GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Belnapia rosea CPCC 100156

Best path

MAL11, susB, glk

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
MAL11 maltose permease
susB alpha-glucosidase (maltase) BLR02_RS13820 BLR02_RS01805
glk glucokinase BLR02_RS12205 BLR02_RS06040
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) BLR02_RS19230
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK maltose ABC transporter, ATPase component AglK BLR02_RS15665 BLR02_RS07875
aglK' glucose ABC transporter, ATPase component (AglK) BLR02_RS15665 BLR02_RS07875
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BLR02_RS17280 BLR02_RS16045
edd phosphogluconate dehydratase BLR02_RS03715 BLR02_RS21720
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase BLR02_RS21990
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) BLR02_RS15665 BLR02_RS19775
gnl gluconolactonase BLR02_RS12260 BLR02_RS16110
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) BLR02_RS07865 BLR02_RS22755
gtsC glucose ABC transporter, permease component 2 (GtsC) BLR02_RS15660 BLR02_RS27610
gtsD glucose ABC transporter, ATPase component (GtsD) BLR02_RS15665 BLR02_RS07875
kguD 2-keto-6-phosphogluconate reductase BLR02_RS09805 BLR02_RS21370
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter BLR02_RS22360
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) BLR02_RS15655
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 BLR02_RS15655 BLR02_RS07865
malF_Sm maltose ABC transporter, permease component 1
malF_Ss maltose ABC transporter, permease component 1 BLR02_RS17325
malG maltose ABC transporter, permease component 2 (MalG) BLR02_RS27610 BLR02_RS06625
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 BLR02_RS15660 BLR02_RS07860
malG_Sm maltose ABC transporter, permease component 2 BLR02_RS27610 BLR02_RS07860
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK BLR02_RS15665 BLR02_RS07875
malK1 maltose ABC transporter, ATPase component BLR02_RS15665 BLR02_RS07875
malK_Aa maltose ABC transporter, ATPase component BLR02_RS15665 BLR02_RS07875
malK_Bb maltose ABC transporter, ATPase component BLR02_RS15665 BLR02_RS00310
malK_Sm maltose ABC transporter, ATPase component BLR02_RS15665 BLR02_RS07875
malK_Ss maltose ABC transporter, ATPase component BLR02_RS01065 BLR02_RS08365
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) BLR02_RS00885 BLR02_RS02520
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
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 BLR02_RS00310 BLR02_RS07875
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase
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) BLR02_RS27605 BLR02_RS07865
thuG maltose ABC transporter, permease component 2 (ThuG) BLR02_RS27610 BLR02_RS07860
thuK maltose ABC transporter, ATPase component ThuK BLR02_RS15665 BLR02_RS07875

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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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