GapMind for catabolism of small carbon sources

 

sucrose catabolism in Megamonas funiformis YIT 11815

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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) HMPREF9454_RS03450 HMPREF9454_RS03470
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components HMPREF9454_RS08300 HMPREF9454_RS06610
1pfk 1-phosphofructokinase HMPREF9454_RS08295
fba fructose 1,6-bisphosphate aldolase HMPREF9454_RS06040 HMPREF9454_RS06615
tpi triose-phosphate isomerase HMPREF9454_RS03395 HMPREF9454_RS03400
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)
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK sucrose ABC transporter, ATPase component AglK HMPREF9454_RS05390 HMPREF9454_RS01120
aglK' glucose ABC transporter, ATPase component (AglK) HMPREF9454_RS05390 HMPREF9454_RS01120
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 HMPREF9454_RS05390 HMPREF9454_RS00035
bglF glucose PTS, enzyme II (BCA components, BglF) HMPREF9454_RS08705
BT1758 fructose transporter
crr glucose PTS, enzyme IIA HMPREF9454_RS00490 HMPREF9454_RS01155
cscB sucrose:H+ symporter CscB HMPREF9454_RS03465 HMPREF9454_RS10290
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HMPREF9454_RS07595
edd phosphogluconate dehydratase HMPREF9454_RS09720
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA
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 HMPREF9454_RS08300 HMPREF9454_RS06610
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 HMPREF9454_RS06605
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 HMPREF9454_RS09390
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component HMPREF9454_RS08300 HMPREF9454_RS06605
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component HMPREF9454_RS08300 HMPREF9454_RS06610
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component HMPREF9454_RS06610 HMPREF9454_RS08300
fruK fructose ABC transporter, ATPase component FruK
fruP fructose porter FruP HMPREF9454_RS03085 HMPREF9454_RS06625
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase HMPREF9454_RS10010 HMPREF9454_RS09960
gdh quinoprotein glucose dehydrogenase
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP HMPREF9454_RS09490 HMPREF9454_RS09235
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) HMPREF9454_RS05390 HMPREF9454_RS00035
glk glucokinase HMPREF9454_RS09110 HMPREF9454_RS10520
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) HMPREF9454_RS05390 HMPREF9454_RS01120
kguD 2-keto-6-phosphogluconate reductase HMPREF9454_RS06920 HMPREF9454_RS03270
kguK 2-ketogluconokinase HMPREF9454_RS07600
kguT 2-ketogluconate transporter HMPREF9454_RS08595
levD fructose PTS system (fructose 6-phosphate forming), EII-A component HMPREF9454_RS07880 HMPREF9454_RS08335
levDE fructose PTS system (fructose 6-phosphate forming), EII-AB component
levE fructose PTS system (fructose 6-phosphate forming), EII-B component HMPREF9454_RS07875
levF fructose PTS system (fructose 6-phosphate forming), EII-C component HMPREF9454_RS07870
levG fructose PTS system (fructose 6-phosphate forming), EII-D component HMPREF9454_RS07865 HMPREF9454_RS10755
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC HMPREF9454_RS07870
manZ glucose PTS, enzyme EIID HMPREF9454_RS07865 HMPREF9454_RS10755
MFS-glucose glucose transporter, MFS superfamily HMPREF9454_RS09490 HMPREF9454_RS09235
mglA glucose ABC transporter, ATP-binding component (MglA) HMPREF9454_RS00035
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase HMPREF9454_RS10380 HMPREF9454_RS05940
ptsG glucose PTS, enzyme IICB HMPREF9454_RS07765 HMPREF9454_RS01155
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) HMPREF9454_RS01155 HMPREF9454_RS07765
ptsS sucrose phosphotransferase enzyme EII-BCA HMPREF9454_RS08705
sacP sucrose phosphotransferase enzyme EII-BC HMPREF9454_RS05575 HMPREF9454_RS08705
scrB sucrose-6-phosphate hydrolase HMPREF9454_RS03470 HMPREF9454_RS03450
scrK fructokinase HMPREF9454_RS09110 HMPREF9454_RS07600
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter HMPREF9454_RS09235 HMPREF9454_RS09490
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)
thuK sucrose ABC transporter, ATPase component ThuK HMPREF9454_RS05390 HMPREF9454_RS01120
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