GapMind for catabolism of small carbon sources

 

Definition of D-maltose catabolism

As rules and steps, or see full text

Rules

Overview: Maltose utilization in GapMind is based on the MetaCyc pathway via maltose phosphorylase (link), or a phosphotransferase system followed by 6-phospho-alphaglucosidase, or a phosphotransferase system followed by a phosphatase back to maltose followed by maltose phosphorylase, or hydrolysis by alpha-glucosidase after uptake, or periplasmic hydrolysis by alpha-glucosidase followed by glucose utilization.

Steps

malE: maltose ABC transporter, substrate-binding component MalE

malF: maltose ABC transporter, permease component 1 (MalF)

malG: maltose ABC transporter, permease component 2 (MalG)

malK: maltose ABC transporter, ATPase component MalK

thuE: maltose ABC transporter, substrate-binding component ThuE

thuF: maltose ABC transporter, permease component 1 (ThuF)

thuG: maltose ABC transporter, permease component 2 (ThuG)

thuK: maltose ABC transporter, ATPase component ThuK

malE1: maltose ABC transporter, substrate-binding component (MalE1/MalE2)

malF1: maltose ABC transporter, permease component 1 (MalF1)

malG1: maltose ABC transporter, permease component 2 (MalG1/MalG2)

malK1: maltose ABC transporter, ATPase component

malX_Sm: maltose ABC transporter, substrate-binding component

malF_Sm: maltose ABC transporter, permease component 1

malG_Sm: maltose ABC transporter, permease component 2

malK_Sm: maltose ABC transporter, ATPase component

musE: maltose ABC transporter, substrate-binding component MusE

musF: maltose ABC transporter, permease component 1 (MusF)

musG: maltose ABC transporter, permease component 2 (MusG)

musK: maltose ABC transporter, ATPase component MusK

musI: maltose ABC transporter, uncharacterized membrane component MusI

malE_Aa: maltose ABC transporter, substrate-binding component

malF_Aa: maltose ABC transporter, permease component 1

malG_Aa: maltose ABC transporter, permease component 2

malK_Aa: maltose ABC transporter, ATPase component

aglE: maltose ABC transporter, substrate-binding component AglK

aglF: maltose ABC transporter, permease component 1 (AglF)

aglG: maltose ABC transporter, permease component 2 (AglG)

aglK: maltose ABC transporter, ATPase component AglK

malEF_Bb: maltose ABC transporter, fused substrate-binding and permease component 1

malG_Bb: maltose ABC transporter, permease component 2

malK_Bb: maltose ABC transporter, ATPase component

malE_Ss: maltose ABC transporter, substrate-binding component

malF_Ss: maltose ABC transporter, permease component 1

malG_Ss: maltose ABC transporter, permease component 2

malK_Ss: maltose ABC transporter, ATPase component

malEIICBA: maltose phosphotransferase system, EII-CBA components

malEIICB: maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715

malEIIA: maltose phosphotransferase system, EII-A component (PtsG/YpqE/GamP)

MAL11: maltose permease

SUC2: maltose:H+ symporter

SUT1: maltose:H+ symporter

cscB: maltose permease

malAP: maltose permease

malI: maltose transporter

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

malP: maltose phosphorylase

pgmB: beta-phosphoglucomutase

malA: 6-phospho-alphaglucosidase

mapP: maltose 6'-phosphate phosphatase

susB: alpha-glucosidase (maltase)

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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, 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