GapMind for catabolism of small carbon sources

 

sucrose catabolism in Acidovorax sp. GW101-3H11

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase)
gtsA glucose ABC transporter, substrate-binding component (GtsA) Ac3H11_2062
gtsB glucose ABC transporter, permease component 1 (GtsB) Ac3H11_2064
gtsC glucose ABC transporter, permease component 2 (GtsC) Ac3H11_2065
gtsD glucose ABC transporter, ATPase component (GtsD) Ac3H11_2066 Ac3H11_4785
glk glucokinase Ac3H11_2067 Ac3H11_2882
Alternative steps:
1pfk 1-phosphofructokinase Ac3H11_779
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) Ac3H11_2065 Ac3H11_794
aglG' glucose ABC transporter, permease component 2 (AglG) Ac3H11_2065
aglK sucrose ABC transporter, ATPase component AglK Ac3H11_2941 Ac3H11_4785
aglK' glucose ABC transporter, ATPase component (AglK) Ac3H11_2941 Ac3H11_2066
araS fructose ABC transporter, substrate-binding component AraS
araT fructose ABC transporter, permease component 2 (AraT)
araU fructose ABC transporter, permease component 1 (AraU) Ac3H11_2065
araV fructose ABC transporter, ATPase component AraV Ac3H11_4785 Ac3H11_2941
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 Ac3H11_2083 Ac3H11_601
edd phosphogluconate dehydratase Ac3H11_2082 Ac3H11_954
fba fructose 1,6-bisphosphate aldolase Ac3H11_658
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA Ac3H11_3037 Ac3H11_607
frcB fructose ABC transporter, substrate-binding component FrcB Ac3H11_3035 Ac3H11_2879
frcC fructose ABC transporter, permease component FrcC Ac3H11_3036 Ac3H11_1841
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
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) Ac3H11_1841 Ac3H11_606
fruG fructose ABC transporter, permease component 2 (FruG) Ac3H11_605 Ac3H11_2880
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components Ac3H11_2115
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
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 Ac3H11_607 Ac3H11_609
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Ac3H11_2872 Ac3H11_3427
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase Ac3H11_3541 Ac3H11_1882
gdh quinoprotein glucose dehydrogenase Ac3H11_2201
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) Ac3H11_2065
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) Ac3H11_2066 Ac3H11_4785
gnl gluconolactonase Ac3H11_615 Ac3H11_2081
kguD 2-keto-6-phosphogluconate reductase Ac3H11_2599 Ac3H11_2341
kguK 2-ketogluconokinase Ac3H11_700
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) Ac3H11_609 Ac3H11_2881
mglB glucose ABC transporter, substrate-binding component Ac3H11_610
mglC glucose ABC transporter, permease component (MglC) Ac3H11_608 Ac3H11_1841
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Ac3H11_2215 Ac3H11_444
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
scrK fructokinase Ac3H11_3034 Ac3H11_2936
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET Ac3H11_671
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) Ac3H11_793 Ac3H11_2943
thuG sucrose ABC transporter, permease component 2 (ThuG) Ac3H11_794 Ac3H11_2942
thuK sucrose ABC transporter, ATPase component ThuK Ac3H11_2941 Ac3H11_4785
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase Ac3H11_1454 Ac3H11_4404

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