GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Sinorhizobium meliloti 1021

Best path

bgl, aglE', aglF', aglG', aglK', 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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase SMc03160
aglE' glucose ABC transporter, substrate-binding component (AglE) SMc03061
aglF' glucose ABC transporter, permease component 1 (AglF) SMc03062 SM_b20232
aglG' glucose ABC transporter, permease component 2 (AglG) SMc03063 SMc04257
aglK' glucose ABC transporter, ATPase component (AglK) SMc03065 SM_b21605
glk glucokinase SMc02835 SMc03109
Alternative steps:
ascB 6-phosphocellobiose hydrolase SM_b21463 SMc03160
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) SM_b21038
cbtC cellobiose ABC transporter, permease component 2 (CbtC) SM_b21198
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) SMa2081 SM_b20141
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) SM_b20111 SMa2079
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) SM_b21653 SMc02472
cebG cellobiose ABC transporter, permease component 2 (CebG) SM_b20969 SM_b20233
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 SMc03153 SMc02043
edd phosphogluconate dehydratase SMc03068 SMc04045
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit SM_b20402 SMc00086
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase SMc00110 SMa0564
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) SM_b20419 SMc01608
gnl gluconolactonase SMa0196 SM_b20453
gtsA glucose ABC transporter, substrate-binding component (GtsA) SMc04396 SMc04259
gtsB glucose ABC transporter, permease component 1 (GtsB) SMc04395 SMc04258
gtsC glucose ABC transporter, permease component 2 (GtsC) SMc04394 SMc04257
gtsD glucose ABC transporter, ATPase component (GtsD) SM_b20661 SMc04393
kguD 2-keto-6-phosphogluconate reductase SMc01943 SMa2137
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) SM_b20894 SM_b20904
mglB glucose ABC transporter, substrate-binding component SM_b20895 SM_b20902
mglC glucose ABC transporter, permease component (MglC) SM_b20893 SM_b20903
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) SM_b20326 SM_b21459
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) SMc01979 SM_b21105
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) SMc04136 SM_b20970
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) SMc04137 SM_b20632
msiK cellobiose ABC transporter, ATPase component SM_b20661 SM_b21106
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase SMc03925 SM_b21081
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component SMc04256 SM_b21605
SMc04257 cellobiose ABC transporter, permease component 1 SMc04257 SMc04394
SMc04258 cellobiose ABC transporter, permease component 2 SMc04258 SMc04395
SMc04259 cellobiose ABC transporter, substrate-binding protein SMc04259 SMc04396
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 SM_b20111 SMa1434
TM0028 cellobiose ABC transporter, ATPase component 1 SMa1371 SMa2079
TM0029 cellobiose ABC transporter, permease component 2 SMc04035 SMc02028
TM0030 cellobiose ABC transporter, permease component 1 SMa0467 SMc00787
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