GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Sphingomonas koreensis DSMZ 15582

Best path

malI, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
malI maltose transporter Ga0059261_1585
susB alpha-glucosidase (maltase) Ga0059261_1581 Ga0059261_1579
glk glucokinase Ga0059261_0355 Ga0059261_1776
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)
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK maltose ABC transporter, ATPase component AglK Ga0059261_3668 Ga0059261_0562
aglK' glucose ABC transporter, ATPase component (AglK) Ga0059261_3668 Ga0059261_0562
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA Ga0059261_1646
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Ga0059261_0356 Ga0059261_1625
edd phosphogluconate dehydratase Ga0059261_0354 Ga0059261_4216
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) Ga0059261_3874 Ga0059261_1321
gnl gluconolactonase Ga0059261_1893
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) Ga0059261_3668 Ga0059261_3874
kguD 2-keto-6-phosphogluconate reductase Ga0059261_2669 Ga0059261_2264
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) Ga0059261_1647 Ga0059261_1646
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 Ga0059261_1647
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)
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
malG_Sm maltose ABC transporter, permease component 2
malG_Ss maltose ABC transporter, permease component 2
malK maltose ABC transporter, ATPase component MalK Ga0059261_3668 Ga0059261_1321
malK1 maltose ABC transporter, ATPase component Ga0059261_1321
malK_Aa maltose ABC transporter, ATPase component Ga0059261_2293
malK_Bb maltose ABC transporter, ATPase component Ga0059261_0341 Ga0059261_3668
malK_Sm maltose ABC transporter, ATPase component Ga0059261_3874 Ga0059261_1321
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 Ga0059261_1891 Ga0059261_0767
mglA glucose ABC transporter, ATP-binding component (MglA) Ga0059261_2542 Ga0059261_3276
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 Ga0059261_2293
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase
ptsG glucose PTS, enzyme IICB Ga0059261_1647
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) Ga0059261_1647
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter Ga0059261_1623
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)
thuG maltose ABC transporter, permease component 2 (ThuG)
thuK maltose ABC transporter, ATPase component ThuK Ga0059261_3668 Ga0059261_3874

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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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