GapMind for catabolism of small carbon sources

 

D-glucose catabolism in Thioclava dalianensis DLFJ1-1

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE' glucose ABC transporter, substrate-binding component (AglE) DL1_RS08730
aglF' glucose ABC transporter, permease component 1 (AglF) DL1_RS08735
aglG' glucose ABC transporter, permease component 2 (AglG) DL1_RS08740 DL1_RS05835
aglK' glucose ABC transporter, ATPase component (AglK) DL1_RS08750 DL1_RS04020
glk glucokinase DL1_RS08715 DL1_RS03520
Alternative steps:
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase DL1_RS12885 DL1_RS05975
edd phosphogluconate dehydratase DL1_RS12880 DL1_RS11965
gadh1 gluconate 2-dehydrogenase flavoprotein subunit DL1_RS19555
gadh2 gluconate 2-dehydrogenase cytochrome c subunit DL1_RS19560 DL1_RS20615
gadh3 gluconate 2-dehydrogenase subunit 3 DL1_RS19550
gdh quinoprotein glucose dehydrogenase DL1_RS02300 DL1_RS06520
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) DL1_RS08740
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) DL1_RS14385 DL1_RS02775
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) DL1_RS05845
gtsB glucose ABC transporter, permease component 1 (GtsB) DL1_RS05840 DL1_RS05995
gtsC glucose ABC transporter, permease component 2 (GtsC) DL1_RS05835 DL1_RS05990
gtsD glucose ABC transporter, ATPase component (GtsD) DL1_RS14385 DL1_RS05830
kguD 2-keto-6-phosphogluconate reductase DL1_RS07935 DL1_RS07735
kguK 2-ketogluconokinase DL1_RS12510
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) DL1_RS09090 DL1_RS17670
mglB glucose ABC transporter, substrate-binding component DL1_RS03525 DL1_RS09085
mglC glucose ABC transporter, permease component (MglC) DL1_RS03530 DL1_RS09095
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 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