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 (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