GapMind for catabolism of small carbon sources

 

D-glucose catabolism in Pseudomonas simiae WCS417

Best path

gtsA, gtsB, gtsC, gtsD, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA glucose ABC transporter, substrate-binding component (GtsA) PS417_22145
gtsB glucose ABC transporter, permease component 1 (GtsB) PS417_22140
gtsC glucose ABC transporter, permease component 2 (GtsC) PS417_22135
gtsD glucose ABC transporter, ATPase component (GtsD) PS417_22130 PS417_12700
glk glucokinase PS417_22685
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) PS417_22135 PS417_16225
aglK' glucose ABC transporter, ATPase component (AglK) PS417_12700 PS417_22130
bglF glucose PTS, enzyme II (BCA components, BglF) PS417_23050
crr glucose PTS, enzyme IIA PS417_23035 PS417_22995
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PS417_22100 PS417_00160
edd phosphogluconate dehydratase PS417_22690 PS417_26890
gadh1 gluconate 2-dehydrogenase flavoprotein subunit PS417_00265
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PS417_00270 PS417_10880
gadh3 gluconate 2-dehydrogenase subunit 3 PS417_00260
gdh quinoprotein glucose dehydrogenase PS417_05300 PS417_10960
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) PS417_27115 PS417_25760
gnl gluconolactonase PS417_15140 PS417_14855
kguD 2-keto-6-phosphogluconate reductase PS417_04730 PS417_12555
kguK 2-ketogluconokinase PS417_12565
kguT 2-ketogluconate transporter PS417_12560 PS417_10835
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily PS417_04925
mglA glucose ABC transporter, ATP-binding component (MglA) PS417_11890 PS417_13635
mglB glucose ABC transporter, substrate-binding component PS417_10940 PS417_11885
mglC glucose ABC transporter, permease component (MglC) PS417_10930 PS417_12060
PAST-A proton-associated sugar transporter A
ptsG glucose PTS, enzyme IICB PS417_23000
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) PS417_23000
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 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, 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