GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

bgl, mglA, mglB, mglC, glk

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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase AU252_RS10135 AU252_RS00470
mglA glucose ABC transporter, ATP-binding component (MglA) AU252_RS04575 AU252_RS07280
mglB glucose ABC transporter, substrate-binding component AU252_RS09315 AU252_RS04585
mglC glucose ABC transporter, permease component (MglC) AU252_RS09325 AU252_RS04580
glk glucokinase AU252_RS02620 AU252_RS02430
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) AU252_RS07845
aglF' glucose ABC transporter, permease component 1 (AglF) AU252_RS07840
aglG' glucose ABC transporter, permease component 2 (AglG) AU252_RS07835 AU252_RS17820
aglK' glucose ABC transporter, ATPase component (AglK) AU252_RS06475 AU252_RS11300
ascB 6-phosphocellobiose hydrolase AU252_RS17260 AU252_RS16845
bglF glucose PTS, enzyme II (BCA components, BglF)
bglG cellobiose PTS system, EII-BC or EII-BCA components
bglT cellobiose transporter BglT AU252_RS07645
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) AU252_RS07910
cbtC cellobiose ABC transporter, permease component 2 (CbtC) AU252_RS07905
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) AU252_RS07900 AU252_RS12580
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) AU252_RS07895 AU252_RS10130
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) AU252_RS13135 AU252_RS14405
cebG cellobiose ABC transporter, permease component 2 (CebG) AU252_RS15865 AU252_RS16970
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 AU252_RS11915
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AU252_RS16240 AU252_RS14180
edd phosphogluconate dehydratase AU252_RS19105
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase AU252_RS19095
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) AU252_RS07835
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) AU252_RS06475 AU252_RS11300
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) AU252_RS14430 AU252_RS09550
gtsC glucose ABC transporter, permease component 2 (GtsC) AU252_RS16500 AU252_RS17820
gtsD glucose ABC transporter, ATPase component (GtsD) AU252_RS06475 AU252_RS13340
kguD 2-keto-6-phosphogluconate reductase AU252_RS16225 AU252_RS07215
kguK 2-ketogluconokinase AU252_RS16245 AU252_RS14185
kguT 2-ketogluconate transporter AU252_RS05895
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily AU252_RS11015 AU252_RS05985
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) AU252_RS09970 AU252_RS17825
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) AU252_RS05310 AU252_RS17820
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) AU252_RS15860 AU252_RS14690
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) AU252_RS14730 AU252_RS15865
msiK cellobiose ABC transporter, ATPase component AU252_RS06475 AU252_RS13340
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase AU252_RS09065 AU252_RS03935
ptsG glucose PTS, enzyme IICB AU252_RS11925
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AU252_RS11925
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component AU252_RS06475 AU252_RS11300
SMc04257 cellobiose ABC transporter, permease component 1 AU252_RS07835 AU252_RS14425
SMc04258 cellobiose ABC transporter, permease component 2
SMc04259 cellobiose ABC transporter, substrate-binding protein
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 AU252_RS07895 AU252_RS09195
TM0028 cellobiose ABC transporter, ATPase component 1 AU252_RS12580 AU252_RS12585
TM0029 cellobiose ABC transporter, permease component 2 AU252_RS07905
TM0030 cellobiose ABC transporter, permease component 1 AU252_RS07910 AU252_RS17670
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 Apr 09 2024. 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 (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