D-cellobiose catabolism in Mesorhizobium ciceri biovar biserrulae WSM1271

GapMind for catabolism of small carbon sources

D-cellobiose catabolism in Mesorhizobium ciceri biovar biserrulae WSM1271

Best path

SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, glk

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 (42 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
SMc04256	cellobiose ABC transporter, ATPase component	MESCI_RS08530	MESCI_RS22115
SMc04257	cellobiose ABC transporter, permease component 1	MESCI_RS08525	MESCI_RS09320
SMc04258	cellobiose ABC transporter, permease component 2	MESCI_RS08520	MESCI_RS09325
SMc04259	cellobiose ABC transporter, substrate-binding protein	MESCI_RS08515	MESCI_RS09330
cbp	cellobiose phosphorylase
pgmA	alpha-phosphoglucomutase	MESCI_RS24750	MESCI_RS24680
glk	glucokinase	MESCI_RS26005	MESCI_RS03760
Alternative steps:
aglE'	glucose ABC transporter, substrate-binding component (AglE)	MESCI_RS01955
aglF'	glucose ABC transporter, permease component 1 (AglF)	MESCI_RS01960
aglG'	glucose ABC transporter, permease component 2 (AglG)	MESCI_RS01965	MESCI_RS08525
aglK'	glucose ABC transporter, ATPase component (AglK)	MESCI_RS01975	MESCI_RS11840
ascB	6-phosphocellobiose hydrolase	MESCI_RS11855
bgl	cellobiase
bglF	glucose PTS, enzyme II (BCA components, BglF)
bglG	cellobiose PTS system, EII-BC or EII-BCA components
bglT	cellobiose transporter BglT
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)	MESCI_RS03325
cbtC	cellobiose ABC transporter, permease component 2 (CbtC)
cbtD	cellobiose ABC transporter, ATPase component 1 (CbtD)	MESCI_RS19810	MESCI_RS19805
cbtF	cellobiose ABC transporter, ATPase component 2 (CbtF)	MESCI_RS28535	MESCI_RS01315
cdt	cellobiose transporter cdt-1/cdt-2
cebE	cellobiose ABC transporter, substrate-binding component CebE
cebF	cellobiose ABC transporter, permease component 1 (CebF)	MESCI_RS11830	MESCI_RS12495
cebG	cellobiose ABC transporter, permease component 2 (CebG)	MESCI_RS31200	MESCI_RS12490
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	MESCI_RS09545	MESCI_RS03645
edd	phosphogluconate dehydratase	MESCI_RS12090	MESCI_RS17555
gadh1	gluconate 2-dehydrogenase flavoprotein subunit	MESCI_RS20485
gadh2	gluconate 2-dehydrogenase cytochrome c subunit	MESCI_RS20490	MESCI_RS27410
gadh3	gluconate 2-dehydrogenase subunit 3	MESCI_RS20480
gdh	quinoprotein glucose dehydrogenase	MESCI_RS16065
glcS	glucose ABC transporter, substrate-binding component (GlcS)
glcT	glucose ABC transporter, permease component 1 (GlcT)
glcU	glucose ABC transporter, permease component 2 (GlcU)	MESCI_RS01965
glcU'	Glucose uptake protein GlcU
glcV	glucose ABC transporter, ATPase component (GclV)	MESCI_RS31190	MESCI_RS15170
gnl	gluconolactonase	MESCI_RS05305	MESCI_RS04855
gtsA	glucose ABC transporter, substrate-binding component (GtsA)	MESCI_RS09330	MESCI_RS08515
gtsB	glucose ABC transporter, permease component 1 (GtsB)	MESCI_RS09325	MESCI_RS08520
gtsC	glucose ABC transporter, permease component 2 (GtsC)	MESCI_RS09320	MESCI_RS08525
gtsD	glucose ABC transporter, ATPase component (GtsD)	MESCI_RS20830	MESCI_RS09315
kguD	2-keto-6-phosphogluconate reductase	MESCI_RS10265	MESCI_RS06505
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
mglA	glucose ABC transporter, ATP-binding component (MglA)	MESCI_RS29835	MESCI_RS08455
mglB	glucose ABC transporter, substrate-binding component	MESCI_RS07085	MESCI_RS29830
mglC	glucose ABC transporter, permease component (MglC)	MESCI_RS29840	MESCI_RS07090
msdB1	cellobiose ABC transporter, permease component 1 (MsdB1)	MESCI_RS12495	MESCI_RS15160
msdB2	cellobiose ABC transporter, permease component 2 (MsdB2)	MESCI_RS12490	MESCI_RS20835
msdC1	cellobiose ABC transporter, permease component 1 (MsdC1)	MESCI_RS11830	MESCI_RS07795
msdC2	cellobiose ABC transporter, permease component 1 (MsdC2)	MESCI_RS01965
msiK	cellobiose ABC transporter, ATPase component	MESCI_RS26050	MESCI_RS22115
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
TM0027	cellobiose ABC transporter, ATPase component 2	MESCI_RS03310	MESCI_RS00580
TM0028	cellobiose ABC transporter, ATPase component 1	MESCI_RS28540	MESCI_RS28535
TM0029	cellobiose ABC transporter, permease component 2	MESCI_RS17175	MESCI_RS01325
TM0030	cellobiose ABC transporter, permease component 1	MESCI_RS03325	MESCI_RS00595
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 Apr 09 2024. 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 2024 update 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