GapMind for catabolism of small carbon sources

 

sucrose catabolism in Rhodococcus qingshengii djl-6-2

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ams sucrose hydrolase (invertase) C1M55_RS18885
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components C1M55_RS13985
1pfk 1-phosphofructokinase C1M55_RS13990 C1M55_RS18150
fba fructose 1,6-bisphosphate aldolase C1M55_RS07165
tpi triose-phosphate isomerase C1M55_RS15105 C1M55_RS15100
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) C1M55_RS20460 C1M55_RS30220
aglG' glucose ABC transporter, permease component 2 (AglG) C1M55_RS20460 C1M55_RS30220
aglK sucrose ABC transporter, ATPase component AglK C1M55_RS20455 C1M55_RS18155
aglK' glucose ABC transporter, ATPase component (AglK) C1M55_RS20455 C1M55_RS30235
araS fructose ABC transporter, substrate-binding component AraS
araT fructose ABC transporter, permease component 2 (AraT)
araU fructose ABC transporter, permease component 1 (AraU) C1M55_RS20465
araV fructose ABC transporter, ATPase component AraV C1M55_RS18505 C1M55_RS30235
bglF glucose PTS, enzyme II (BCA components, BglF)
BT1758 fructose transporter
crr glucose PTS, enzyme IIA C1M55_RS19670
cscB sucrose:H+ symporter CscB
eda 2-keto-3-deoxygluconate 6-phosphate aldolase
edd phosphogluconate dehydratase C1M55_RS25540
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA C1M55_RS26590 C1M55_RS10275
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC C1M55_RS26585
frt1 fructose:H+ symporter Frt1
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components C1M55_RS13985
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) C1M55_RS26585
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components C1M55_RS19650 C1M55_RS14000
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component C1M55_RS13985
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component C1M55_RS13985
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component C1M55_RS13985
fruK fructose ABC transporter, ATPase component FruK
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 C1M55_RS22115 C1M55_RS06585
gdh quinoprotein glucose dehydrogenase C1M55_RS29555 C1M55_RS21725
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP C1M55_RS14300
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) C1M55_RS20455 C1M55_RS25125
glk glucokinase C1M55_RS14200 C1M55_RS17630
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) C1M55_RS30220 C1M55_RS25135
gtsD glucose ABC transporter, ATPase component (GtsD) C1M55_RS30235 C1M55_RS20455
kguD 2-keto-6-phosphogluconate reductase C1M55_RS12520 C1M55_RS01490
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter C1M55_RS00110
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 C1M55_RS14300
mglA glucose ABC transporter, ATP-binding component (MglA) C1M55_RS26590 C1M55_RS10275
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) C1M55_RS26585
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase C1M55_RS11860 C1M55_RS10455
ptsG glucose PTS, enzyme IICB C1M55_RS19660
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) C1M55_RS19660
ptsS sucrose phosphotransferase enzyme EII-BCA
sacP sucrose phosphotransferase enzyme EII-BC
scrB sucrose-6-phosphate hydrolase
scrK fructokinase C1M55_RS18150 C1M55_RS10205
scrP sucrose phosphorylase
scrT sucrose permease ScrT
SemiSWEET Sugar transporter SemiSWEET
Slc2a5 fructose:H+ symporter C1M55_RS14300
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 C1M55_RS30230
thuF sucrose ABC transporter, permease component 1 (ThuF) C1M55_RS30225 C1M55_RS20465
thuG sucrose ABC transporter, permease component 2 (ThuG) C1M55_RS20460 C1M55_RS30220
thuK sucrose ABC transporter, ATPase component ThuK C1M55_RS30235 C1M55_RS20455
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.

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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