D-glucose catabolism in Rhizobium grahamii CCGE 502

GapMind for catabolism of small carbon sources

D-glucose catabolism in Rhizobium grahamii CCGE 502

Best path

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.

all: glucose-utilization
glucose-utilization:

glucose-transport and glk
or glucose-PTS
or gdh, gnl, gadh1, gadh2, gadh3, kguT, kguK, kguD, edd and eda
Comment: Glucose can be taken up and then phosphorylated to glucose 6-phosphate by the kinase glk. Or, both uptake and phosphorylation are catalyzed by a PTS system. Or, glucose is oxidized to glucono-1,5-lactone in the periplasm (by gdh), hydrolyzed to gluconate (by gnl), oxidized to 2-ketogluconate (by gadh123), taken up by kguT, phosphorylated to 2-dehydro-6-phosphogluconate (by kguK), reduced to gluconate 6-phosphate (by kguD), dehydrated by edd to 2-dehydro-3-deoxy-gluconate 6-phosphate, and cleaved by aldolase eda to pyruvate and D-glyceraldehyde 3-phosphate.

glucose-PTS:

ptsG-crr
or bglF
or ptsG and crr
or manX, manY and manZ

glucose-transport:

MFS-glucose
or SSS-glucose
or glcU'
or PAST-A
or SemiSWEET
or SWEET1
or mglA, mglB and mglC
or gtsA, gtsB, gtsC and gtsD
or glcS, glcT, glcU and glcV
or aglE', aglF', aglG' and aglK'
Comment: Transporters and PTS systems were analyzed uzing query: transporter:glucose:D-glucose:D-glucopyranose:ALPHA-GLUCOSE:GLC:CPD-15374

39 steps (22 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
aglE'	glucose ABC transporter, substrate-binding component (AglE)	RGCCGE502_RS03550
aglF'	glucose ABC transporter, permease component 1 (AglF)	RGCCGE502_RS03555	RGCCGE502_RS33570
aglG'	glucose ABC transporter, permease component 2 (AglG)	RGCCGE502_RS03560	RGCCGE502_RS11200
aglK'	glucose ABC transporter, ATPase component (AglK)	RGCCGE502_RS03570	RGCCGE502_RS00770
glk	glucokinase	RGCCGE502_RS01160	RGCCGE502_RS24705
Alternative steps:
bglF	glucose PTS, enzyme II (BCA components, BglF)
crr	glucose PTS, enzyme IIA
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	RGCCGE502_RS25095	RGCCGE502_RS04210
edd	phosphogluconate dehydratase	RGCCGE502_RS03580	RGCCGE502_RS05625
gadh1	gluconate 2-dehydrogenase flavoprotein subunit
gadh2	gluconate 2-dehydrogenase cytochrome c subunit	RGCCGE502_RS25475	RGCCGE502_RS05735
gadh3	gluconate 2-dehydrogenase subunit 3
gdh	quinoprotein glucose dehydrogenase	RGCCGE502_RS05815	RGCCGE502_RS13235
glcS	glucose ABC transporter, substrate-binding component (GlcS)
glcT	glucose ABC transporter, permease component 1 (GlcT)
glcU	glucose ABC transporter, permease component 2 (GlcU)	RGCCGE502_RS29355	RGCCGE502_RS03560
glcU'	Glucose uptake protein GlcU
glcV	glucose ABC transporter, ATPase component (GclV)	RGCCGE502_RS01685	RGCCGE502_RS29365
gnl	gluconolactonase	RGCCGE502_RS24660
gtsA	glucose ABC transporter, substrate-binding component (GtsA)	RGCCGE502_RS11765	RGCCGE502_RS11210
gtsB	glucose ABC transporter, permease component 1 (GtsB)	RGCCGE502_RS11760	RGCCGE502_RS11205
gtsC	glucose ABC transporter, permease component 2 (GtsC)	RGCCGE502_RS11755	RGCCGE502_RS11200
gtsD	glucose ABC transporter, ATPase component (GtsD)	RGCCGE502_RS11750	RGCCGE502_RS01685
kguD	2-keto-6-phosphogluconate reductase	RGCCGE502_RS14500	RGCCGE502_RS26155
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	RGCCGE502_RS12300
mglA	glucose ABC transporter, ATP-binding component (MglA)	RGCCGE502_RS14015	RGCCGE502_RS14060
mglB	glucose ABC transporter, substrate-binding component	RGCCGE502_RS14020	RGCCGE502_RS14050
mglC	glucose ABC transporter, permease component (MglC)	RGCCGE502_RS14010	RGCCGE502_RS14055
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	RGCCGE502_RS17420
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources