GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Marinomonas arctica 328

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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE maltose ABC transporter, substrate-binding component AglK DK187_RS03320
aglF maltose ABC transporter, permease component 1 (AglF) DK187_RS03325 DK187_RS11930
aglG maltose ABC transporter, permease component 2 (AglG) DK187_RS03330 DK187_RS11925
aglK maltose ABC transporter, ATPase component AglK DK187_RS03335 DK187_RS20415
susB alpha-glucosidase (maltase) DK187_RS03340 DK187_RS13285
glk glucokinase DK187_RS01540
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) DK187_RS03320
aglF' glucose ABC transporter, permease component 1 (AglF) DK187_RS03325 DK187_RS04620
aglG' glucose ABC transporter, permease component 2 (AglG) DK187_RS03330 DK187_RS17250
aglK' glucose ABC transporter, ATPase component (AglK) DK187_RS03335 DK187_RS11940
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase DK187_RS01530 DK187_RS11900
edd phosphogluconate dehydratase DK187_RS13445 DK187_RS19975
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase DK187_RS01750 DK187_RS10780
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) DK187_RS16035 DK187_RS18225
gnl gluconolactonase DK187_RS03545 DK187_RS11895
gtsA glucose ABC transporter, substrate-binding component (GtsA) DK187_RS03300 DK187_RS17240
gtsB glucose ABC transporter, permease component 1 (GtsB) DK187_RS03295 DK187_RS17245
gtsC glucose ABC transporter, permease component 2 (GtsC) DK187_RS03290 DK187_RS17250
gtsD glucose ABC transporter, ATPase component (GtsD) DK187_RS03285 DK187_RS04605
kguD 2-keto-6-phosphogluconate reductase DK187_RS16380 DK187_RS15435
kguK 2-ketogluconokinase DK187_RS16375
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) DK187_RS02520 DK187_RS16025
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 DK187_RS02520 DK187_RS09385
malF_Sm maltose ABC transporter, permease component 1
malF_Ss maltose ABC transporter, permease component 1
malG maltose ABC transporter, permease component 2 (MalG) DK187_RS02525 DK187_RS03330
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 DK187_RS02525 DK187_RS11060
malG_Bb maltose ABC transporter, permease component 2 DK187_RS02525 DK187_RS03330
malG_Sm maltose ABC transporter, permease component 2 DK187_RS02525
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK DK187_RS04605 DK187_RS20415
malK1 maltose ABC transporter, ATPase component DK187_RS03285 DK187_RS04605
malK_Aa maltose ABC transporter, ATPase component DK187_RS03285 DK187_RS09375
malK_Bb maltose ABC transporter, ATPase component DK187_RS03285 DK187_RS04605
malK_Sm maltose ABC transporter, ATPase component DK187_RS03285 DK187_RS11940
malK_Ss maltose ABC transporter, ATPase component DK187_RS03000 DK187_RS12290
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 DK187_RS15015 DK187_RS08940
mglA glucose ABC transporter, ATP-binding component (MglA) DK187_RS20555 DK187_RS16470
mglB glucose ABC transporter, substrate-binding component DK187_RS20550 DK187_RS04280
mglC glucose ABC transporter, permease component (MglC) DK187_RS20560 DK187_RS04270
musE maltose ABC transporter, substrate-binding component MusE
musF maltose ABC transporter, permease component 1 (MusF)
musG maltose ABC transporter, permease component 2 (MusG) DK187_RS09460
musI maltose ABC transporter, uncharacterized membrane component MusI
musK maltose ABC transporter, ATPase component MusK DK187_RS09450 DK187_RS16035
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase DK187_RS10645
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 DK187_RS02515
thuF maltose ABC transporter, permease component 1 (ThuF) DK187_RS02520 DK187_RS09385
thuG maltose ABC transporter, permease component 2 (ThuG) DK187_RS02525 DK187_RS09460
thuK maltose ABC transporter, ATPase component ThuK DK187_RS03335 DK187_RS02530

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