GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Escherichia coli BW25113

Best path

malE, malF, malG, malK, susB, glk

Also see fitness data for the top candidates

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.

89 steps (53 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
malE maltose ABC transporter, substrate-binding component MalE b4034
malF maltose ABC transporter, permease component 1 (MalF) b4033 b3452
malG maltose ABC transporter, permease component 2 (MalG) b4032 b1312
malK maltose ABC transporter, ATPase component MalK b4035 b3450
susB alpha-glucosidase (maltase) b3080 b0403
glk glucokinase b2388 b0394
Alternative steps:
aglE maltose ABC transporter, substrate-binding component AglK
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF maltose ABC transporter, permease component 1 (AglF)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG maltose ABC transporter, permease component 2 (AglG) b4032
aglG' glucose ABC transporter, permease component 2 (AglG) b4032
aglK maltose ABC transporter, ATPase component AglK b4035 b3450
aglK' glucose ABC transporter, ATPase component (AglK) b4035 b3450
bglF glucose PTS, enzyme II (BCA components, BglF) b3722 b2715
crr glucose PTS, enzyme IIA b2417 b0679
cscB maltose permease b0343
eda 2-keto-3-deoxygluconate 6-phosphate aldolase b1850 b4477
edd phosphogluconate dehydratase b1851 b3771
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase b0124 b0837
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) b0262 b4035
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) b1312 b4032
gtsD glucose ABC transporter, ATPase component (GtsD) b4035 b3450
kguD 2-keto-6-phosphogluconate reductase b3553 b2913
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
MAL11 maltose permease
malA 6-phospho-alphaglucosidase b1734
malAP maltose permease
malE1 maltose ABC transporter, substrate-binding component (MalE1/MalE2) b4034
malE_Aa maltose ABC transporter, substrate-binding component b4034
malE_Ss maltose ABC transporter, substrate-binding component
malEF_Bb maltose ABC transporter, fused substrate-binding and permease component 1
malEIIA maltose phosphotransferase system, EII-A component (PtsG/YpqE/GamP) b0679 b1101
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 b1101 b0679
malEIICBA maltose phosphotransferase system, EII-CBA components b0679 b1101
malF1 maltose ABC transporter, permease component 1 (MalF1) b4033
malF_Aa maltose ABC transporter, permease component 1 b4033 b1311
malF_Sm maltose ABC transporter, permease component 1 b4033
malF_Ss maltose ABC transporter, permease component 1
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 b4032 b1312
malG_Bb maltose ABC transporter, permease component 2 b1312 b4032
malG_Sm maltose ABC transporter, permease component 2 b1312 b4032
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK1 maltose ABC transporter, ATPase component b3450 b4035
malK_Aa maltose ABC transporter, ATPase component b3450 b4035
malK_Bb maltose ABC transporter, ATPase component b4035 b3450
malK_Sm maltose ABC transporter, ATPase component b3450 b4035
malK_Ss maltose ABC transporter, ATPase component b1246 b3541
malP maltose phosphorylase b1316
malX_Sm maltose ABC transporter, substrate-binding component
manX glucose PTS, enzyme EIIAB b1817
manY glucose PTS, enzyme EIIC b1818
manZ glucose PTS, enzyme EIID b1819 b3140
mapP maltose 6'-phosphate phosphatase
MFS-glucose glucose transporter, MFS superfamily b2943 b2841
mglA glucose ABC transporter, ATP-binding component (MglA) b2149 b3567
mglB glucose ABC transporter, substrate-binding component b2150 b3566
mglC glucose ABC transporter, permease component (MglC) b2148 b3750
musE maltose ABC transporter, substrate-binding component MusE
musF maltose ABC transporter, permease component 1 (MusF)
musG maltose ABC transporter, permease component 2 (MusG)
musI maltose ABC transporter, uncharacterized membrane component MusI
musK maltose ABC transporter, ATPase component MusK b3450 b4035
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase b1317 b2690
ptsG glucose PTS, enzyme IICB b1101 b0679
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) b0679 b1101
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter b3679
SUC2 maltose:H+ symporter
SUT1 maltose:H+ symporter
SWEET1 bidirectional sugar transporter SWEET1
thuE maltose ABC transporter, substrate-binding component ThuE
thuF maltose ABC transporter, permease component 1 (ThuF) b1311 b4033
thuG maltose ABC transporter, permease component 2 (ThuG) b1312 b4032
thuK maltose ABC transporter, ATPase component ThuK b4035 b3450

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 17 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 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