GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Pseudomonas fluorescens FW300-N2E2

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase Pf6N2E2_2809
gtsA glucose ABC transporter, substrate-binding component (GtsA) Pf6N2E2_2892
gtsB glucose ABC transporter, permease component 1 (GtsB) Pf6N2E2_2891
gtsC glucose ABC transporter, permease component 2 (GtsC) Pf6N2E2_2890 Pf6N2E2_1648
gtsD glucose ABC transporter, ATPase component (GtsD) Pf6N2E2_2889 Pf6N2E2_807
glk glucokinase Pf6N2E2_2897
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) Pf6N2E2_2890 Pf6N2E2_106
aglK' glucose ABC transporter, ATPase component (AglK) Pf6N2E2_807 Pf6N2E2_1960
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) Pf6N2E2_3424
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) Pf6N2E2_1812 Pf6N2E2_3425
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) Pf6N2E2_3314 Pf6N2E2_3426
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) Pf6N2E2_1648
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 Pf6N2E2_2883 Pf6N2E2_5976
edd phosphogluconate dehydratase Pf6N2E2_2898 Pf6N2E2_1668
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Pf6N2E2_1903 Pf6N2E2_4408
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Pf6N2E2_5442 Pf6N2E2_1939
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) Pf6N2E2_4815 Pf6N2E2_4515
gnl gluconolactonase Pf6N2E2_614 Pf6N2E2_318
kguD 2-keto-6-phosphogluconate reductase Pf6N2E2_5310 Pf6N2E2_627
kguK 2-ketogluconokinase Pf6N2E2_629
kguT 2-ketogluconate transporter Pf6N2E2_628 Pf6N2E2_1312
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily Pf6N2E2_883 Pf6N2E2_1003
mglA glucose ABC transporter, ATP-binding component (MglA) Pf6N2E2_523 Pf6N2E2_1456
mglB glucose ABC transporter, substrate-binding component Pf6N2E2_1455 Pf6N2E2_1015
mglC glucose ABC transporter, permease component (MglC) Pf6N2E2_524 Pf6N2E2_1457
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) Pf6N2E2_1647
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) Pf6N2E2_1648 Pf6N2E2_2890
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2)
msiK cellobiose ABC transporter, ATPase component Pf6N2E2_807 Pf6N2E2_1960
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Pf6N2E2_1059 Pf6N2E2_4374
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component Pf6N2E2_2889 Pf6N2E2_807
SMc04257 cellobiose ABC transporter, permease component 1 Pf6N2E2_2890
SMc04258 cellobiose ABC transporter, permease component 2 Pf6N2E2_2891
SMc04259 cellobiose ABC transporter, substrate-binding protein Pf6N2E2_2892
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 Pf6N2E2_1813 Pf6N2E2_2033
TM0028 cellobiose ABC transporter, ATPase component 1 Pf6N2E2_3314 Pf6N2E2_1813
TM0029 cellobiose ABC transporter, permease component 2
TM0030 cellobiose ABC transporter, permease component 1 Pf6N2E2_3311 Pf6N2E2_3423
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, 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