GapMind for catabolism of small carbon sources

 

D-glucose catabolism in Collinsella tanakaei YIT 12063

Best path

manX, manY, manZ

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
manX glucose PTS, enzyme EIIAB HMPREF9452_RS00200 HMPREF9452_RS03890
manY glucose PTS, enzyme EIIC HMPREF9452_RS00205 HMPREF9452_RS04740
manZ glucose PTS, enzyme EIID HMPREF9452_RS00210 HMPREF9452_RS04785
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) HMPREF9452_RS09060 HMPREF9452_RS00665
bglF glucose PTS, enzyme II (BCA components, BglF) HMPREF9452_RS02295 HMPREF9452_RS07370
crr glucose PTS, enzyme IIA HMPREF9452_RS00875 HMPREF9452_RS06255
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HMPREF9452_RS03910 HMPREF9452_RS08955
edd phosphogluconate dehydratase HMPREF9452_RS05330 HMPREF9452_RS00690
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase
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) HMPREF9452_RS06235 HMPREF9452_RS09060
glk glucokinase HMPREF9452_RS05275
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)
gtsD glucose ABC transporter, ATPase component (GtsD) HMPREF9452_RS02825 HMPREF9452_RS08560
kguD 2-keto-6-phosphogluconate reductase HMPREF9452_RS05340
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) HMPREF9452_RS06110 HMPREF9452_RS08755
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
ptsG glucose PTS, enzyme IICB HMPREF9452_RS09360
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) HMPREF9452_RS09360
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