GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Phaeobacter inhibens BS107

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase PGA1_c07840
aglE' glucose ABC transporter, substrate-binding component (AglE) PGA1_c07860
aglF' glucose ABC transporter, permease component 1 (AglF) PGA1_c07870
aglG' glucose ABC transporter, permease component 2 (AglG) PGA1_c07880 PGA1_78p00180
aglK' glucose ABC transporter, ATPase component (AglK) PGA1_c07900 PGA1_c16680
glk glucokinase PGA1_c05420 PGA1_262p00420
Alternative steps:
ascB 6-phosphocellobiose hydrolase PGA1_c07840
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) PGA1_262p00880
cbtC cellobiose ABC transporter, permease component 2 (CbtC)
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) PGA1_262p01730 PGA1_262p01010
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) PGA1_262p00340 PGA1_262p01000
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) PGA1_c07400 PGA1_c30820
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 PGA1_c28010 PGA1_c07350
edd phosphogluconate dehydratase PGA1_c28000 PGA1_c07380
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase PGA1_c15880
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) PGA1_c02740 PGA1_c27320
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) PGA1_c19500 PGA1_78p00160
gtsB glucose ABC transporter, permease component 1 (GtsB) PGA1_c19490 PGA1_78p00170
gtsC glucose ABC transporter, permease component 2 (GtsC) PGA1_c19480 PGA1_78p00180
gtsD glucose ABC transporter, ATPase component (GtsD) PGA1_c19470 PGA1_c16680
kguD 2-keto-6-phosphogluconate reductase PGA1_c28260 PGA1_c24680
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) PGA1_262p00450 PGA1_c23060
mglB glucose ABC transporter, substrate-binding component PGA1_262p00430
mglC glucose ABC transporter, permease component (MglC) PGA1_262p00440 PGA1_c28050
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) PGA1_c16700
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) PGA1_c16690 PGA1_c30820
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) PGA1_c02720
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) PGA1_c30820 PGA1_c07880
msiK cellobiose ABC transporter, ATPase component PGA1_c02740 PGA1_c07440
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PGA1_c24340 PGA1_c06550
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component PGA1_78p00190 PGA1_c19470
SMc04257 cellobiose ABC transporter, permease component 1 PGA1_78p00180 PGA1_c19480
SMc04258 cellobiose ABC transporter, permease component 2 PGA1_78p00170 PGA1_c19490
SMc04259 cellobiose ABC transporter, substrate-binding protein PGA1_78p00160 PGA1_c19500
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 PGA1_c06820 PGA1_262p01000
TM0028 cellobiose ABC transporter, ATPase component 1 PGA1_c06810 PGA1_262p01730
TM0029 cellobiose ABC transporter, permease component 2 PGA1_c16290 PGA1_c06800
TM0030 cellobiose ABC transporter, permease component 1 PGA1_c06790
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