GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Klebsiella michiganensis M5al

Best path

bgl, mglA, mglB, mglC, 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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase BWI76_RS19510 BWI76_RS11890
mglA glucose ABC transporter, ATP-binding component (MglA) BWI76_RS19640 BWI76_RS07240
mglB glucose ABC transporter, substrate-binding component BWI76_RS19645 BWI76_RS27030
mglC glucose ABC transporter, permease component (MglC) BWI76_RS19635 BWI76_RS14865
glk glucokinase BWI76_RS20510 BWI76_RS22415
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF) BWI76_RS03135
aglG' glucose ABC transporter, permease component 2 (AglG) BWI76_RS01820
aglK' glucose ABC transporter, ATPase component (AglK) BWI76_RS01840 BWI76_RS06690
ascB 6-phosphocellobiose hydrolase BWI76_RS19550 BWI76_RS23855
bglF glucose PTS, enzyme II (BCA components, BglF) BWI76_RS19555 BWI76_RS07290
bglG cellobiose PTS system, EII-BC or EII-BCA components BWI76_RS22290 BWI76_RS19555
bglT cellobiose transporter BglT BWI76_RS27490 BWI76_RS27595
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) BWI76_RS26870 BWI76_RS17225
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) BWI76_RS26865 BWI76_RS17220
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) BWI76_RS23380 BWI76_RS03135
cebG cellobiose ABC transporter, permease component 2 (CebG) BWI76_RS17835 BWI76_RS26295
celEIIA cellobiose PTS system, EII-A component BWI76_RS11735 BWI76_RS22410
celEIIB cellobiose PTS system, EII-B component BWI76_RS11725 BWI76_RS01520
celEIIC cellobiose PTS system, EII-C component BWI76_RS11730 BWI76_RS14945
crr glucose PTS, enzyme IIA BWI76_RS20655 BWI76_RS08220
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BWI76_RS18095 BWI76_RS27940
edd phosphogluconate dehydratase BWI76_RS18100 BWI76_RS00975
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase BWI76_RS04950 BWI76_RS13270
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) BWI76_RS09465 BWI76_RS06035
gnl gluconolactonase BWI76_RS23720 BWI76_RS21470
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) BWI76_RS23380
gtsC glucose ABC transporter, permease component 2 (GtsC) BWI76_RS17835 BWI76_RS06705
gtsD glucose ABC transporter, ATPase component (GtsD) BWI76_RS03270 BWI76_RS06690
kguD 2-keto-6-phosphogluconate reductase BWI76_RS26960 BWI76_RS27925
kguK 2-ketogluconokinase BWI76_RS26950 BWI76_RS07325
kguT 2-ketogluconate transporter BWI76_RS26955 BWI76_RS06145
manX glucose PTS, enzyme EIIAB BWI76_RS17890 BWI76_RS01735
manY glucose PTS, enzyme EIIC BWI76_RS17895 BWI76_RS01730
manZ glucose PTS, enzyme EIID BWI76_RS17900 BWI76_RS01725
MFS-glucose glucose transporter, MFS superfamily BWI76_RS24055 BWI76_RS17580
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1)
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2)
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) BWI76_RS17840 BWI76_RS03135
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) BWI76_RS23385
msiK cellobiose ABC transporter, ATPase component BWI76_RS26290 BWI76_RS17830
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BWI76_RS08290 BWI76_RS25130
ptsG glucose PTS, enzyme IICB BWI76_RS11130 BWI76_RS08220
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BWI76_RS11130 BWI76_RS08220
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component BWI76_RS26290 BWI76_RS06690
SMc04257 cellobiose ABC transporter, permease component 1
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 BWI76_RS07535 BWI76_RS12010
TM0028 cellobiose ABC transporter, ATPase component 1 BWI76_RS07535 BWI76_RS17225
TM0029 cellobiose ABC transporter, permease component 2
TM0030 cellobiose ABC transporter, permease component 1 BWI76_RS07525 BWI76_RS19200
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