GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Pseudomonas putida KT2440

Best path

bgl, gtsA, gtsB, gtsC, gtsD, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase PP_1403
gtsA glucose ABC transporter, substrate-binding component (GtsA) PP_1015
gtsB glucose ABC transporter, permease component 1 (GtsB) PP_1016
gtsC glucose ABC transporter, permease component 2 (GtsC) PP_1017
gtsD glucose ABC transporter, ATPase component (GtsD) PP_1018 PP_0411
glk glucokinase PP_1011
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) PP_1017 PP_2263
aglK' glucose ABC transporter, ATPase component (AglK) PP_1018 PP_5179
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) PP_3221
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) PP_0879 PP_0878
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) PP_0878 PP_4453
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)
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 PP_1024
edd phosphogluconate dehydratase PP_1010 PP_5128
gadh1 gluconate 2-dehydrogenase flavoprotein subunit PP_3383
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PP_3382 PP_3623
gadh3 gluconate 2-dehydrogenase subunit 3 PP_3384
gdh quinoprotein glucose dehydrogenase PP_1444 PP_3569
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) PP_0411 PP_5179
gnl gluconolactonase PP_2021 PP_3180
kguD 2-keto-6-phosphogluconate reductase PP_3376 PP_1261
kguK 2-ketogluconokinase PP_3378
kguT 2-ketogluconate transporter PP_3377 PP_3176
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) PP_2759 PP_2455
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) PP_2761 PP_2456
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1)
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) PP_1017
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2)
msiK cellobiose ABC transporter, ATPase component PP_1018 PP_1484
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PP_3578 PP_5288
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component PP_1018 PP_0411
SMc04257 cellobiose ABC transporter, permease component 1 PP_1017
SMc04258 cellobiose ABC transporter, permease component 2 PP_1016
SMc04259 cellobiose ABC transporter, substrate-binding protein PP_1015
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 PP_4150 PP_0878
TM0028 cellobiose ABC transporter, ATPase component 1 PP_0878 PP_0879
TM0029 cellobiose ABC transporter, permease component 2 PP_4454
TM0030 cellobiose ABC transporter, permease component 1 PP_0881 PP_4455
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