GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Shewanella sp. ANA-3

Best path

malI, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
malI maltose transporter Shewana3_1925
susB alpha-glucosidase (maltase) Shewana3_2311 Shewana3_1931
glk glucokinase Shewana3_2790 Shewana3_2698
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)
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK maltose ABC transporter, ATPase component AglK Shewana3_3096 Shewana3_3192
aglK' glucose ABC transporter, ATPase component (AglK) Shewana3_3096 Shewana3_3192
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA Shewana3_2258
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Shewana3_2148
edd phosphogluconate dehydratase Shewana3_2149 Shewana3_0358
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase
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) Shewana3_3192 Shewana3_3096
gnl gluconolactonase Shewana3_2088
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) Shewana3_3096 Shewana3_3192
kguD 2-keto-6-phosphogluconate reductase Shewana3_3416 Shewana3_1476
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
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) Shewana3_2822 Shewana3_2258
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 Shewana3_2822
malEIICBA maltose phosphotransferase system, EII-CBA components Shewana3_2822
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)
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
malK maltose ABC transporter, ATPase component MalK Shewana3_3096 Shewana3_3192
malK1 maltose ABC transporter, ATPase component Shewana3_3096 Shewana3_3192
malK_Aa maltose ABC transporter, ATPase component Shewana3_3096 Shewana3_3192
malK_Bb maltose ABC transporter, ATPase component Shewana3_3192 Shewana3_3096
malK_Sm maltose ABC transporter, ATPase component Shewana3_3096 Shewana3_3192
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 Shewana3_2310 Shewana3_2696
mglA glucose ABC transporter, ATP-binding component (MglA) Shewana3_2074 Shewana3_3096
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) Shewana3_2076 Shewana3_2075
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 Shewana3_3096 Shewana3_3192
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase Shewana3_2067
ptsG glucose PTS, enzyme IICB Shewana3_2822
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) Shewana3_2822
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)
thuG maltose ABC transporter, permease component 2 (ThuG)
thuK maltose ABC transporter, ATPase component ThuK Shewana3_3096 Shewana3_3192

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