GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Marivita geojedonensis DPG-138

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aglE maltose ABC transporter, substrate-binding component AglK MGEO_RS13920
aglF maltose ABC transporter, permease component 1 (AglF) MGEO_RS13915 MGEO_RS13975
aglG maltose ABC transporter, permease component 2 (AglG) MGEO_RS13910 MGEO_RS11960
aglK maltose ABC transporter, ATPase component AglK MGEO_RS13900 MGEO_RS10860
susB alpha-glucosidase (maltase) MGEO_RS13905
glk glucokinase MGEO_RS13935
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) MGEO_RS13920
aglF' glucose ABC transporter, permease component 1 (AglF) MGEO_RS13915
aglG' glucose ABC transporter, permease component 2 (AglG) MGEO_RS13910
aglK' glucose ABC transporter, ATPase component (AglK) MGEO_RS13900 MGEO_RS10860
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase MGEO_RS10990 MGEO_RS13950
edd phosphogluconate dehydratase MGEO_RS10995 MGEO_RS17335
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit MGEO_RS06505
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase MGEO_RS14445
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) MGEO_RS08400 MGEO_RS01120
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) MGEO_RS11970
gtsB glucose ABC transporter, permease component 1 (GtsB) MGEO_RS11965 MGEO_RS00455
gtsC glucose ABC transporter, permease component 2 (GtsC) MGEO_RS11960 MGEO_RS00450
gtsD glucose ABC transporter, ATPase component (GtsD) MGEO_RS11955 MGEO_RS12095
kguD 2-keto-6-phosphogluconate reductase MGEO_RS02170 MGEO_RS00570
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) MGEO_RS11960 MGEO_RS13910
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 MGEO_RS08415
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 MGEO_RS13900 MGEO_RS13990
malK1 maltose ABC transporter, ATPase component MGEO_RS08400 MGEO_RS11955
malK_Aa maltose ABC transporter, ATPase component MGEO_RS10860 MGEO_RS13990
malK_Bb maltose ABC transporter, ATPase component MGEO_RS10860 MGEO_RS13990
malK_Sm maltose ABC transporter, ATPase component MGEO_RS08400 MGEO_RS13990
malK_Ss maltose ABC transporter, ATPase component MGEO_RS14290
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) MGEO_RS05035 MGEO_RS05335
mglB glucose ABC transporter, substrate-binding component MGEO_RS12245
mglC glucose ABC transporter, permease component (MglC) MGEO_RS12240 MGEO_RS05025
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 MGEO_RS10860 MGEO_RS13990
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) MGEO_RS10850 MGEO_RS00455
thuG maltose ABC transporter, permease component 2 (ThuG) MGEO_RS08415 MGEO_RS02750
thuK maltose ABC transporter, ATPase component ThuK MGEO_RS13900 MGEO_RS02745

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.

Links

Downloads

Related tools

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