GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Rhodobacter viridis JA737

Best path

aglE, aglF, aglG, aglK, 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
aglE maltose ABC transporter, substrate-binding component AglK C8J30_RS01970
aglF maltose ABC transporter, permease component 1 (AglF) C8J30_RS01975
aglG maltose ABC transporter, permease component 2 (AglG) C8J30_RS01980
aglK maltose ABC transporter, ATPase component AglK C8J30_RS01990 C8J30_RS03245
susB alpha-glucosidase (maltase) C8J30_RS01985 C8J30_RS02110
glk glucokinase C8J30_RS01955 C8J30_RS04445
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) C8J30_RS01970
aglF' glucose ABC transporter, permease component 1 (AglF) C8J30_RS01975
aglG' glucose ABC transporter, permease component 2 (AglG) C8J30_RS01980
aglK' glucose ABC transporter, ATPase component (AglK) C8J30_RS01990 C8J30_RS03245
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase C8J30_RS09810
edd phosphogluconate dehydratase C8J30_RS09805 C8J30_RS14975
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase
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) C8J30_RS08100 C8J30_RS09730
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) C8J30_RS01980
gtsD glucose ABC transporter, ATPase component (GtsD) C8J30_RS03245 C8J30_RS01990
kguD 2-keto-6-phosphogluconate reductase C8J30_RS11315 C8J30_RS06910
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)
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) C8J30_RS01980 C8J30_RS02700
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 C8J30_RS01980
malG_Bb maltose ABC transporter, permease component 2 C8J30_RS01980
malG_Sm maltose ABC transporter, permease component 2
malG_Ss maltose ABC transporter, permease component 2 C8J30_RS17485
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK C8J30_RS01990 C8J30_RS03245
malK1 maltose ABC transporter, ATPase component C8J30_RS01990 C8J30_RS08100
malK_Aa maltose ABC transporter, ATPase component C8J30_RS03245 C8J30_RS01990
malK_Bb maltose ABC transporter, ATPase component C8J30_RS03245 C8J30_RS01990
malK_Sm maltose ABC transporter, ATPase component C8J30_RS03245 C8J30_RS01990
malK_Ss maltose ABC transporter, ATPase component
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) C8J30_RS04460 C8J30_RS14105
mglB glucose ABC transporter, substrate-binding component C8J30_RS04450 C8J30_RS14110
mglC glucose ABC transporter, permease component (MglC) C8J30_RS04455 C8J30_RS10880
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 C8J30_RS01990 C8J30_RS08100
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) C8J30_RS03235
thuG maltose ABC transporter, permease component 2 (ThuG) C8J30_RS01980
thuK maltose ABC transporter, ATPase component ThuK C8J30_RS01990 C8J30_RS03245

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