GapMind for catabolism of small carbon sources

 

sucrose catabolism in Alkalihalobacterium alkalinitrilicum DSM 22532

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) BK574_RS07610 BK574_RS15505
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components BK574_RS21980
1pfk 1-phosphofructokinase BK574_RS21975
fba fructose 1,6-bisphosphate aldolase BK574_RS19135 BK574_RS25200
tpi triose-phosphate isomerase BK574_RS20795 BK574_RS20790
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 BK574_RS17060 BK574_RS01510
aglK' glucose ABC transporter, ATPase component (AglK) BK574_RS17060 BK574_RS01510
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 BK574_RS17060 BK574_RS11415
bglF glucose PTS, enzyme II (BCA components, BglF) BK574_RS07620
BT1758 fructose transporter
crr glucose PTS, enzyme IIA BK574_RS22665 BK574_RS10715
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BK574_RS09410 BK574_RS15640
edd phosphogluconate dehydratase BK574_RS03330 BK574_RS05060
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA BK574_RS01730 BK574_RS00955
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC BK574_RS01735
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components BK574_RS21980
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 BK574_RS22675
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component BK574_RS21980
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component BK574_RS21980
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component BK574_RS21980
fruK fructose ABC transporter, ATPase component FruK BK574_RS01730 BK574_RS00955
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 BK574_RS19705 BK574_RS19795
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) BK574_RS17060 BK574_RS11415
glk glucokinase BK574_RS12335 BK574_RS14475
gnl gluconolactonase BK574_RS04175
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) BK574_RS17060 BK574_RS01510
kguD 2-keto-6-phosphogluconate reductase BK574_RS21120 BK574_RS21465
kguK 2-ketogluconokinase BK574_RS15635 BK574_RS02545
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) BK574_RS01730 BK574_RS00955
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) BK574_RS01735
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BK574_RS14130 BK574_RS17175
ptsG glucose PTS, enzyme IICB BK574_RS22665
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BK574_RS22665
ptsS sucrose phosphotransferase enzyme EII-BCA BK574_RS15510 BK574_RS07620
sacP sucrose phosphotransferase enzyme EII-BC BK574_RS07620 BK574_RS15510
scrB sucrose-6-phosphate hydrolase BK574_RS07610
scrK fructokinase BK574_RS07615 BK574_RS02545
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)
thuG sucrose ABC transporter, permease component 2 (ThuG)
thuK sucrose ABC transporter, ATPase component ThuK BK574_RS17060 BK574_RS01510
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 Apr 09 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