GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3261 Pf1N1B4_3419
gtsA glucose ABC transporter, substrate-binding component (GtsA) Pf1N1B4_596
gtsB glucose ABC transporter, permease component 1 (GtsB) Pf1N1B4_595
gtsC glucose ABC transporter, permease component 2 (GtsC) Pf1N1B4_594 Pf1N1B4_5114
gtsD glucose ABC transporter, ATPase component (GtsD) Pf1N1B4_593 Pf1N1B4_5115
glk glucokinase Pf1N1B4_600
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) Pf1N1B4_4011 Pf1N1B4_594
aglK' glucose ABC transporter, ATPase component (AglK) Pf1N1B4_4847 Pf1N1B4_5115
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)
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) Pf1N1B4_5104 Pf1N1B4_1127
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) Pf1N1B4_1127 Pf1N1B4_5105
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) Pf1N1B4_5114 Pf1N1B4_594
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 Pf1N1B4_833
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf1N1B4_587 Pf1N1B4_399
edd phosphogluconate dehydratase Pf1N1B4_601 Pf1N1B4_2303
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Pf1N1B4_821 Pf1N1B4_5582
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) Pf1N1B4_594
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) Pf1N1B4_2538 Pf1N1B4_4352
gnl gluconolactonase Pf1N1B4_4626 Pf1N1B4_4510
kguD 2-keto-6-phosphogluconate reductase Pf1N1B4_1004 Pf1N1B4_4763
kguK 2-ketogluconokinase Pf1N1B4_4765
kguT 2-ketogluconate transporter Pf1N1B4_4764 Pf1N1B4_5000
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) Pf1N1B4_4286 Pf1N1B4_410
mglB glucose ABC transporter, substrate-binding component Pf1N1B4_4386
mglC glucose ABC transporter, permease component (MglC) Pf1N1B4_4287 Pf1N1B4_409
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) Pf1N1B4_5113
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) Pf1N1B4_5114
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2)
msiK cellobiose ABC transporter, ATPase component Pf1N1B4_593 Pf1N1B4_4847
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Pf1N1B4_4886 Pf1N1B4_2122
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component Pf1N1B4_593 Pf1N1B4_4847
SMc04257 cellobiose ABC transporter, permease component 1 Pf1N1B4_594
SMc04258 cellobiose ABC transporter, permease component 2 Pf1N1B4_595
SMc04259 cellobiose ABC transporter, substrate-binding protein Pf1N1B4_596
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 Pf1N1B4_1127 Pf1N1B4_5629
TM0028 cellobiose ABC transporter, ATPase component 1 Pf1N1B4_1127 Pf1N1B4_5104
TM0029 cellobiose ABC transporter, permease component 2
TM0030 cellobiose ABC transporter, permease component 1 Pf1N1B4_1124 Pf1N1B4_5102
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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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