GapMind for catabolism of small carbon sources

 

D-glucose catabolism in Dinoroseobacter shibae DFL-12

Best path

aglE', aglF', aglG', aglK', glk

Also see fitness data for the top candidates

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE' glucose ABC transporter, substrate-binding component (AglE) Dshi_1652
aglF' glucose ABC transporter, permease component 1 (AglF) Dshi_1651
aglG' glucose ABC transporter, permease component 2 (AglG) Dshi_1650 Dshi_0549
aglK' glucose ABC transporter, ATPase component (AglK) Dshi_1648 Dshi_1357
glk glucokinase Dshi_1655 Dshi_2001
Alternative steps:
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Dshi_1768 Dshi_1241
edd phosphogluconate dehydratase Dshi_1769 Dshi_0129
gadh1 gluconate 2-dehydrogenase flavoprotein subunit Dshi_3895
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Dshi_4060 Dshi_3784
gadh3 gluconate 2-dehydrogenase subunit 3 Dshi_3896
gdh quinoprotein glucose dehydrogenase Dshi_2294 Dshi_1523
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) Dshi_3141 Dshi_2017
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) Dshi_1246 Dshi_1650
gtsD glucose ABC transporter, ATPase component (GtsD) Dshi_1416 Dshi_1250
kguD 2-keto-6-phosphogluconate reductase Dshi_2970 Dshi_2643
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
mglA glucose ABC transporter, ATP-binding component (MglA) Dshi_1998 Dshi_2433
mglB glucose ABC transporter, substrate-binding component Dshi_2000
mglC glucose ABC transporter, permease component (MglC) Dshi_1999 Dshi_2431
PAST-A proton-associated sugar transporter A
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter Dshi_3906 Dshi_3904
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 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 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