GapMind for catabolism of small carbon sources

 

sucrose catabolism in Herbaspirillum seropedicae SmR1

Best path

ams, mglA, mglB, mglC, glk

Also see fitness data for the top candidates

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 (39 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) HSERO_RS05195 HSERO_RS05250
mglB glucose ABC transporter, substrate-binding component HSERO_RS05190 HSERO_RS22460
mglC glucose ABC transporter, permease component (MglC) HSERO_RS05200 HSERO_RS05325
glk glucokinase HSERO_RS17870
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) HSERO_RS01335 HSERO_RS22745
aglG' glucose ABC transporter, permease component 2 (AglG) HSERO_RS01335 HSERO_RS22745
aglK sucrose ABC transporter, ATPase component AglK HSERO_RS22750 HSERO_RS02210
aglK' glucose ABC transporter, ATPase component (AglK) HSERO_RS01355 HSERO_RS02210
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 HSERO_RS16715 HSERO_RS22645
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 HSERO_RS05525 HSERO_RS05155
edd phosphogluconate dehydratase HSERO_RS05520 HSERO_RS16705
fba fructose 1,6-bisphosphate aldolase HSERO_RS03355
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA HSERO_RS03640 HSERO_RS05250
frcB fructose ABC transporter, substrate-binding component FrcB HSERO_RS03635 HSERO_RS05315
frcC fructose ABC transporter, permease component FrcC HSERO_RS03645 HSERO_RS05255
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
fruE fructose ABC transporter, substrate-binding component FruE
fruF fructose ABC transporter, permease component 1 (FruF) HSERO_RS05180 HSERO_RS03645
fruG fructose ABC transporter, permease component 2 (FruG) HSERO_RS05185 HSERO_RS05255
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components HSERO_RS00450
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component HSERO_RS19525
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 HSERO_RS05175 HSERO_RS03640
fruP fructose porter FruP
gadh1 gluconate 2-dehydrogenase flavoprotein subunit HSERO_RS22385 HSERO_RS16740
gadh2 gluconate 2-dehydrogenase cytochrome c subunit HSERO_RS16735 HSERO_RS22390
gadh3 gluconate 2-dehydrogenase subunit 3 HSERO_RS16745 HSERO_RS22380
galU glucose 1-phosphate uridylyltransferase HSERO_RS10830 HSERO_RS13375
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) HSERO_RS11145 HSERO_RS22750
gnl gluconolactonase HSERO_RS20090 HSERO_RS19370
gtsA glucose ABC transporter, substrate-binding component (GtsA) HSERO_RS22730
gtsB glucose ABC transporter, permease component 1 (GtsB) HSERO_RS18950 HSERO_RS01340
gtsC glucose ABC transporter, permease component 2 (GtsC) HSERO_RS01335 HSERO_RS22745
gtsD glucose ABC transporter, ATPase component (GtsD) HSERO_RS16715 HSERO_RS02210
kguD 2-keto-6-phosphogluconate reductase HSERO_RS07550 HSERO_RS08110
kguK 2-ketogluconokinase HSERO_RS07545
kguT 2-ketogluconate transporter HSERO_RS21145 HSERO_RS22270
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
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase HSERO_RS13360 HSERO_RS02355
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 HSERO_RS02180 HSERO_RS08715
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) HSERO_RS15495 HSERO_RS16725
thuG sucrose ABC transporter, permease component 2 (ThuG) HSERO_RS16730 HSERO_RS02200
thuK sucrose ABC transporter, ATPase component ThuK HSERO_RS02210 HSERO_RS16715
TMT1 heteromeric sucrose:H+ symporter, TMT1 component
TMT2 heteromeric sucrose:H+ symporter, TMT2 component
tpi triose-phosphate isomerase HSERO_RS08805 HSERO_RS03345

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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