GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Pseudomonas fluorescens FW300-N2C3

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase AO356_04805
gtsA glucose ABC transporter, substrate-binding component (GtsA) AO356_05195
gtsB glucose ABC transporter, permease component 1 (GtsB) AO356_05190
gtsC glucose ABC transporter, permease component 2 (GtsC) AO356_05185 AO356_28580
gtsD glucose ABC transporter, ATPase component (GtsD) AO356_05180 AO356_28585
glk glucokinase AO356_05215
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) AO356_05185 AO356_21625
aglK' glucose ABC transporter, ATPase component (AglK) AO356_27685 AO356_00010
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) AO356_07710
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) AO356_29385 AO356_07270
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) AO356_07275 AO356_07720
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 AO356_17540
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO356_05150 AO356_20285
edd phosphogluconate dehydratase AO356_05220 AO356_28760
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AO356_30205
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase AO356_17600 AO356_30385
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) AO356_14385 AO356_13165
gnl gluconolactonase AO356_24610 AO356_23060
kguD 2-keto-6-phosphogluconate reductase AO356_16925 AO356_24675
kguK 2-ketogluconokinase AO356_24685
kguT 2-ketogluconate transporter AO356_24680 AO356_22860
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily AO356_27270
mglA glucose ABC transporter, ATP-binding component (MglA) AO356_23205 AO356_28510
mglB glucose ABC transporter, substrate-binding component AO356_28505 AO356_23200
mglC glucose ABC transporter, permease component (MglC) AO356_23210 AO356_28515
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) AO356_28575
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) AO356_28580 AO356_05185
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2)
msiK cellobiose ABC transporter, ATPase component AO356_27685 AO356_00010
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase AO356_27065 AO356_12530
ptsG glucose PTS, enzyme IICB AO356_17535
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AO356_17535
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component AO356_05180 AO356_27685
SMc04257 cellobiose ABC transporter, permease component 1 AO356_05185
SMc04258 cellobiose ABC transporter, permease component 2 AO356_05190
SMc04259 cellobiose ABC transporter, substrate-binding protein AO356_05195
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 AO356_29390 AO356_07275
TM0028 cellobiose ABC transporter, ATPase component 1 AO356_07275 AO356_29390
TM0029 cellobiose ABC transporter, permease component 2
TM0030 cellobiose ABC transporter, permease component 1 AO356_07260 AO356_07705
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.

Links

Downloads

Related tools

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