
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) RSPH17029_RS20300
gtsC glucose ABC transporter, permease component 2 (GtsC) RSPH17029_RS07675
gtsD glucose ABC transporter, ATPase component (GtsD) RSPH17029_RS20290 RSPH17029_RS17190
kguD 2-keto-6-phosphogluconate reductase RSPH17029_RS15170 RSPH17029_RS05035
kguK 2-ketogluconokinase RSPH17029_RS10785
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) RSPH17029_RS14320 RSPH17029_RS14655
mglB glucose ABC transporter, substrate-binding component RSPH17029_RS14330 RSPH17029_RS17310
mglC glucose ABC transporter, permease component (MglC) RSPH17029_RS14325 RSPH17029_RS13365
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase RSPH17029_RS07735 RSPH17029_RS12575
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) RSPH17029_RS17170 RSPH17029_RS00485
thuG sucrose ABC transporter, permease component 2 (ThuG) RSPH17029_RS17165 RSPH17029_RS08745
thuK sucrose ABC transporter, ATPase component ThuK RSPH17029_RS08750 RSPH17029_RS20290
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase RSPH17029_RS03035 RSPH17029_RS05860

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 Apr 10 2024. 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