GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Pseudomonas fluorescens FW300-N2C3

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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
susB alpha-glucosidase (maltase) AO356_01250
gtsA glucose ABC transporter, substrate-binding component (GtsA) AO356_05195
gtsB glucose ABC transporter, permease component 1 (GtsB) AO356_05190
gtsC glucose ABC transporter, permease component 2 (GtsC) AO356_05185 AO356_28580
gtsD glucose ABC transporter, ATPase component (GtsD) AO356_05180 AO356_28585
glk glucokinase AO356_05215
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) AO356_28580 AO356_21625
aglG' glucose ABC transporter, permease component 2 (AglG) AO356_05185 AO356_21625
aglK maltose ABC transporter, ATPase component AglK AO356_00010 AO356_27685
aglK' glucose ABC transporter, ATPase component (AglK) AO356_27685 AO356_00010
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA AO356_17540
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO356_05150 AO356_20285
edd phosphogluconate dehydratase AO356_05220 AO356_28760
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AO356_30205
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase AO356_17600 AO356_30385
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) AO356_14385 AO356_13165
gnl gluconolactonase AO356_24610 AO356_23060
kguD 2-keto-6-phosphogluconate reductase AO356_16925 AO356_24675
kguK 2-ketogluconokinase AO356_24685
kguT 2-ketogluconate transporter AO356_24680 AO356_22860
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) AO356_17535 AO356_17540
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 AO356_17535
malEIICBA maltose phosphotransferase system, EII-CBA components AO356_17535
malF maltose ABC transporter, permease component 1 (MalF)
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 AO356_28575
malF_Sm maltose ABC transporter, permease component 1
malF_Ss maltose ABC transporter, permease component 1
malG maltose ABC transporter, permease component 2 (MalG) AO356_28580 AO356_27680
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 AO356_28580
malG_Bb maltose ABC transporter, permease component 2 AO356_28580
malG_Sm maltose ABC transporter, permease component 2 AO356_28580
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK AO356_27685 AO356_28585
malK1 maltose ABC transporter, ATPase component AO356_05180 AO356_00010
malK_Aa maltose ABC transporter, ATPase component AO356_05180 AO356_27685
malK_Bb maltose ABC transporter, ATPase component AO356_05180 AO356_27685
malK_Sm maltose ABC transporter, ATPase component AO356_27685 AO356_00010
malK_Ss maltose ABC transporter, ATPase component AO356_07270
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 AO356_27270
mglA glucose ABC transporter, ATP-binding component (MglA) AO356_23205 AO356_28510
mglB glucose ABC transporter, substrate-binding component AO356_28505 AO356_23200
mglC glucose ABC transporter, permease component (MglC) AO356_23210 AO356_28515
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 AO356_05180 AO356_27685
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase AO356_20805
ptsG glucose PTS, enzyme IICB AO356_17535
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AO356_17535
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 AO356_28570
thuF maltose ABC transporter, permease component 1 (ThuF) AO356_28575 AO356_27675
thuG maltose ABC transporter, permease component 2 (ThuG) AO356_28580 AO356_27680
thuK maltose ABC transporter, ATPase component ThuK AO356_00010 AO356_27685

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