GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Pseudomonas simiae WCS417

Best path

susB, gtsA, gtsB, gtsC, gtsD, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
susB alpha-glucosidase (maltase) PS417_23045 PS417_12800
gtsA glucose ABC transporter, substrate-binding component (GtsA) PS417_22145
gtsB glucose ABC transporter, permease component 1 (GtsB) PS417_22140
gtsC glucose ABC transporter, permease component 2 (GtsC) PS417_22135
gtsD glucose ABC transporter, ATPase component (GtsD) PS417_22130 PS417_12700
glk glucokinase PS417_22685
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) PS417_16225 PS417_22135
aglG' glucose ABC transporter, permease component 2 (AglG) PS417_22135 PS417_16225
aglK maltose ABC transporter, ATPase component AglK PS417_12700 PS417_22130
aglK' glucose ABC transporter, ATPase component (AglK) PS417_12700 PS417_22130
bglF glucose PTS, enzyme II (BCA components, BglF) PS417_23050
crr glucose PTS, enzyme IIA PS417_23035 PS417_22995
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PS417_22100 PS417_00160
edd phosphogluconate dehydratase PS417_22690 PS417_26890
gadh1 gluconate 2-dehydrogenase flavoprotein subunit PS417_00265
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PS417_00270 PS417_10880
gadh3 gluconate 2-dehydrogenase subunit 3 PS417_00260
gdh quinoprotein glucose dehydrogenase PS417_05300 PS417_10960
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) PS417_27115 PS417_25760
gnl gluconolactonase PS417_15140 PS417_14855
kguD 2-keto-6-phosphogluconate reductase PS417_04730 PS417_12555
kguK 2-ketogluconokinase PS417_12565
kguT 2-ketogluconate transporter PS417_12560 PS417_10835
MAL11 maltose permease
malA 6-phospho-alphaglucosidase
malAP maltose permease
malE maltose ABC transporter, substrate-binding component MalE
malE1 maltose ABC transporter, substrate-binding component (MalE1/MalE2)
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) PS417_23000 PS417_22995
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 PS417_23000
malEIICBA maltose phosphotransferase system, EII-CBA components PS417_23000
malF maltose ABC transporter, permease component 1 (MalF)
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1
malF_Sm maltose ABC transporter, permease component 1
malF_Ss maltose ABC transporter, permease component 1
malG maltose ABC transporter, permease component 2 (MalG) PS417_12705
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2
malG_Bb maltose ABC transporter, permease component 2
malG_Sm maltose ABC transporter, permease component 2
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK PS417_12700 PS417_22130
malK1 maltose ABC transporter, ATPase component PS417_22130 PS417_12700
malK_Aa maltose ABC transporter, ATPase component PS417_22130 PS417_12700
malK_Bb maltose ABC transporter, ATPase component PS417_22130 PS417_12700
malK_Sm maltose ABC transporter, ATPase component PS417_12700 PS417_22130
malK_Ss maltose ABC transporter, ATPase component PS417_08075 PS417_04045
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 PS417_04925
mglA glucose ABC transporter, ATP-binding component (MglA) PS417_11890 PS417_13635
mglB glucose ABC transporter, substrate-binding component PS417_10940 PS417_11885
mglC glucose ABC transporter, permease component (MglC) PS417_10930 PS417_12060
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 PS417_22130 PS417_12700
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase PS417_21150
ptsG glucose PTS, enzyme IICB PS417_23000
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) PS417_23000
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) PS417_12710 PS417_16230
thuG maltose ABC transporter, permease component 2 (ThuG) PS417_12705 PS417_16225
thuK maltose ABC transporter, ATPase component ThuK PS417_12700 PS417_22130

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, 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