GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Ochrobactrum thiophenivorans DSM 7216

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase
mglA glucose ABC transporter, ATP-binding component (MglA) CEV31_RS02580 CEV31_RS17305
mglB glucose ABC transporter, substrate-binding component CEV31_RS02585 CEV31_RS17260
mglC glucose ABC transporter, permease component (MglC) CEV31_RS02575 CEV31_RS09010
glk glucokinase CEV31_RS07005 CEV31_RS18970
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF) CEV31_RS07180
aglG' glucose ABC transporter, permease component 2 (AglG) CEV31_RS16735 CEV31_RS14070
aglK' glucose ABC transporter, ATPase component (AglK) CEV31_RS15275 CEV31_RS06775
ascB 6-phosphocellobiose hydrolase
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) CEV31_RS15720
cbtC cellobiose ABC transporter, permease component 2 (CbtC) CEV31_RS17235 CEV31_RS15715
cbtD cellobiose ABC transporter, ATPase component 1 (CbtD) CEV31_RS18935 CEV31_RS09385
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) CEV31_RS18940 CEV31_RS19570
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) CEV31_RS14075
cebG cellobiose ABC transporter, permease component 2 (CebG) CEV31_RS14430
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 CEV31_RS13155
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CEV31_RS20745 CEV31_RS18545
edd phosphogluconate dehydratase CEV31_RS15685 CEV31_RS06110
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit CEV31_RS09840 CEV31_RS08410
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase CEV31_RS06685 CEV31_RS03435
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) CEV31_RS14655 CEV31_RS17415
gnl gluconolactonase CEV31_RS19470 CEV31_RS14210
gtsA glucose ABC transporter, substrate-binding component (GtsA) CEV31_RS09330
gtsB glucose ABC transporter, permease component 1 (GtsB) CEV31_RS09335 CEV31_RS14435
gtsC glucose ABC transporter, permease component 2 (GtsC) CEV31_RS09340 CEV31_RS07125
gtsD glucose ABC transporter, ATPase component (GtsD) CEV31_RS09345 CEV31_RS17415
kguD 2-keto-6-phosphogluconate reductase CEV31_RS03240 CEV31_RS05585
kguK 2-ketogluconokinase
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 CEV31_RS19855
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) CEV31_RS14435 CEV31_RS07130
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) CEV31_RS07125 CEV31_RS14430
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) CEV31_RS14665 CEV31_RS06765
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2)
msiK cellobiose ABC transporter, ATPase component CEV31_RS17415 CEV31_RS07190
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase CEV31_RS05910 CEV31_RS03255
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component CEV31_RS09345 CEV31_RS07190
SMc04257 cellobiose ABC transporter, permease component 1 CEV31_RS09340 CEV31_RS17420
SMc04258 cellobiose ABC transporter, permease component 2 CEV31_RS09335
SMc04259 cellobiose ABC transporter, substrate-binding protein CEV31_RS09330
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 CEV31_RS15105 CEV31_RS18940
TM0028 cellobiose ABC transporter, ATPase component 1 CEV31_RS18935 CEV31_RS19565
TM0029 cellobiose ABC transporter, permease component 2 CEV31_RS15715 CEV31_RS18930
TM0030 cellobiose ABC transporter, permease component 1 CEV31_RS02310 CEV31_RS18995
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.

Links

Downloads

Related tools

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