GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Klebsiella michiganensis M5al

Best path

malE, malF, malG, malK, 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 (58 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
malE maltose ABC transporter, substrate-binding component MalE BWI76_RS01830
malF maltose ABC transporter, permease component 1 (MalF) BWI76_RS01825
malG maltose ABC transporter, permease component 2 (MalG) BWI76_RS01820 BWI76_RS06705
malK maltose ABC transporter, ATPase component MalK BWI76_RS01840 BWI76_RS06690
susB alpha-glucosidase (maltase) BWI76_RS06250 BWI76_RS02960
glk glucokinase BWI76_RS20510 BWI76_RS22415
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) BWI76_RS03135
aglF' glucose ABC transporter, permease component 1 (AglF) BWI76_RS03135
aglG maltose ABC transporter, permease component 2 (AglG) BWI76_RS17835 BWI76_RS06705
aglG' glucose ABC transporter, permease component 2 (AglG) BWI76_RS01820
aglK maltose ABC transporter, ATPase component AglK BWI76_RS01840 BWI76_RS06690
aglK' glucose ABC transporter, ATPase component (AglK) BWI76_RS01840 BWI76_RS06690
bglF glucose PTS, enzyme II (BCA components, BglF) BWI76_RS19555 BWI76_RS07290
crr glucose PTS, enzyme IIA BWI76_RS20655 BWI76_RS08220
cscB maltose permease BWI76_RS23415 BWI76_RS09125
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BWI76_RS18095 BWI76_RS27940
edd phosphogluconate dehydratase BWI76_RS18100 BWI76_RS00975
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase BWI76_RS04950 BWI76_RS13270
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) BWI76_RS09465 BWI76_RS06035
gnl gluconolactonase BWI76_RS23720 BWI76_RS21470
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) BWI76_RS23380
gtsC glucose ABC transporter, permease component 2 (GtsC) BWI76_RS17835 BWI76_RS06705
gtsD glucose ABC transporter, ATPase component (GtsD) BWI76_RS03270 BWI76_RS06690
kguD 2-keto-6-phosphogluconate reductase BWI76_RS26960 BWI76_RS27925
kguK 2-ketogluconokinase BWI76_RS26950 BWI76_RS07325
kguT 2-ketogluconate transporter BWI76_RS26955 BWI76_RS06145
MAL11 maltose permease
malA 6-phospho-alphaglucosidase BWI76_RS27880 BWI76_RS18685
malAP maltose permease
malE1 maltose ABC transporter, substrate-binding component (MalE1/MalE2) BWI76_RS06695 BWI76_RS01830
malE_Aa maltose ABC transporter, substrate-binding component BWI76_RS01830
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) BWI76_RS08220 BWI76_RS11130
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 BWI76_RS11130 BWI76_RS27535
malEIICBA maltose phosphotransferase system, EII-CBA components BWI76_RS08220 BWI76_RS11130
malF1 maltose ABC transporter, permease component 1 (MalF1) BWI76_RS01825
malF_Aa maltose ABC transporter, permease component 1 BWI76_RS06700 BWI76_RS03245
malF_Sm maltose ABC transporter, permease component 1 BWI76_RS03245 BWI76_RS06700
malF_Ss maltose ABC transporter, permease component 1
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 BWI76_RS06705 BWI76_RS03240
malG_Bb maltose ABC transporter, permease component 2 BWI76_RS06705 BWI76_RS03240
malG_Sm maltose ABC transporter, permease component 2 BWI76_RS03240 BWI76_RS06705
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK1 maltose ABC transporter, ATPase component BWI76_RS03270 BWI76_RS23390
malK_Aa maltose ABC transporter, ATPase component BWI76_RS03270 BWI76_RS17830
malK_Bb maltose ABC transporter, ATPase component BWI76_RS06690 BWI76_RS26290
malK_Sm maltose ABC transporter, ATPase component BWI76_RS03270 BWI76_RS26290
malK_Ss maltose ABC transporter, ATPase component BWI76_RS17225 BWI76_RS26870
malP maltose phosphorylase
malX_Sm maltose ABC transporter, substrate-binding component
manX glucose PTS, enzyme EIIAB BWI76_RS17890 BWI76_RS01735
manY glucose PTS, enzyme EIIC BWI76_RS17895 BWI76_RS01730
manZ glucose PTS, enzyme EIID BWI76_RS17900 BWI76_RS01725
mapP maltose 6'-phosphate phosphatase
MFS-glucose glucose transporter, MFS superfamily BWI76_RS24055 BWI76_RS17580
mglA glucose ABC transporter, ATP-binding component (MglA) BWI76_RS19640 BWI76_RS07240
mglB glucose ABC transporter, substrate-binding component BWI76_RS19645 BWI76_RS27030
mglC glucose ABC transporter, permease component (MglC) BWI76_RS19635 BWI76_RS14865
musE maltose ABC transporter, substrate-binding component MusE
musF maltose ABC transporter, permease component 1 (MusF) BWI76_RS17840
musG maltose ABC transporter, permease component 2 (MusG)
musI maltose ABC transporter, uncharacterized membrane component MusI
musK maltose ABC transporter, ATPase component MusK BWI76_RS17830 BWI76_RS26290
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase BWI76_RS11780
ptsG glucose PTS, enzyme IICB BWI76_RS11130 BWI76_RS08220
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BWI76_RS11130 BWI76_RS08220
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) BWI76_RS23380 BWI76_RS17840
thuG maltose ABC transporter, permease component 2 (ThuG) BWI76_RS03240 BWI76_RS06705
thuK maltose ABC transporter, ATPase component ThuK BWI76_RS03270 BWI76_RS01840

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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