D-cellobiose catabolism in Pleomorphomonas diazotrophica R5-392

GapMind for catabolism of small carbon sources

D-cellobiose catabolism in Pleomorphomonas diazotrophica R5-392

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 (49 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
SMc04256	cellobiose ABC transporter, ATPase component	CXZ10_RS07065	CXZ10_RS05140
SMc04257	cellobiose ABC transporter, permease component 1	CXZ10_RS07070	CXZ10_RS11805
SMc04258	cellobiose ABC transporter, permease component 2	CXZ10_RS07075	CXZ10_RS11810
SMc04259	cellobiose ABC transporter, substrate-binding protein	CXZ10_RS07080	CXZ10_RS11815
cbp	cellobiose phosphorylase	CXZ10_RS12315
pgmA	alpha-phosphoglucomutase	CXZ10_RS00810	CXZ10_RS10600
glk	glucokinase	CXZ10_RS16730	CXZ10_RS13525
Alternative steps:
aglE'	glucose ABC transporter, substrate-binding component (AglE)	CXZ10_RS00685
aglF'	glucose ABC transporter, permease component 1 (AglF)	CXZ10_RS00680	CXZ10_RS13320
aglG'	glucose ABC transporter, permease component 2 (AglG)	CXZ10_RS00675	CXZ10_RS11805
aglK'	glucose ABC transporter, ATPase component (AglK)	CXZ10_RS06160	CXZ10_RS17790
ascB	6-phosphocellobiose hydrolase	CXZ10_RS08725	CXZ10_RS11820
bgl	cellobiase	CXZ10_RS13805	CXZ10_RS09770
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)	CXZ10_RS09500	CXZ10_RS09385
cbtC	cellobiose ABC transporter, permease component 2 (CbtC)	CXZ10_RS13045
cbtD	cellobiose ABC transporter, ATPase component 1 (CbtD)	CXZ10_RS17895	CXZ10_RS09510
cbtF	cellobiose ABC transporter, ATPase component 2 (CbtF)	CXZ10_RS17890	CXZ10_RS01675
cdt	cellobiose transporter cdt-1/cdt-2
cebE	cellobiose ABC transporter, substrate-binding component CebE
cebF	cellobiose ABC transporter, permease component 1 (CebF)	CXZ10_RS02435	CXZ10_RS13540
cebG	cellobiose ABC transporter, permease component 2 (CebG)	CXZ10_RS10380	CXZ10_RS13135
celEIIA	cellobiose PTS system, EII-A component
celEIIB	cellobiose PTS system, EII-B component
celEIIC	cellobiose PTS system, EII-C component	CXZ10_RS21100
crr	glucose PTS, enzyme IIA	CXZ10_RS02705	CXZ10_RS08605
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	CXZ10_RS09975
edd	phosphogluconate dehydratase	CXZ10_RS07100	CXZ10_RS08790
gadh1	gluconate 2-dehydrogenase flavoprotein subunit
gadh2	gluconate 2-dehydrogenase cytochrome c subunit
gadh3	gluconate 2-dehydrogenase subunit 3
gdh	quinoprotein glucose dehydrogenase	CXZ10_RS03410	CXZ10_RS03850
glcS	glucose ABC transporter, substrate-binding component (GlcS)
glcT	glucose ABC transporter, permease component 1 (GlcT)	CXZ10_RS11810
glcU	glucose ABC transporter, permease component 2 (GlcU)	CXZ10_RS07345
glcU'	Glucose uptake protein GlcU
glcV	glucose ABC transporter, ATPase component (GclV)	CXZ10_RS10880	CXZ10_RS12995
gnl	gluconolactonase	CXZ10_RS16410
gtsA	glucose ABC transporter, substrate-binding component (GtsA)	CXZ10_RS11815	CXZ10_RS07080
gtsB	glucose ABC transporter, permease component 1 (GtsB)	CXZ10_RS11810	CXZ10_RS07075
gtsC	glucose ABC transporter, permease component 2 (GtsC)	CXZ10_RS11805	CXZ10_RS07070
gtsD	glucose ABC transporter, ATPase component (GtsD)	CXZ10_RS13555	CXZ10_RS03855
kguD	2-keto-6-phosphogluconate reductase	CXZ10_RS16405	CXZ10_RS13995
kguK	2-ketogluconokinase	CXZ10_RS19125	CXZ10_RS08150
kguT	2-ketogluconate transporter	CXZ10_RS15815
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)	CXZ10_RS18795	CXZ10_RS07200
mglB	glucose ABC transporter, substrate-binding component	CXZ10_RS20985	CXZ10_RS04255
mglC	glucose ABC transporter, permease component (MglC)	CXZ10_RS11515	CXZ10_RS15995
msdB1	cellobiose ABC transporter, permease component 1 (MsdB1)	CXZ10_RS06145	CXZ10_RS17775
msdB2	cellobiose ABC transporter, permease component 2 (MsdB2)	CXZ10_RS19060	CXZ10_RS05150
msdC1	cellobiose ABC transporter, permease component 1 (MsdC1)	CXZ10_RS16065	CXZ10_RS04655
msdC2	cellobiose ABC transporter, permease component 1 (MsdC2)	CXZ10_RS05150	CXZ10_RS04660
msiK	cellobiose ABC transporter, ATPase component	CXZ10_RS07355	CXZ10_RS13555
PAST-A	proton-associated sugar transporter A
ptsG	glucose PTS, enzyme IICB	CXZ10_RS02710
ptsG-crr	glucose PTS, enzyme II (CBA components, PtsG)	CXZ10_RS02710
SemiSWEET	Sugar transporter SemiSWEET
SSS-glucose	Sodium/glucose cotransporter
SWEET1	bidirectional sugar transporter SWEET1
TM0027	cellobiose ABC transporter, ATPase component 2	CXZ10_RS09400	CXZ10_RS09515
TM0028	cellobiose ABC transporter, ATPase component 1	CXZ10_RS09395	CXZ10_RS09510
TM0029	cellobiose ABC transporter, permease component 2	CXZ10_RS09390	CXZ10_RS09505
TM0030	cellobiose ABC transporter, permease component 1	CXZ10_RS09385	CXZ10_RS09500
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