GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Sinorhizobium meliloti 1021

Best path

thuE, thuF, thuG, thuK, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
thuE maltose ABC transporter, substrate-binding component ThuE SM_b20325 SM_b21461
thuF maltose ABC transporter, permease component 1 (ThuF) SM_b20326 SM_b21459
thuG maltose ABC transporter, permease component 2 (ThuG) SM_b20327 SM_b21458
thuK maltose ABC transporter, ATPase component ThuK SMc03065 SM_b20328
susB alpha-glucosidase (maltase) SMc03064 SMc01532
glk glucokinase SMc02835 SMc03109
Alternative steps:
aglE maltose ABC transporter, substrate-binding component AglK SMc03061
aglE' glucose ABC transporter, substrate-binding component (AglE) SMc03061
aglF maltose ABC transporter, permease component 1 (AglF) SMc03062 SM_b20232
aglF' glucose ABC transporter, permease component 1 (AglF) SMc03062 SM_b20232
aglG maltose ABC transporter, permease component 2 (AglG) SMc03063 SMc04257
aglG' glucose ABC transporter, permease component 2 (AglG) SMc03063 SMc04257
aglK maltose ABC transporter, ATPase component AglK SMc03065 SMc04140
aglK' glucose ABC transporter, ATPase component (AglK) SMc03065 SM_b21605
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase SMc03153 SMc02043
edd phosphogluconate dehydratase SMc03068 SMc04045
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit SM_b20402 SMc00086
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase SMc00110 SMa0564
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) SM_b20419 SMc01608
gnl gluconolactonase SMa0196 SM_b20453
gtsA glucose ABC transporter, substrate-binding component (GtsA) SMc04396 SMc04259
gtsB glucose ABC transporter, permease component 1 (GtsB) SMc04395 SMc04258
gtsC glucose ABC transporter, permease component 2 (GtsC) SMc04394 SMc04257
gtsD glucose ABC transporter, ATPase component (GtsD) SM_b20661 SMc04393
kguD 2-keto-6-phosphogluconate reductase SMc01943 SMa2137
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)
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715
malEIICBA maltose phosphotransferase system, EII-CBA components
malF maltose ABC transporter, permease component 1 (MalF) SMc01978
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 SM_b20326 SM_b21459
malF_Sm maltose ABC transporter, permease component 1 SMc01978
malF_Ss maltose ABC transporter, permease component 1
malG maltose ABC transporter, permease component 2 (MalG) SMc01979 SMc04137
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 SMc01979 SM_b20327
malG_Bb maltose ABC transporter, permease component 2 SMc01979 SM_b21105
malG_Sm maltose ABC transporter, permease component 2 SMc01979 SMc04137
malG_Ss maltose ABC transporter, permease component 2 SMc02028
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK SMc04140 SM_b21152
malK1 maltose ABC transporter, ATPase component SM_b20661 SM_b21106
malK_Aa maltose ABC transporter, ATPase component SM_b20661 SM_b21106
malK_Bb maltose ABC transporter, ATPase component SM_b20002 SM_b21106
malK_Sm maltose ABC transporter, ATPase component SM_b21106 SM_b20661
malK_Ss maltose ABC transporter, ATPase component SMa0298
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) SM_b20894 SM_b20904
mglB glucose ABC transporter, substrate-binding component SM_b20895 SM_b20902
mglC glucose ABC transporter, permease component (MglC) SM_b20893 SM_b20903
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 SM_b20661 SMc02474
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase SMc01502 SM_b21214
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

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