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 (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