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 (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