D-cellobiose catabolism in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

D-cellobiose catabolism in Ruegeria conchae TW15

Best path

Rules

Overview: MetaCyc does not list any pathways for cellobiose utilization, but the major catabolic enzymes are believed to be intracellular cellobiase, periplasmic cellobiase, cellobiose-6-phosphate hydrolase, or cellobiose phosphorylase (PMID:28535986). These pathways all lead to glucose-6-phosphate, which is a central metabolic intermediate. There also may be a 3-ketoglucoside pathway in some Bacteroidetes, but this is not characterized.

all:

bgl and glucose-utilization
or cellobiose-transport, bgl and glk
or cellobiose-transport, cbp, pgmA and glk
or cellobiose-PTS, ascB and glk
Comment: Cellobiose may be cleaved to two glucose in the periplasm (by bgl). Or, after transport, cellobiose may be cleaved in the cytoplasm and then the glucose is phosphorylated by glk. Or cellobiose is cleaved by cellobiose phosphorylase (cbp), into glucose and alpha-glucose-1-phosphate; alpha-phosphoglucomutase (pgmA) converts the glucose-1-P to glucose-6-phosphate and glucokinase converts glucose to glucose-6-phosphate. Or, after transport and phosphorylation by a PTS system, 6-phosphocellobiose hydrolase forms glucose and glucose-6-phosphate, and glucokinase converts the glucose to glucose-6-phosphate.

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

cellobiose-PTS:

bglG
or celEIIA, celEIIB and celEIIC

cellobiose-transport:

TM0031, TM0030, TM0029, TM0028 and TM0027
or cbtA, cbtB, cbtC, cbtD and cbtF
or cebE, cebF, cebG and msiK
or SMc04256, SMc04257, SMc04258 and SMc04259
or cbpB, msdB1 and msdB2
or cbpC, msdC1 and msdC2
or cdt
or bglT
Comment: Transporters and PTS systems were identified uing query: transporter:cellobiose:D-cellobiose:CPD-15976:beta-glucoside:beta-glucosides. But, some of the beta-glucoside transporters might not be cellobiose transporters. Omitted TCDB 4.A.1.2.15 = LGAS_1755 = ART98417 (see curated BLAST for PTS vs. GCF_000014425.1), "PTS 19CBA" in PMC2848229 (Francl et al 2010); this was not actually shown to be a cellobiose transporter (and, the main one in this organism is TC 4.A.1.2.14 = LGAS_1669). Omitted TM1219:TM1223, listed as a probable cellobiose porter: the SBP TM1223 is reported to bind beta,1-4-mannobiose only (PMC1392961).

