GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Pantoea rwandensis LMG 26275

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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase HA51_RS02740 HA51_RS18300
mglA glucose ABC transporter, ATP-binding component (MglA) HA51_RS22600 HA51_RS15895
mglB glucose ABC transporter, substrate-binding component HA51_RS22605 HA51_RS05640
mglC glucose ABC transporter, permease component (MglC) HA51_RS22595 HA51_RS05185
glk glucokinase HA51_RS10880 HA51_RS17370
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) HA51_RS18875
aglK' glucose ABC transporter, ATPase component (AglK) HA51_RS09990 HA51_RS18870
ascB 6-phosphocellobiose hydrolase HA51_RS01080 HA51_RS21600
bglF glucose PTS, enzyme II (BCA components, BglF) HA51_RS20050 HA51_RS04935
bglG cellobiose PTS system, EII-BC or EII-BCA components HA51_RS01085 HA51_RS20050
bglT cellobiose transporter BglT HA51_RS07515 HA51_RS08910
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) HA51_RS05940 HA51_RS05850
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) HA51_RS05945 HA51_RS05845
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) HA51_RS09970 HA51_RS18875
celEIIA cellobiose PTS system, EII-A component HA51_RS12310 HA51_RS17500
celEIIB cellobiose PTS system, EII-B component HA51_RS12305 HA51_RS17510
celEIIC cellobiose PTS system, EII-C component HA51_RS12320 HA51_RS17505
crr glucose PTS, enzyme IIA HA51_RS26435
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HA51_RS10460 HA51_RS05430
edd phosphogluconate dehydratase HA51_RS25625
gadh1 gluconate 2-dehydrogenase flavoprotein subunit HA51_RS18510 HA51_RS25120
gadh2 gluconate 2-dehydrogenase cytochrome c subunit HA51_RS18505 HA51_RS25125
gadh3 gluconate 2-dehydrogenase subunit 3 HA51_RS18515 HA51_RS25115
gdh quinoprotein glucose dehydrogenase HA51_RS10020 HA51_RS19005
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) HA51_RS18870 HA51_RS00345
gnl gluconolactonase HA51_RS02640 HA51_RS19865
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) HA51_RS09975
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) HA51_RS18870 HA51_RS03335
kguD 2-keto-6-phosphogluconate reductase HA51_RS05510 HA51_RS25715
kguK 2-ketogluconokinase HA51_RS05520 HA51_RS00260
kguT 2-ketogluconate transporter HA51_RS05515 HA51_RS02315
manX glucose PTS, enzyme EIIAB HA51_RS10605
manY glucose PTS, enzyme EIIC HA51_RS10600
manZ glucose PTS, enzyme EIID HA51_RS10595
MFS-glucose glucose transporter, MFS superfamily HA51_RS21365 HA51_RS04135
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) HA51_RS03320
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2)
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2)
msiK cellobiose ABC transporter, ATPase component HA51_RS18870 HA51_RS09990
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase HA51_RS24100 HA51_RS09435
ptsG glucose PTS, enzyme IICB HA51_RS14550 HA51_RS02255
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) HA51_RS02255 HA51_RS14550
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component HA51_RS09990 HA51_RS18870
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 HA51_RS08835 HA51_RS05945
TM0028 cellobiose ABC transporter, ATPase component 1 HA51_RS08230 HA51_RS08550
TM0029 cellobiose ABC transporter, permease component 2 HA51_RS13960
TM0030 cellobiose ABC transporter, permease component 1 HA51_RS05835 HA51_RS25040
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 24 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