GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Rhizobium etli CFN 42

Best path

thuE, thuF, thuG, thuK, 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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
thuE maltose ABC transporter, substrate-binding component ThuE RHE_RS27520
thuF maltose ABC transporter, permease component 1 (ThuF) RHE_RS27515 RHE_RS17260
thuG maltose ABC transporter, permease component 2 (ThuG) RHE_RS27510 RHE_RS24525
thuK maltose ABC transporter, ATPase component ThuK RHE_RS03540 RHE_RS27505
susB alpha-glucosidase (maltase) RHE_RS03535 RHE_RS15830
glk glucokinase RHE_RS00875 RHE_RS07925
Alternative steps:
aglE maltose ABC transporter, substrate-binding component AglK RHE_RS03520
aglE' glucose ABC transporter, substrate-binding component (AglE) RHE_RS03520
aglF maltose ABC transporter, permease component 1 (AglF) RHE_RS03525 RHE_RS26925
aglF' glucose ABC transporter, permease component 1 (AglF) RHE_RS03525 RHE_RS07945
aglG maltose ABC transporter, permease component 2 (AglG) RHE_RS03530 RHE_RS12570
aglG' glucose ABC transporter, permease component 2 (AglG) RHE_RS03530 RHE_RS12570
aglK maltose ABC transporter, ATPase component AglK RHE_RS03540 RHE_RS00440
aglK' glucose ABC transporter, ATPase component (AglK) RHE_RS03540 RHE_RS27950
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase RHE_RS18590 RHE_RS04295
edd phosphogluconate dehydratase RHE_RS03550 RHE_RS16175
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit RHE_RS04980 RHE_RS06225
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase RHE_RS06265 RHE_RS17355
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) RHE_RS03530
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) RHE_RS03620 RHE_RS14790
gnl gluconolactonase RHE_RS18940 RHE_RS28940
gtsA glucose ABC transporter, substrate-binding component (GtsA) RHE_RS18965 RHE_RS08805
gtsB glucose ABC transporter, permease component 1 (GtsB) RHE_RS18960 RHE_RS12575
gtsC glucose ABC transporter, permease component 2 (GtsC) RHE_RS18955 RHE_RS12570
gtsD glucose ABC transporter, ATPase component (GtsD) RHE_RS18950 RHE_RS08820
kguD 2-keto-6-phosphogluconate reductase RHE_RS28405 RHE_RS23565
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 RHE_RS27515 RHE_RS26900
malF_Sm maltose ABC transporter, permease component 1
malF_Ss maltose ABC transporter, permease component 1 RHE_RS25760
malG maltose ABC transporter, permease component 2 (MalG) RHE_RS24525 RHE_RS29395
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 RHE_RS25310 RHE_RS24525
malG_Bb maltose ABC transporter, permease component 2 RHE_RS25310 RHE_RS24525
malG_Sm maltose ABC transporter, permease component 2 RHE_RS24525 RHE_RS25310
malG_Ss maltose ABC transporter, permease component 2 RHE_RS25755 RHE_RS27675
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK RHE_RS03540 RHE_RS22750
malK1 maltose ABC transporter, ATPase component RHE_RS28085 RHE_RS26890
malK_Aa maltose ABC transporter, ATPase component RHE_RS28085 RHE_RS25880
malK_Bb maltose ABC transporter, ATPase component RHE_RS12565 RHE_RS23370
malK_Sm maltose ABC transporter, ATPase component RHE_RS28085 RHE_RS22750
malK_Ss maltose ABC transporter, ATPase component RHE_RS03060 RHE_RS25015
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) RHE_RS16195 RHE_RS27550
mglB glucose ABC transporter, substrate-binding component RHE_RS16200 RHE_RS16235
mglC glucose ABC transporter, permease component (MglC) RHE_RS16190 RHE_RS16240
musE maltose ABC transporter, substrate-binding component MusE
musF maltose ABC transporter, permease component 1 (MusF) RHE_RS28070 RHE_RS00425
musG maltose ABC transporter, permease component 2 (MusG) RHE_RS23035 RHE_RS14805
musI maltose ABC transporter, uncharacterized membrane component MusI
musK maltose ABC transporter, ATPase component MusK RHE_RS25880 RHE_RS26890
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase RHE_RS18805
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

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 Apr 09 2024. 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