GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
susB alpha-glucosidase (maltase) H281DRAFT_02777 H281DRAFT_06049
gtsA glucose ABC transporter, substrate-binding component (GtsA) H281DRAFT_00166 H281DRAFT_01454
gtsB glucose ABC transporter, permease component 1 (GtsB) H281DRAFT_00167 H281DRAFT_01453
gtsC glucose ABC transporter, permease component 2 (GtsC) H281DRAFT_00168 H281DRAFT_01452
gtsD glucose ABC transporter, ATPase component (GtsD) H281DRAFT_00169 H281DRAFT_03749
glk glucokinase H281DRAFT_00163
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) H281DRAFT_03232 H281DRAFT_02632
aglG' glucose ABC transporter, permease component 2 (AglG) H281DRAFT_00168 H281DRAFT_03232
aglK maltose ABC transporter, ATPase component AglK H281DRAFT_04155 H281DRAFT_03228
aglK' glucose ABC transporter, ATPase component (AglK) H281DRAFT_04155 H281DRAFT_03228
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA H281DRAFT_01852 H281DRAFT_01977
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase H281DRAFT_04277 H281DRAFT_06295
edd phosphogluconate dehydratase H281DRAFT_04278 H281DRAFT_00127
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit H281DRAFT_04220 H281DRAFT_05401
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase H281DRAFT_03298 H281DRAFT_00328
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) H281DRAFT_01452 H281DRAFT_00168
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) H281DRAFT_05887 H281DRAFT_05405
gnl gluconolactonase H281DRAFT_00300 H281DRAFT_05949
kguD 2-keto-6-phosphogluconate reductase H281DRAFT_05213 H281DRAFT_04333
kguK 2-ketogluconokinase H281DRAFT_05211
kguT 2-ketogluconate transporter H281DRAFT_05212 H281DRAFT_00211
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) H281DRAFT_01853 H281DRAFT_01976
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 H281DRAFT_01853 H281DRAFT_01976
malEIICBA maltose phosphotransferase system, EII-CBA components H281DRAFT_01853 H281DRAFT_01976
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) H281DRAFT_03745 H281DRAFT_04157
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 H281DRAFT_05890
malG_Bb maltose ABC transporter, permease component 2 H281DRAFT_03745 H281DRAFT_05890
malG_Sm maltose ABC transporter, permease component 2
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK H281DRAFT_04155 H281DRAFT_02629
malK1 maltose ABC transporter, ATPase component H281DRAFT_00169 H281DRAFT_03749
malK_Aa maltose ABC transporter, ATPase component H281DRAFT_04155 H281DRAFT_00169
malK_Bb maltose ABC transporter, ATPase component H281DRAFT_05701 H281DRAFT_00169
malK_Sm maltose ABC transporter, ATPase component H281DRAFT_03749 H281DRAFT_04155
malK_Ss maltose ABC transporter, ATPase component H281DRAFT_04094 H281DRAFT_01032
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) H281DRAFT_02712 H281DRAFT_00426
mglB glucose ABC transporter, substrate-binding component H281DRAFT_03877 H281DRAFT_02713
mglC glucose ABC transporter, permease component (MglC) H281DRAFT_02714 H281DRAFT_04148
musE maltose ABC transporter, substrate-binding component MusE
musF maltose ABC transporter, permease component 1 (MusF) H281DRAFT_05891
musG maltose ABC transporter, permease component 2 (MusG)
musI maltose ABC transporter, uncharacterized membrane component MusI
musK maltose ABC transporter, ATPase component MusK H281DRAFT_05701 H281DRAFT_00169
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase H281DRAFT_04156
ptsG glucose PTS, enzyme IICB H281DRAFT_01853 H281DRAFT_01976
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) H281DRAFT_01853 H281DRAFT_01976
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) H281DRAFT_05891 H281DRAFT_03746
thuG maltose ABC transporter, permease component 2 (ThuG) H281DRAFT_05890 H281DRAFT_04157
thuK maltose ABC transporter, ATPase component ThuK H281DRAFT_04155 H281DRAFT_03228

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