GapMind for catabolism of small carbon sources

 

Definition of sucrose catabolism

As rules and steps, or see full text

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.

Steps

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

aglE: sucrose ABC transporter, substrate-binding component AglK

aglF: sucrose ABC transporter, permease component 1 (AglF)

aglG: sucrose ABC transporter, permease component 2 (AglG)

aglK: sucrose ABC transporter, ATPase component AglK

sacP: sucrose phosphotransferase enzyme EII-BC

ptsS: sucrose phosphotransferase enzyme EII-BCA

TMT1: heteromeric sucrose:H+ symporter, TMT1 component

TMT2: heteromeric sucrose:H+ symporter, TMT2 component

sut: sucrose:proton symporter SUT/SUC

SLC45A2: sucrose transporter

scrT: sucrose permease ScrT

sut1: alpha-glucoside permease Sut1

cscB: sucrose:H+ symporter CscB

SLC45A3: sucrose:H+ symporter

SLC45A4: sucrose:H+ symporter

scrB: sucrose-6-phosphate hydrolase

MFS-glucose: glucose transporter, MFS superfamily

SSS-glucose: Sodium/glucose cotransporter

glcU': Glucose uptake protein GlcU

PAST-A: proton-associated sugar transporter A

SemiSWEET: Sugar transporter SemiSWEET

SWEET1: bidirectional sugar transporter SWEET1

mglA: glucose ABC transporter, ATP-binding component (MglA)

mglB: glucose ABC transporter, substrate-binding component

mglC: glucose ABC transporter, permease component (MglC)

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)

glcS: glucose ABC transporter, substrate-binding component (GlcS)

glcT: glucose ABC transporter, permease component 1 (GlcT)

glcU: glucose ABC transporter, permease component 2 (GlcU)

glcV: glucose ABC transporter, ATPase component (GclV)

aglE': glucose ABC transporter, substrate-binding component (AglE)

aglF': glucose ABC transporter, permease component 1 (AglF)

aglG': glucose ABC transporter, permease component 2 (AglG)

aglK': glucose ABC transporter, ATPase component (AglK)

ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)

bglF: glucose PTS, enzyme II (BCA components, BglF)

ptsG: glucose PTS, enzyme IICB

crr: glucose PTS, enzyme IIA

manX: glucose PTS, enzyme EIIAB

manY: glucose PTS, enzyme EIIC

manZ: glucose PTS, enzyme EIID

gdh: quinoprotein glucose dehydrogenase

gnl: gluconolactonase

gadh1: gluconate 2-dehydrogenase flavoprotein subunit

gadh2: gluconate 2-dehydrogenase cytochrome c subunit

gadh3: gluconate 2-dehydrogenase subunit 3

kguT: 2-ketogluconate transporter

kguK: 2-ketogluconokinase

kguD: 2-keto-6-phosphogluconate reductase

edd: phosphogluconate dehydratase

eda: 2-keto-3-deoxygluconate 6-phosphate aldolase

glk: glucokinase

levD: fructose PTS system (fructose 6-phosphate forming), EII-A 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

levDE: fructose PTS system (fructose 6-phosphate forming), EII-AB component

araV: fructose ABC transporter, ATPase component AraV

araU: fructose ABC transporter, permease component 1 (AraU)

araT: fructose ABC transporter, permease component 2 (AraT)

araS: fructose ABC transporter, substrate-binding component AraS

fruE: fructose ABC transporter, substrate-binding component FruE

fruF: fructose ABC transporter, permease component 1 (FruF)

fruG: fructose ABC transporter, permease component 2 (FruG)

fruK: fructose ABC transporter, ATPase component FruK

frcA: fructose ABC transporter, ATPase component FrcA

frcB: fructose ABC transporter, substrate-binding component FrcB

frcC: fructose ABC transporter, permease component FrcC

Slc2a5: fructose:H+ symporter

ffz: fructose facilitator (uniporter)

glcP: fructose:H+ symporter GlcP

ght6: high-affinity fructose transporter ght6

STP6: sugar transport protein 6

THT2A: fructose THT2A

frt1: fructose:H+ symporter Frt1

fruP: fructose porter FruP

BT1758: fructose transporter

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

fruI: fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components

fruD: fructose-specific PTS system (fructose 1-phosphate forming), EII-A component

fruII-A: fructose-specific PTS system (fructose 1-phosphate forming), EII-A component

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

fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components

1pfk: 1-phosphofructokinase

fba: fructose 1,6-bisphosphate aldolase

tpi: triose-phosphate isomerase

scrK: fructokinase

SUS: sucrose synthase

galU: glucose 1-phosphate uridylyltransferase

pgmA: alpha-phosphoglucomutase

ams: sucrose hydrolase (invertase)

scrP: sucrose phosphorylase

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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