73 steps (39 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
bgl	cellobiase	G7G_RS0120470	G7G_RS23700
gtsA	glucose ABC transporter, substrate-binding component (GtsA)	G7G_RS0103670	G7G_RS0117185
gtsB	glucose ABC transporter, permease component 1 (GtsB)	G7G_RS0103675	G7G_RS0117190
gtsC	glucose ABC transporter, permease component 2 (GtsC)	G7G_RS0103680	G7G_RS0117195
gtsD	glucose ABC transporter, ATPase component (GtsD)	G7G_RS0103685	G7G_RS0110555
glk	glucokinase	G7G_RS23700	G7G_RS0115580
Alternative steps:
aglE'	glucose ABC transporter, substrate-binding component (AglE)	G7G_RS0120460
aglF'	glucose ABC transporter, permease component 1 (AglF)	G7G_RS0120455
aglG'	glucose ABC transporter, permease component 2 (AglG)	G7G_RS0120450	G7G_RS0117195
aglK'	glucose ABC transporter, ATPase component (AglK)	G7G_RS0120440	G7G_RS0115470
ascB	6-phosphocellobiose hydrolase	G7G_RS0120470
bglF	glucose PTS, enzyme II (BCA components, BglF)
bglG	cellobiose PTS system, EII-BC or EII-BCA components
bglT	cellobiose transporter BglT
cbp	cellobiose phosphorylase
cbpB	cellobiose ABC transporter, substrate-binding component CpbB
cbpC	cellobiose ABC transporter, substrate-binding component CbpC
cbtA	cellobiose ABC transporter, substrate-binding component CbtA
cbtB	cellobiose ABC transporter, permease component 1 (CbtB)
cbtC	cellobiose ABC transporter, permease component 2 (CbtC)	G7G_RS0121580
cbtD	cellobiose ABC transporter, ATPase component 1 (CbtD)	G7G_RS0120955	G7G_RS0121585
cbtF	cellobiose ABC transporter, ATPase component 2 (CbtF)	G7G_RS0120960	G7G_RS0117765
cdt	cellobiose transporter cdt-1/cdt-2
cebE	cellobiose ABC transporter, substrate-binding component CebE
cebF	cellobiose ABC transporter, permease component 1 (CebF)
cebG	cellobiose ABC transporter, permease component 2 (CebG)	G7G_RS0111295
celEIIA	cellobiose PTS system, EII-A component
celEIIB	cellobiose PTS system, EII-B component
celEIIC	cellobiose PTS system, EII-C component
crr	glucose PTS, enzyme IIA
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	G7G_RS0112140	G7G_RS0100605
edd	phosphogluconate dehydratase	G7G_RS0112135	G7G_RS0117165
gadh1	gluconate 2-dehydrogenase flavoprotein subunit
gadh2	gluconate 2-dehydrogenase cytochrome c subunit	G7G_RS0100695
gadh3	gluconate 2-dehydrogenase subunit 3
gdh	quinoprotein glucose dehydrogenase	G7G_RS0107420
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)	G7G_RS0114935	G7G_RS0115525
gnl	gluconolactonase	G7G_RS0100425
kguD	2-keto-6-phosphogluconate reductase	G7G_RS0120600	G7G_RS0120345
kguK	2-ketogluconokinase	G7G_RS0119975	G7G_RS22610
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)	G7G_RS0115595	G7G_RS0100415
mglB	glucose ABC transporter, substrate-binding component	G7G_RS0115585
mglC	glucose ABC transporter, permease component (MglC)	G7G_RS0115590	G7G_RS0100410
msdB1	cellobiose ABC transporter, permease component 1 (MsdB1)	G7G_RS0115485
msdB2	cellobiose ABC transporter, permease component 2 (MsdB2)	G7G_RS0110560	G7G_RS0111295
msdC1	cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2	cellobiose ABC transporter, permease component 1 (MsdC2)	G7G_RS0120450
msiK	cellobiose ABC transporter, ATPase component	G7G_RS0111275	G7G_RS0121175
PAST-A	proton-associated sugar transporter A
pgmA	alpha-phosphoglucomutase	G7G_RS0112845	G7G_RS0105430
ptsG	glucose PTS, enzyme IICB
ptsG-crr	glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET	Sugar transporter SemiSWEET
SMc04256	cellobiose ABC transporter, ATPase component	G7G_RS0117200	G7G_RS0103685
SMc04257	cellobiose ABC transporter, permease component 1	G7G_RS0117195	G7G_RS0103680
SMc04258	cellobiose ABC transporter, permease component 2	G7G_RS0117190	G7G_RS0103675
SMc04259	cellobiose ABC transporter, substrate-binding protein	G7G_RS0117185	G7G_RS0103670
SSS-glucose	Sodium/glucose cotransporter
SWEET1	bidirectional sugar transporter SWEET1
TM0027	cellobiose ABC transporter, ATPase component 2	G7G_RS0109785	G7G_RS0111035
TM0028	cellobiose ABC transporter, ATPase component 1	G7G_RS0120955	G7G_RS0111210
TM0029	cellobiose ABC transporter, permease component 2	G7G_RS0103555	G7G_RS0120950
TM0030	cellobiose ABC transporter, permease component 1	G7G_RS0117775	G7G_RS0111025
TM0031	cellobiose ABC transporter, substrate-binding component

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

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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:

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