GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Burkholderia phytofirmans PsJN

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase BPHYT_RS29195
gtsA glucose ABC transporter, substrate-binding component (GtsA) BPHYT_RS00415 BPHYT_RS05025
gtsB glucose ABC transporter, permease component 1 (GtsB) BPHYT_RS05030 BPHYT_RS29185
gtsC glucose ABC transporter, permease component 2 (GtsC) BPHYT_RS05035 BPHYT_RS29180
gtsD glucose ABC transporter, ATPase component (GtsD) BPHYT_RS05040 BPHYT_RS35680
glk glucokinase BPHYT_RS05010
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) BPHYT_RS05035 BPHYT_RS22780
aglK' glucose ABC transporter, ATPase component (AglK) BPHYT_RS16095 BPHYT_RS22760
ascB 6-phosphocellobiose hydrolase BPHYT_RS29195
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) BPHYT_RS31200 BPHYT_RS18675
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) BPHYT_RS18670 BPHYT_RS22030
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) BPHYT_RS22775
cebG cellobiose ABC transporter, permease component 2 (CebG) BPHYT_RS17465
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 BPHYT_RS02740
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BPHYT_RS16730 BPHYT_RS16945
edd phosphogluconate dehydratase BPHYT_RS16735 BPHYT_RS04815
gadh1 gluconate 2-dehydrogenase flavoprotein subunit BPHYT_RS23025 BPHYT_RS30780
gadh2 gluconate 2-dehydrogenase cytochrome c subunit BPHYT_RS23020 BPHYT_RS01060
gadh3 gluconate 2-dehydrogenase subunit 3 BPHYT_RS23030 BPHYT_RS01070
gdh quinoprotein glucose dehydrogenase BPHYT_RS08325
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) BPHYT_RS05035
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) BPHYT_RS24660 BPHYT_RS08805
gnl gluconolactonase BPHYT_RS06110 BPHYT_RS21245
kguD 2-keto-6-phosphogluconate reductase BPHYT_RS11290 BPHYT_RS14520
kguK 2-ketogluconokinase BPHYT_RS11300
kguT 2-ketogluconate transporter BPHYT_RS11295 BPHYT_RS10985
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) BPHYT_RS27185 BPHYT_RS20740
mglB glucose ABC transporter, substrate-binding component BPHYT_RS32820
mglC glucose ABC transporter, permease component (MglC) BPHYT_RS16055 BPHYT_RS27190
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) BPHYT_RS27975
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) BPHYT_RS35660 BPHYT_RS27970
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) BPHYT_RS17460
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2)
msiK cellobiose ABC transporter, ATPase component BPHYT_RS17470 BPHYT_RS16095
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BPHYT_RS04470 BPHYT_RS14155
ptsG glucose PTS, enzyme IICB BPHYT_RS02745
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BPHYT_RS02745
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component BPHYT_RS29175 BPHYT_RS05040
SMc04257 cellobiose ABC transporter, permease component 1 BPHYT_RS29180 BPHYT_RS05035
SMc04258 cellobiose ABC transporter, permease component 2 BPHYT_RS29185 BPHYT_RS05030
SMc04259 cellobiose ABC transporter, substrate-binding protein BPHYT_RS29190 BPHYT_RS00415
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 BPHYT_RS18670 BPHYT_RS22035
TM0028 cellobiose ABC transporter, ATPase component 1 BPHYT_RS31200 BPHYT_RS22030
TM0029 cellobiose ABC transporter, permease component 2
TM0030 cellobiose ABC transporter, permease component 1 BPHYT_RS31190 BPHYT_RS18685
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 (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