GapMind for catabolism of small carbon sources

 

sucrose catabolism in Mucilaginibacter mallensis MP1X4

Best path

ams, glcP, scrK

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) BLU33_RS21000 BLU33_RS15220
glcP fructose:H+ symporter GlcP BLU33_RS15240 BLU33_RS04945
scrK fructokinase BLU33_RS05060 BLU33_RS15235
Alternative steps:
1pfk 1-phosphofructokinase
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)
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK sucrose ABC transporter, ATPase component AglK BLU33_RS19840 BLU33_RS05275
aglK' glucose ABC transporter, ATPase component (AglK) BLU33_RS19840 BLU33_RS05275
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 BLU33_RS00530 BLU33_RS19840
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 BLU33_RS12875
edd phosphogluconate dehydratase BLU33_RS19300
fba fructose 1,6-bisphosphate aldolase BLU33_RS08550 BLU33_RS02565
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA BLU33_RS15970 BLU33_RS11360
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC
frt1 fructose:H+ symporter Frt1 BLU33_RS04860 BLU33_RS04945
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)
fruG fructose ABC transporter, permease component 2 (FruG)
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components BLU33_RS11285
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
fruP fructose porter FruP BLU33_RS11040 BLU33_RS11695
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase
gdh quinoprotein glucose dehydrogenase BLU33_RS13310
ght6 high-affinity fructose transporter ght6
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) BLU33_RS00530 BLU33_RS19840
glk glucokinase BLU33_RS02715 BLU33_RS17875
gnl gluconolactonase BLU33_RS22265 BLU33_RS17565
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) BLU33_RS19840 BLU33_RS14325
kguD 2-keto-6-phosphogluconate reductase BLU33_RS10820 BLU33_RS17605
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 BLU33_RS11275
levF fructose PTS system (fructose 6-phosphate forming), EII-C component BLU33_RS11280
levG fructose PTS system (fructose 6-phosphate forming), EII-D component BLU33_RS11280
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC BLU33_RS11280
manZ glucose PTS, enzyme EIID BLU33_RS11280
MFS-glucose glucose transporter, MFS superfamily BLU33_RS04860 BLU33_RS04945
mglA glucose ABC transporter, ATP-binding component (MglA) BLU33_RS17430 BLU33_RS14325
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BLU33_RS13775 BLU33_RS08520
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 BLU33_RS05585
Slc2a5 fructose:H+ symporter BLU33_RS04945 BLU33_RS15240
SLC45A2 sucrose transporter
SLC45A3 sucrose:H+ symporter
SLC45A4 sucrose:H+ symporter
SSS-glucose Sodium/glucose cotransporter BLU33_RS02755 BLU33_RS02975
STP6 sugar transport protein 6 BLU33_RS04860 BLU33_RS15240
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)
thuK sucrose ABC transporter, ATPase component ThuK BLU33_RS19840 BLU33_RS14325
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase BLU33_RS16125 BLU33_RS02380

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.

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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