GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Pseudomonas stutzeri RCH2

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
malE maltose ABC transporter, substrate-binding component MalE Psest_0863
malF maltose ABC transporter, permease component 1 (MalF) Psest_0864
malG maltose ABC transporter, permease component 2 (MalG) Psest_0865 Psest_1898
malK maltose ABC transporter, ATPase component MalK Psest_0871 Psest_1899
susB alpha-glucosidase (maltase) Psest_0870 Psest_3785
glk glucokinase Psest_0850 Psest_1893
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) Psest_1898 Psest_0865
aglG' glucose ABC transporter, permease component 2 (AglG) Psest_1898 Psest_0865
aglK maltose ABC transporter, ATPase component AglK Psest_0871 Psest_1899
aglK' glucose ABC transporter, ATPase component (AglK) Psest_0871 Psest_1899
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Psest_0854 Psest_1998
edd phosphogluconate dehydratase Psest_1892 Psest_0849
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Psest_2914 Psest_2915
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) Psest_3658 Psest_0871
gnl gluconolactonase Psest_4141 Psest_0364
gtsA glucose ABC transporter, substrate-binding component (GtsA) Psest_1896
gtsB glucose ABC transporter, permease component 1 (GtsB) Psest_1897
gtsC glucose ABC transporter, permease component 2 (GtsC) Psest_1898
gtsD glucose ABC transporter, ATPase component (GtsD) Psest_1899 Psest_0871
kguD 2-keto-6-phosphogluconate reductase Psest_0378 Psest_0431
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
MAL11 maltose permease
malA 6-phospho-alphaglucosidase
malAP maltose permease
malE1 maltose ABC transporter, substrate-binding component (MalE1/MalE2) Psest_0863
malE_Aa maltose ABC transporter, substrate-binding component
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)
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715
malEIICBA maltose phosphotransferase system, EII-CBA components
malF1 maltose ABC transporter, permease component 1 (MalF1) Psest_0864
malF_Aa maltose ABC transporter, permease component 1 Psest_0864
malF_Sm maltose ABC transporter, permease component 1 Psest_0864
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 Psest_0865
malG_Bb maltose ABC transporter, permease component 2 Psest_0865
malG_Sm maltose ABC transporter, permease component 2 Psest_0865
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK1 maltose ABC transporter, ATPase component Psest_1899 Psest_0871
malK_Aa maltose ABC transporter, ATPase component Psest_0871 Psest_1899
malK_Bb maltose ABC transporter, ATPase component Psest_1899 Psest_0871
malK_Sm maltose ABC transporter, ATPase component Psest_0871 Psest_1899
malK_Ss maltose ABC transporter, ATPase component
malP maltose phosphorylase
malX_Sm maltose ABC transporter, substrate-binding component
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mapP maltose 6'-phosphate phosphatase
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) Psest_1392 Psest_1309
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
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 Psest_1899 Psest_0871
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
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) Psest_0864
thuG maltose ABC transporter, permease component 2 (ThuG) Psest_0865 Psest_4061
thuK maltose ABC transporter, ATPase component ThuK Psest_0871 Psest_1899

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