GapMind for catabolism of small carbon sources

 

D-glucose catabolism in Cereibacter sphaeroides ATCC 17029

Best path

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

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE' glucose ABC transporter, substrate-binding component (AglE) RSPH17029_RS07685
aglF' glucose ABC transporter, permease component 1 (AglF) RSPH17029_RS07680
aglG' glucose ABC transporter, permease component 2 (AglG) RSPH17029_RS07675 RSPH17029_RS06705
aglK' glucose ABC transporter, ATPase component (AglK) RSPH17029_RS07670 RSPH17029_RS00495
glk glucokinase RSPH17029_RS07695 RSPH17029_RS00375
Alternative steps:
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase RSPH17029_RS06600 RSPH17029_RS20365
edd phosphogluconate dehydratase RSPH17029_RS06605 RSPH17029_RS18285
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit RSPH17029_RS07210
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase RSPH17029_RS06740 RSPH17029_RS17905
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) RSPH17029_RS08750 RSPH17029_RS00495
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) RSPH17029_RS20300
gtsC glucose ABC transporter, permease component 2 (GtsC) RSPH17029_RS07675
gtsD glucose ABC transporter, ATPase component (GtsD) RSPH17029_RS20290 RSPH17029_RS17190
kguD 2-keto-6-phosphogluconate reductase RSPH17029_RS15170 RSPH17029_RS05035
kguK 2-ketogluconokinase RSPH17029_RS10785
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) RSPH17029_RS14320 RSPH17029_RS14655
mglB glucose ABC transporter, substrate-binding component RSPH17029_RS14330 RSPH17029_RS17310
mglC glucose ABC transporter, permease component (MglC) RSPH17029_RS14325 RSPH17029_RS13365
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
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 Apr 10 2024. 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