GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Dyella japonica UNC79MFTsu3.2

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
malI maltose transporter N515DRAFT_3387
susB alpha-glucosidase (maltase) N515DRAFT_3393 N515DRAFT_3389
glk glucokinase N515DRAFT_4210 N515DRAFT_0393
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) N515DRAFT_3134
aglF' glucose ABC transporter, permease component 1 (AglF) N515DRAFT_3134
aglG maltose ABC transporter, permease component 2 (AglG) N515DRAFT_3133
aglG' glucose ABC transporter, permease component 2 (AglG) N515DRAFT_3133
aglK maltose ABC transporter, ATPase component AglK N515DRAFT_4212 N515DRAFT_1562
aglK' glucose ABC transporter, ATPase component (AglK) N515DRAFT_4212 N515DRAFT_1562
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase N515DRAFT_3178 N515DRAFT_1232
edd phosphogluconate dehydratase N515DRAFT_3177
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit N515DRAFT_0703 N515DRAFT_2297
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase N515DRAFT_0461
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) N515DRAFT_4212 N515DRAFT_1562
gnl gluconolactonase N515DRAFT_1229
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) N515DRAFT_3133
gtsD glucose ABC transporter, ATPase component (GtsD) N515DRAFT_4212 N515DRAFT_1562
kguD 2-keto-6-phosphogluconate reductase N515DRAFT_0108 N515DRAFT_3581
kguK 2-ketogluconokinase N515DRAFT_0916
kguT 2-ketogluconate transporter N515DRAFT_2085
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)
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 N515DRAFT_3134
malF_Sm maltose ABC transporter, permease component 1
malF_Ss maltose ABC transporter, permease component 1
malG maltose ABC transporter, permease component 2 (MalG) N515DRAFT_1560
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 N515DRAFT_3133
malG_Sm maltose ABC transporter, permease component 2 N515DRAFT_3133
malG_Ss maltose ABC transporter, permease component 2
malK maltose ABC transporter, ATPase component MalK N515DRAFT_4212 N515DRAFT_1562
malK1 maltose ABC transporter, ATPase component N515DRAFT_4212 N515DRAFT_1562
malK_Aa maltose ABC transporter, ATPase component N515DRAFT_4212 N515DRAFT_1562
malK_Bb maltose ABC transporter, ATPase component N515DRAFT_4212 N515DRAFT_1562
malK_Sm maltose ABC transporter, ATPase component N515DRAFT_4212 N515DRAFT_1562
malK_Ss maltose ABC transporter, ATPase component
malP maltose phosphorylase N515DRAFT_1906
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 N515DRAFT_1228 N515DRAFT_0382
mglA glucose ABC transporter, ATP-binding component (MglA) N515DRAFT_3232 N515DRAFT_2413
mglB glucose ABC transporter, substrate-binding component N515DRAFT_3231
mglC glucose ABC transporter, permease component (MglC) N515DRAFT_3233 N515DRAFT_2415
musE maltose ABC transporter, substrate-binding component MusE
musF maltose ABC transporter, permease component 1 (MusF) N515DRAFT_3134
musG maltose ABC transporter, permease component 2 (MusG)
musI maltose ABC transporter, uncharacterized membrane component MusI
musK maltose ABC transporter, ATPase component MusK N515DRAFT_4212 N515DRAFT_1562
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase N515DRAFT_1906
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) N515DRAFT_3134
thuG maltose ABC transporter, permease component 2 (ThuG) N515DRAFT_3133
thuK maltose ABC transporter, ATPase component ThuK N515DRAFT_4212 N515DRAFT_1562

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