GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Azospirillum thiophilum BV-S

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase AL072_RS30145 AL072_RS15155
mglA glucose ABC transporter, ATP-binding component (MglA) AL072_RS30960 AL072_RS26290
mglB glucose ABC transporter, substrate-binding component AL072_RS30965 AL072_RS26300
mglC glucose ABC transporter, permease component (MglC) AL072_RS30955 AL072_RS26295
glk glucokinase AL072_RS02695 AL072_RS29570
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) AL072_RS00990 AL072_RS19185
ascB 6-phosphocellobiose hydrolase AL072_RS30035 AL072_RS24890
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) AL072_RS19055 AL072_RS17815
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) AL072_RS20665 AL072_RS17915
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
celEIIB cellobiose PTS system, EII-B component
celEIIC cellobiose PTS system, EII-C component
crr glucose PTS, enzyme IIA AL072_RS17560
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AL072_RS15650 AL072_RS28850
edd phosphogluconate dehydratase AL072_RS14175 AL072_RS23425
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AL072_RS29735
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase AL072_RS30155 AL072_RS22775
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) AL072_RS24545 AL072_RS00990
gnl gluconolactonase AL072_RS26020 AL072_RS30975
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) AL072_RS00995 AL072_RS19180
gtsD glucose ABC transporter, ATPase component (GtsD) AL072_RS00990 AL072_RS19185
kguD 2-keto-6-phosphogluconate reductase AL072_RS05440 AL072_RS13725
kguK 2-ketogluconokinase AL072_RS19200
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
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1)
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) AL072_RS19180
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1)
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2) AL072_RS00995
msiK cellobiose ABC transporter, ATPase component AL072_RS00990 AL072_RS19185
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase AL072_RS23680 AL072_RS28605
ptsG glucose PTS, enzyme IICB AL072_RS17555
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AL072_RS17555
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component AL072_RS00990 AL072_RS19185
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 AL072_RS17915 AL072_RS20665
TM0028 cellobiose ABC transporter, ATPase component 1 AL072_RS17915 AL072_RS17910
TM0029 cellobiose ABC transporter, permease component 2 AL072_RS15190 AL072_RS23080
TM0030 cellobiose ABC transporter, permease component 1 AL072_RS15195 AL072_RS20680
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