GapMind for catabolism of small carbon sources

 

D-glucose catabolism in Neiella marina J221

Best path

ptsG, crr

Rules

Overview: In most bacteria, glucose is consumed via glucose 6-phosphate, which is a central metabolic intermediate. It can also be oxidized to 2-ketogluconate in the periplasm before uptake and conversion to gluconate 6-phosphate (link). Periplasmic oxidation to gluconate, uptake, and phosphorylation by gnuK is also a potential path to gluconate-6-phosphate, but is not included in GapMind because it is not known to be the major path for glucose utilization in a prokaryote.

39 steps (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ptsG glucose PTS, enzyme IICB CBE68_RS17710 CBE68_RS17695
crr glucose PTS, enzyme IIA CBE68_RS11180 CBE68_RS17690
Alternative steps:
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) CBE68_RS16355 CBE68_RS09785
bglF glucose PTS, enzyme II (BCA components, BglF)
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CBE68_RS10100 CBE68_RS14635
edd phosphogluconate dehydratase CBE68_RS01310
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase CBE68_RS15740
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) CBE68_RS16355 CBE68_RS09785
glk glucokinase CBE68_RS03760 CBE68_RS08895
gnl gluconolactonase CBE68_RS04335 CBE68_RS16720
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) CBE68_RS16355 CBE68_RS09785
kguD 2-keto-6-phosphogluconate reductase CBE68_RS03630 CBE68_RS05435
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily CBE68_RS06295 CBE68_RS15430
mglA glucose ABC transporter, ATP-binding component (MglA) CBE68_RS02095 CBE68_RS06860
mglB glucose ABC transporter, substrate-binding component CBE68_RS02090
mglC glucose ABC transporter, permease component (MglC) CBE68_RS02100
PAST-A proton-associated sugar transporter A
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) CBE68_RS17695 CBE68_RS17710
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1

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