GapMind for catabolism of small carbon sources

 

sucrose catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

ams, mglA, mglB, mglC, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase)
mglA glucose ABC transporter, ATP-binding component (MglA) CEV31_RS02580 CEV31_RS17305
mglB glucose ABC transporter, substrate-binding component CEV31_RS02585 CEV31_RS17260
mglC glucose ABC transporter, permease component (MglC) CEV31_RS02575 CEV31_RS09010
glk glucokinase CEV31_RS07005 CEV31_RS18970
Alternative steps:
1pfk 1-phosphofructokinase CEV31_RS20260
aglE sucrose ABC transporter, substrate-binding component AglK
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF sucrose ABC transporter, permease component 1 (AglF) CEV31_RS07180
aglF' glucose ABC transporter, permease component 1 (AglF) CEV31_RS07180
aglG sucrose ABC transporter, permease component 2 (AglG) CEV31_RS09340 CEV31_RS17420
aglG' glucose ABC transporter, permease component 2 (AglG) CEV31_RS16735 CEV31_RS14070
aglK sucrose ABC transporter, ATPase component AglK CEV31_RS15275 CEV31_RS16725
aglK' glucose ABC transporter, ATPase component (AglK) CEV31_RS15275 CEV31_RS06775
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 CEV31_RS20275 CEV31_RS17415
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA CEV31_RS13155
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CEV31_RS20745 CEV31_RS18545
edd phosphogluconate dehydratase CEV31_RS15685 CEV31_RS06110
fba fructose 1,6-bisphosphate aldolase CEV31_RS08915
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA CEV31_RS18950 CEV31_RS17305
frcB fructose ABC transporter, substrate-binding component FrcB CEV31_RS18960
frcC fructose ABC transporter, permease component FrcC CEV31_RS18955 CEV31_RS19245
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 CEV31_RS06410
fruE fructose ABC transporter, substrate-binding component FruE CEV31_RS02615
fruF fructose ABC transporter, permease component 1 (FruF) CEV31_RS02625 CEV31_RS09010
fruG fructose ABC transporter, permease component 2 (FruG) CEV31_RS02630 CEV31_RS08970
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components CEV31_RS04205
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component CEV31_RS06410
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 CEV31_RS02620 CEV31_RS18890
fruP fructose porter FruP CEV31_RS19855
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit CEV31_RS09840 CEV31_RS08410
gadh3 gluconate 2-dehydrogenase subunit 3
galU glucose 1-phosphate uridylyltransferase CEV31_RS20680
gdh quinoprotein glucose dehydrogenase CEV31_RS06685 CEV31_RS03435
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) CEV31_RS14655 CEV31_RS17415
gnl gluconolactonase CEV31_RS19470 CEV31_RS14210
gtsA glucose ABC transporter, substrate-binding component (GtsA) CEV31_RS09330
gtsB glucose ABC transporter, permease component 1 (GtsB) CEV31_RS09335 CEV31_RS14435
gtsC glucose ABC transporter, permease component 2 (GtsC) CEV31_RS09340 CEV31_RS07125
gtsD glucose ABC transporter, ATPase component (GtsD) CEV31_RS09345 CEV31_RS17415
kguD 2-keto-6-phosphogluconate reductase CEV31_RS03240 CEV31_RS05585
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
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 CEV31_RS19855
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase CEV31_RS05910 CEV31_RS03255
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 CEV31_RS06180 CEV31_RS18970
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) CEV31_RS14435 CEV31_RS16740
thuG sucrose ABC transporter, permease component 2 (ThuG) CEV31_RS14430 CEV31_RS17420
thuK sucrose ABC transporter, ATPase component ThuK CEV31_RS15275 CEV31_RS17415
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase CEV31_RS12005 CEV31_RS08925

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