GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Phyllobacterium leguminum ORS 1419

Best path

SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, 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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SMc04256 cellobiose ABC transporter, ATPase component C7477_RS15000 C7477_RS00560
SMc04257 cellobiose ABC transporter, permease component 1 C7477_RS15005 C7477_RS00555
SMc04258 cellobiose ABC transporter, permease component 2 C7477_RS15010 C7477_RS00550
SMc04259 cellobiose ABC transporter, substrate-binding protein C7477_RS15020 C7477_RS00540
cbp cellobiose phosphorylase
pgmA alpha-phosphoglucomutase C7477_RS05195 C7477_RS06840
glk glucokinase C7477_RS11585 C7477_RS02345
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) C7477_RS15025
aglF' glucose ABC transporter, permease component 1 (AglF) C7477_RS15030
aglG' glucose ABC transporter, permease component 2 (AglG) C7477_RS15035 C7477_RS15005
aglK' glucose ABC transporter, ATPase component (AglK) C7477_RS15040 C7477_RS15575
ascB 6-phosphocellobiose hydrolase
bgl cellobiase
bglF glucose PTS, enzyme II (BCA components, BglF)
bglG cellobiose PTS system, EII-BC or EII-BCA components
bglT cellobiose transporter BglT
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) C7477_RS16100 C7477_RS10290
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) C7477_RS00200 C7477_RS10290
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) C7477_RS13710 C7477_RS00230
cebG cellobiose ABC transporter, permease component 2 (CebG) C7477_RS00790 C7477_RS15595
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 C7477_RS10820 C7477_RS04405
edd phosphogluconate dehydratase C7477_RS00080 C7477_RS13890
gadh1 gluconate 2-dehydrogenase flavoprotein subunit C7477_RS09995 C7477_RS10280
gadh2 gluconate 2-dehydrogenase cytochrome c subunit C7477_RS10000
gadh3 gluconate 2-dehydrogenase subunit 3 C7477_RS09990
gdh quinoprotein glucose dehydrogenase C7477_RS17580 C7477_RS15800
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) C7477_RS15035
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) C7477_RS13775 C7477_RS10760
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) C7477_RS00540 C7477_RS15020
gtsB glucose ABC transporter, permease component 1 (GtsB) C7477_RS00550 C7477_RS15010
gtsC glucose ABC transporter, permease component 2 (GtsC) C7477_RS00555 C7477_RS15005
gtsD glucose ABC transporter, ATPase component (GtsD) C7477_RS00560 C7477_RS15040
kguD 2-keto-6-phosphogluconate reductase C7477_RS04785 C7477_RS06885
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
mglA glucose ABC transporter, ATP-binding component (MglA) C7477_RS14925 C7477_RS16705
mglB glucose ABC transporter, substrate-binding component C7477_RS14930 C7477_RS16695
mglC glucose ABC transporter, permease component (MglC) C7477_RS14920 C7477_RS16700
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1)
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) C7477_RS09560 C7477_RS13715
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) C7477_RS13785 C7477_RS09780
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) C7477_RS00790
msiK cellobiose ABC transporter, ATPase component C7477_RS13775 C7477_RS15040
PAST-A proton-associated sugar transporter A
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 C7477_RS00200 C7477_RS13365
TM0028 cellobiose ABC transporter, ATPase component 1 C7477_RS16095 C7477_RS16100
TM0029 cellobiose ABC transporter, permease component 2 C7477_RS02090
TM0030 cellobiose ABC transporter, permease component 1 C7477_RS13350 C7477_RS00880
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