GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Nocardiopsis baichengensis YIM 90130

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase C892_RS0106605 C892_RS0108995
mglA glucose ABC transporter, ATP-binding component (MglA) C892_RS0109575 C892_RS0117120
mglB glucose ABC transporter, substrate-binding component C892_RS0109580 C892_RS0113095
mglC glucose ABC transporter, permease component (MglC) C892_RS0109570 C892_RS0117115
glk glucokinase C892_RS0114285 C892_RS0102110
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) C892_RS0108170
aglF' glucose ABC transporter, permease component 1 (AglF) C892_RS0108165 C892_RS0124960
aglG' glucose ABC transporter, permease component 2 (AglG) C892_RS0108160 C892_RS0124955
aglK' glucose ABC transporter, ATPase component (AglK) C892_RS0124970 C892_RS0124950
ascB 6-phosphocellobiose hydrolase C892_RS0104415 C892_RS0105635
bglF glucose PTS, enzyme II (BCA components, BglF) C892_RS0110610
bglG cellobiose PTS system, EII-BC or EII-BCA components C892_RS0110610
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) C892_RS0127905 C892_RS0111560
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) C892_RS0127900 C892_RS0111520
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE C892_RS0109010
cebF cellobiose ABC transporter, permease component 1 (CebF) C892_RS0109005 C892_RS0109600
cebG cellobiose ABC transporter, permease component 2 (CebG) C892_RS0109000 C892_RS0109595
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 C892_RS0123955
eda 2-keto-3-deoxygluconate 6-phosphate aldolase C892_RS0102105
edd phosphogluconate dehydratase C892_RS0102115 C892_RS0126045
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase C892_RS0110725
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) C892_RS0124950 C892_RS0124970
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) C892_RS0124910 C892_RS0123140
gtsC glucose ABC transporter, permease component 2 (GtsC) C892_RS0122530 C892_RS0124955
gtsD glucose ABC transporter, ATPase component (GtsD) C892_RS0124950 C892_RS0124970
kguD 2-keto-6-phosphogluconate reductase C892_RS0126925 C892_RS0101795
kguK 2-ketogluconokinase C892_RS0104700
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 C892_RS0102035
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) C892_RS0109005
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) C892_RS0119340 C892_RS0110280
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) C892_RS0101030 C892_RS0109600
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) C892_RS0101035 C892_RS0109000
msiK cellobiose ABC transporter, ATPase component C892_RS0124950 C892_RS0124970
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase C892_RS0123815 C892_RS0112215
ptsG glucose PTS, enzyme IICB C892_RS0123935
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) C892_RS0123935
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component C892_RS0124950 C892_RS0124970
SMc04257 cellobiose ABC transporter, permease component 1 C892_RS0124955 C892_RS0108160
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 C892_RS0100135 C892_RS0108610
TM0028 cellobiose ABC transporter, ATPase component 1 C892_RS0111520 C892_RS0108610
TM0029 cellobiose ABC transporter, permease component 2 C892_RS0127910
TM0030 cellobiose ABC transporter, permease component 1 C892_RS0127915 C892_RS0108595
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