GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Rhodobacter viridis JA737

Best path

bgl, aglE', aglF', aglG', aglK', 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.

73 steps (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase C8J30_RS01960 C8J30_RS09855
aglE' glucose ABC transporter, substrate-binding component (AglE) C8J30_RS01970
aglF' glucose ABC transporter, permease component 1 (AglF) C8J30_RS01975
aglG' glucose ABC transporter, permease component 2 (AglG) C8J30_RS01980
aglK' glucose ABC transporter, ATPase component (AglK) C8J30_RS01990 C8J30_RS03245
glk glucokinase C8J30_RS01955 C8J30_RS04445
Alternative steps:
ascB 6-phosphocellobiose hydrolase C8J30_RS01960
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)
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) C8J30_RS07575 C8J30_RS07570
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) C8J30_RS07570 C8J30_RS07575
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) C8J30_RS01980
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 C8J30_RS09810
edd phosphogluconate dehydratase C8J30_RS09805 C8J30_RS14975
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) C8J30_RS08100 C8J30_RS09730
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) C8J30_RS01980
gtsD glucose ABC transporter, ATPase component (GtsD) C8J30_RS03245 C8J30_RS01990
kguD 2-keto-6-phosphogluconate reductase C8J30_RS11315 C8J30_RS06910
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) C8J30_RS04460 C8J30_RS14105
mglB glucose ABC transporter, substrate-binding component C8J30_RS04450 C8J30_RS14110
mglC glucose ABC transporter, permease component (MglC) C8J30_RS04455 C8J30_RS10880
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1)
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) C8J30_RS01980 C8J30_RS03240
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) C8J30_RS01980
msiK cellobiose ABC transporter, ATPase component C8J30_RS03245 C8J30_RS01990
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase C8J30_RS02140 C8J30_RS11560
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component C8J30_RS03245 C8J30_RS01990
SMc04257 cellobiose ABC transporter, permease component 1 C8J30_RS01980
SMc04258 cellobiose ABC transporter, permease component 2
SMc04259 cellobiose ABC transporter, substrate-binding protein
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 C8J30_RS07570 C8J30_RS08810
TM0028 cellobiose ABC transporter, ATPase component 1 C8J30_RS07570 C8J30_RS07575
TM0029 cellobiose ABC transporter, permease component 2 C8J30_RS17715
TM0030 cellobiose ABC transporter, permease component 1 C8J30_RS07560 C8J30_RS08420
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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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