GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Thioclava dalianensis DLFJ1-1

Best path

bgl, aglE', aglF', aglG', aglK', 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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase DL1_RS08720 DL1_RS17560
aglE' glucose ABC transporter, substrate-binding component (AglE) DL1_RS08730
aglF' glucose ABC transporter, permease component 1 (AglF) DL1_RS08735
aglG' glucose ABC transporter, permease component 2 (AglG) DL1_RS08740 DL1_RS05835
aglK' glucose ABC transporter, ATPase component (AglK) DL1_RS08750 DL1_RS04020
glk glucokinase DL1_RS08715 DL1_RS03520
Alternative steps:
ascB 6-phosphocellobiose hydrolase DL1_RS08720
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) DL1_RS01380 DL1_RS12010
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) DL1_RS12005 DL1_RS01385
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) DL1_RS17575 DL1_RS05525
cebG cellobiose ABC transporter, permease component 2 (CebG) DL1_RS04015 DL1_RS04150
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 DL1_RS12885 DL1_RS05975
edd phosphogluconate dehydratase DL1_RS12880 DL1_RS11965
gadh1 gluconate 2-dehydrogenase flavoprotein subunit DL1_RS19555
gadh2 gluconate 2-dehydrogenase cytochrome c subunit DL1_RS19560 DL1_RS20615
gadh3 gluconate 2-dehydrogenase subunit 3 DL1_RS19550
gdh quinoprotein glucose dehydrogenase DL1_RS02300 DL1_RS06520
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) DL1_RS08740
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) DL1_RS14385 DL1_RS02775
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) DL1_RS05845
gtsB glucose ABC transporter, permease component 1 (GtsB) DL1_RS05840 DL1_RS05995
gtsC glucose ABC transporter, permease component 2 (GtsC) DL1_RS05835 DL1_RS05990
gtsD glucose ABC transporter, ATPase component (GtsD) DL1_RS14385 DL1_RS05830
kguD 2-keto-6-phosphogluconate reductase DL1_RS07935 DL1_RS07735
kguK 2-ketogluconokinase DL1_RS12510
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) DL1_RS09090 DL1_RS17670
mglB glucose ABC transporter, substrate-binding component DL1_RS03525 DL1_RS09085
mglC glucose ABC transporter, permease component (MglC) DL1_RS03530 DL1_RS09095
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) DL1_RS05525
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) DL1_RS05990 DL1_RS14515
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) DL1_RS04010
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) DL1_RS14390 DL1_RS04015
msiK cellobiose ABC transporter, ATPase component DL1_RS14385 DL1_RS18995
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase DL1_RS00335 DL1_RS05230
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component DL1_RS05830 DL1_RS04020
SMc04257 cellobiose ABC transporter, permease component 1 DL1_RS05835 DL1_RS05990
SMc04258 cellobiose ABC transporter, permease component 2 DL1_RS05840
SMc04259 cellobiose ABC transporter, substrate-binding protein DL1_RS05845
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 DL1_RS13865 DL1_RS00635
TM0028 cellobiose ABC transporter, ATPase component 1 DL1_RS12005 DL1_RS12010
TM0029 cellobiose ABC transporter, permease component 2 DL1_RS11695
TM0030 cellobiose ABC transporter, permease component 1 DL1_RS00650 DL1_RS01375
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