GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism in Amantichitinum ursilacus IGB-41

Best path

bgl, gtsA, gtsB, gtsC, gtsD, 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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgl cellobiase WG78_RS19275 WG78_RS12620
gtsA glucose ABC transporter, substrate-binding component (GtsA) WG78_RS08555 WG78_RS09435
gtsB glucose ABC transporter, permease component 1 (GtsB) WG78_RS08560 WG78_RS05875
gtsC glucose ABC transporter, permease component 2 (GtsC) WG78_RS08565 WG78_RS05870
gtsD glucose ABC transporter, ATPase component (GtsD) WG78_RS08570 WG78_RS08940
glk glucokinase WG78_RS13930 WG78_RS21595
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF) WG78_RS19490
aglG' glucose ABC transporter, permease component 2 (AglG) WG78_RS05870 WG78_RS07485
aglK' glucose ABC transporter, ATPase component (AglK) WG78_RS09695 WG78_RS07490
ascB 6-phosphocellobiose hydrolase WG78_RS07760 WG78_RS04700
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) WG78_RS01500 WG78_RS20220
cbtF cellobiose ABC transporter, ATPase component 2 (CbtF) WG78_RS01495 WG78_RS07660
cdt cellobiose transporter cdt-1/cdt-2
cebE cellobiose ABC transporter, substrate-binding component CebE
cebF cellobiose ABC transporter, permease component 1 (CebF) WG78_RS04690 WG78_RS08950
cebG cellobiose ABC transporter, permease component 2 (CebG) WG78_RS04695 WG78_RS08945
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 WG78_RS10305 WG78_RS13860
eda 2-keto-3-deoxygluconate 6-phosphate aldolase WG78_RS07225 WG78_RS19240
edd phosphogluconate dehydratase WG78_RS08530
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit WG78_RS18875
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) WG78_RS20360 WG78_RS05410
gnl gluconolactonase WG78_RS15705 WG78_RS19225
kguD 2-keto-6-phosphogluconate reductase WG78_RS20980 WG78_RS05195
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 WG78_RS19555
mglA glucose ABC transporter, ATP-binding component (MglA) WG78_RS19010 WG78_RS19930
mglB glucose ABC transporter, substrate-binding component WG78_RS13900
mglC glucose ABC transporter, permease component (MglC) WG78_RS13910 WG78_RS19935
msdB1 cellobiose ABC transporter, permease component 1 (MsdB1) WG78_RS06130 WG78_RS08950
msdB2 cellobiose ABC transporter, permease component 2 (MsdB2) WG78_RS19495 WG78_RS09980
msdC1 cellobiose ABC transporter, permease component 1 (MsdC1) WG78_RS16190
msdC2 cellobiose ABC transporter, permease component 1 (MsdC2)
msiK cellobiose ABC transporter, ATPase component WG78_RS08940 WG78_RS08570
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase WG78_RS09080 WG78_RS02890
ptsG glucose PTS, enzyme IICB WG78_RS13865 WG78_RS06315
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) WG78_RS10305 WG78_RS13865
SemiSWEET Sugar transporter SemiSWEET
SMc04256 cellobiose ABC transporter, ATPase component WG78_RS08570 WG78_RS08940
SMc04257 cellobiose ABC transporter, permease component 1 WG78_RS08565 WG78_RS05870
SMc04258 cellobiose ABC transporter, permease component 2 WG78_RS08560
SMc04259 cellobiose ABC transporter, substrate-binding protein WG78_RS08555 WG78_RS09435
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
TM0027 cellobiose ABC transporter, ATPase component 2 WG78_RS01495 WG78_RS20215
TM0028 cellobiose ABC transporter, ATPase component 1 WG78_RS01495 WG78_RS20215
TM0029 cellobiose ABC transporter, permease component 2 WG78_RS07665
TM0030 cellobiose ABC transporter, permease component 1 WG78_RS20230
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