GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Synechococcus elongatus PCC 7942

Best path

bgl, MFS-glucose, glk

Also see fitness data for the top candidates

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase Synpcc7942_0854 Synpcc7942_0354
MFS-glucose glucose transporter, MFS superfamily
glk glucokinase Synpcc7942_0221 Synpcc7942_2111
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG' glucose ABC transporter, permease component 2 (AglG) Synpcc7942_0471
aglK' glucose ABC transporter, ATPase component (AglK) Synpcc7942_0947 Synpcc7942_0960
ascB 6-phosphocellobiose hydrolase
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) Synpcc7942_0445
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) Synpcc7942_2236 Synpcc7942_1305
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) Synpcc7942_2236 Synpcc7942_1305
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) Synpcc7942_0526
cebG cellobiose ABC transporter, permease component 2 (CebG) Synpcc7942_0471
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 Synpcc7942_0017
edd phosphogluconate dehydratase Synpcc7942_0626
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Synpcc7942_1791
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) Synpcc7942_1680 Synpcc7942_0947
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) Synpcc7942_0949 Synpcc7942_0526
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) Synpcc7942_0960 Synpcc7942_0947
kguD 2-keto-6-phosphogluconate reductase Synpcc7942_1501 Synpcc7942_1347
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mglA glucose ABC transporter, ATP-binding component (MglA) Synpcc7942_2493 Synpcc7942_0427
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) Synpcc7942_0949
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) Synpcc7942_0471 Synpcc7942_0948
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) Synpcc7942_0471
msiK cellobiose ABC transporter, ATPase component Synpcc7942_0960 Synpcc7942_0947
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Synpcc7942_0156 Synpcc7942_2132
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component Synpcc7942_0947 Synpcc7942_0960
SMc04257 cellobiose ABC transporter, permease component 1
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 Synpcc7942_1305 Synpcc7942_2236
TM0028 cellobiose ABC transporter, ATPase component 1 Synpcc7942_2236 Synpcc7942_1305
TM0029 cellobiose ABC transporter, permease component 2 Synpcc7942_0445
TM0030 cellobiose ABC transporter, permease component 1 Synpcc7942_0822
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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