GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Phaeobacter inhibens BS107

Best path

aglE, aglF, aglG, aglK, 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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE maltose ABC transporter, substrate-binding component AglK PGA1_c07860
aglF maltose ABC transporter, permease component 1 (AglF) PGA1_c07870 PGA1_c07410
aglG maltose ABC transporter, permease component 2 (AglG) PGA1_c07880 PGA1_c19480
aglK maltose ABC transporter, ATPase component AglK PGA1_c07900 PGA1_c16680
susB alpha-glucosidase (maltase) PGA1_c07890
glk glucokinase PGA1_c05420 PGA1_262p00420
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) PGA1_c07860
aglF' glucose ABC transporter, permease component 1 (AglF) PGA1_c07870
aglG' glucose ABC transporter, permease component 2 (AglG) PGA1_c07880 PGA1_78p00180
aglK' glucose ABC transporter, ATPase component (AglK) PGA1_c07900 PGA1_c16680
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PGA1_c28010 PGA1_c07350
edd phosphogluconate dehydratase PGA1_c28000 PGA1_c07380
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase PGA1_c15880
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) PGA1_c02740 PGA1_c27320
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) PGA1_c19500 PGA1_78p00160
gtsB glucose ABC transporter, permease component 1 (GtsB) PGA1_c19490 PGA1_78p00170
gtsC glucose ABC transporter, permease component 2 (GtsC) PGA1_c19480 PGA1_78p00180
gtsD glucose ABC transporter, ATPase component (GtsD) PGA1_c19470 PGA1_c16680
kguD 2-keto-6-phosphogluconate reductase PGA1_c28260 PGA1_c24680
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) PGA1_c16700
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 PGA1_c16700
malF_Sm maltose ABC transporter, permease component 1
malF_Ss maltose ABC transporter, permease component 1
malG maltose ABC transporter, permease component 2 (MalG) PGA1_c16690 PGA1_c13190
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 PGA1_c16690
malG_Bb maltose ABC transporter, permease component 2 PGA1_c16690
malG_Sm maltose ABC transporter, permease component 2 PGA1_c16690 PGA1_c07880
malG_Ss maltose ABC transporter, permease component 2 PGA1_c28420
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK PGA1_c16680 PGA1_c07440
malK1 maltose ABC transporter, ATPase component PGA1_c02740 PGA1_c16680
malK_Aa maltose ABC transporter, ATPase component PGA1_c02740 PGA1_c07900
malK_Bb maltose ABC transporter, ATPase component PGA1_c16680 PGA1_78p00190
malK_Sm maltose ABC transporter, ATPase component PGA1_c02740 PGA1_c07440
malK_Ss maltose ABC transporter, ATPase component PGA1_c14150
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) PGA1_262p00450 PGA1_c23060
mglB glucose ABC transporter, substrate-binding component PGA1_262p00430
mglC glucose ABC transporter, permease component (MglC) PGA1_262p00440 PGA1_c28050
musE maltose ABC transporter, substrate-binding component MusE
musF maltose ABC transporter, permease component 1 (MusF) PGA1_c19490
musG maltose ABC transporter, permease component 2 (MusG) PGA1_c27950
musI maltose ABC transporter, uncharacterized membrane component MusI
musK maltose ABC transporter, ATPase component MusK PGA1_c02740 PGA1_c16680
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase PGA1_c29250
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) PGA1_c16700 PGA1_c07410
thuG maltose ABC transporter, permease component 2 (ThuG) PGA1_c27350 PGA1_c16690
thuK maltose ABC transporter, ATPase component ThuK PGA1_c07900 PGA1_c13180

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