GapMind for catabolism of small carbon sources

 

Definition of D-cellobiose catabolism

As rules and steps, or see full text

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.

Steps

TM0031: cellobiose ABC transporter, substrate-binding component

TM0030: cellobiose ABC transporter, permease component 1

TM0029: cellobiose ABC transporter, permease component 2

TM0028: cellobiose ABC transporter, ATPase component 1

TM0027: cellobiose ABC transporter, ATPase component 2

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)

cbtF: cellobiose ABC transporter, ATPase component 2 (CbtF)

cebE: cellobiose ABC transporter, substrate-binding component CebE

cebF: cellobiose ABC transporter, permease component 1 (CebF)

cebG: cellobiose ABC transporter, permease component 2 (CebG)

msiK: cellobiose ABC transporter, ATPase component

SMc04256: cellobiose ABC transporter, ATPase component

SMc04257: cellobiose ABC transporter, permease component 1

SMc04258: cellobiose ABC transporter, permease component 2

SMc04259: cellobiose ABC transporter, substrate-binding protein

cbpB: cellobiose ABC transporter, substrate-binding component CpbB

msdB1: cellobiose ABC transporter, permease component 1 (MsdB1)

msdB2: cellobiose ABC transporter, permease component 2 (MsdB2)

cbpC: cellobiose ABC transporter, substrate-binding component CbpC

msdC1: cellobiose ABC transporter, permease component 1 (MsdC1)

msdC2: cellobiose ABC transporter, permease component 1 (MsdC2)

bglG: cellobiose PTS system, EII-BC or EII-BCA components

celEIIA: cellobiose PTS system, EII-A component

celEIIB: cellobiose PTS system, EII-B component

celEIIC: cellobiose PTS system, EII-C component

cdt: cellobiose transporter cdt-1/cdt-2

bglT: cellobiose transporter BglT

MFS-glucose: glucose transporter, MFS superfamily

SSS-glucose: Sodium/glucose cotransporter

glcU': Glucose uptake protein GlcU

PAST-A: proton-associated sugar transporter A

SemiSWEET: Sugar transporter SemiSWEET

SWEET1: bidirectional sugar transporter SWEET1

mglA: glucose ABC transporter, ATP-binding component (MglA)

mglB: glucose ABC transporter, substrate-binding component

mglC: glucose ABC transporter, permease component (MglC)

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)

glcS: glucose ABC transporter, substrate-binding component (GlcS)

glcT: glucose ABC transporter, permease component 1 (GlcT)

glcU: glucose ABC transporter, permease component 2 (GlcU)

glcV: glucose ABC transporter, ATPase component (GclV)

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)

ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)

bglF: glucose PTS, enzyme II (BCA components, BglF)

ptsG: glucose PTS, enzyme IICB

crr: glucose PTS, enzyme IIA

manX: glucose PTS, enzyme EIIAB

manY: glucose PTS, enzyme EIIC

manZ: glucose PTS, enzyme EIID

gdh: quinoprotein glucose dehydrogenase

gnl: gluconolactonase

gadh1: gluconate 2-dehydrogenase flavoprotein subunit

gadh2: gluconate 2-dehydrogenase cytochrome c subunit

gadh3: gluconate 2-dehydrogenase subunit 3

kguT: 2-ketogluconate transporter

kguK: 2-ketogluconokinase

kguD: 2-keto-6-phosphogluconate reductase

edd: phosphogluconate dehydratase

eda: 2-keto-3-deoxygluconate 6-phosphate aldolase

glk: glucokinase

bgl: cellobiase

cbp: cellobiose phosphorylase

pgmA: alpha-phosphoglucomutase

ascB: 6-phosphocellobiose hydrolase

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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