GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Megamonas funiformis YIT 11815

Best path

bgl, MFS-glucose, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase HMPREF9454_RS07115
MFS-glucose glucose transporter, MFS superfamily HMPREF9454_RS09490 HMPREF9454_RS09235
glk glucokinase HMPREF9454_RS09110 HMPREF9454_RS10520
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)
aglK' glucose ABC transporter, ATPase component (AglK) HMPREF9454_RS05390 HMPREF9454_RS01120
ascB 6-phosphocellobiose hydrolase HMPREF9454_RS07115 HMPREF9454_RS01150
bglF glucose PTS, enzyme II (BCA components, BglF) HMPREF9454_RS08705
bglG cellobiose PTS system, EII-BC or EII-BCA components HMPREF9454_RS08705
bglT cellobiose transporter BglT HMPREF9454_RS02300
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) HMPREF9454_RS05910 HMPREF9454_RS03185
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) HMPREF9454_RS05045 HMPREF9454_RS03175
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) HMPREF9454_RS05045 HMPREF9454_RS03170
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)
celEIIA cellobiose PTS system, EII-A component HMPREF9454_RS12510 HMPREF9454_RS07120
celEIIB cellobiose PTS system, EII-B component HMPREF9454_RS07125
celEIIC cellobiose PTS system, EII-C component HMPREF9454_RS07135
crr glucose PTS, enzyme IIA HMPREF9454_RS00490 HMPREF9454_RS01155
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HMPREF9454_RS07595
edd phosphogluconate dehydratase HMPREF9454_RS09720
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase
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) HMPREF9454_RS05390 HMPREF9454_RS00035
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) HMPREF9454_RS05390 HMPREF9454_RS01120
kguD 2-keto-6-phosphogluconate reductase HMPREF9454_RS06920 HMPREF9454_RS03270
kguK 2-ketogluconokinase HMPREF9454_RS07600
kguT 2-ketogluconate transporter HMPREF9454_RS08595
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC HMPREF9454_RS07870
manZ glucose PTS, enzyme EIID HMPREF9454_RS07865 HMPREF9454_RS10755
mglA glucose ABC transporter, ATP-binding component (MglA) HMPREF9454_RS00035
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1)
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 HMPREF9454_RS05390 HMPREF9454_RS01120
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase HMPREF9454_RS10380 HMPREF9454_RS05940
ptsG glucose PTS, enzyme IICB HMPREF9454_RS07765 HMPREF9454_RS01155
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) HMPREF9454_RS01155 HMPREF9454_RS07765
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component HMPREF9454_RS05390 HMPREF9454_RS01120
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 HMPREF9454_RS05045 HMPREF9454_RS03175
TM0028 cellobiose ABC transporter, ATPase component 1 HMPREF9454_RS05050 HMPREF9454_RS05045
TM0029 cellobiose ABC transporter, permease component 2
TM0030 cellobiose ABC transporter, permease component 1 HMPREF9454_RS03190
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