GapMind for catabolism of small carbon sources

 

trehalose catabolism in Lentibacillus jeotgali Grbi

Best path

treF, MFS-glucose, glk

Rules

Overview: Trehalose degradation is based on MetaCyc pathways I via trehalose-6-phosphate hydrolase (link), II via cytoplasmic trehalase (link), III via trehalose-6-phosphate phosphorylase (link), IV via inverting trehalose phosphorylase (link), V via trehalose phosphorylase (link), VI via periplasmic trehalase (link), as well as trehalose degradation via 3-ketotrehalose (PMID:33657378).

74 steps (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase ON01_RS02165
MFS-glucose glucose transporter, MFS superfamily ON01_RS14040 ON01_RS16370
glk glucokinase ON01_RS10435 ON01_RS13930
Alternative steps:
aglE trehalose ABC transporter, substrate-binding component AglE
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF trehalose ABC transporter, permease component 1 (AglF)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG trehalose ABC transporter, permease component 2 (AglG)
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK trehalose ABC trehalose, ATPase component AglK ON01_RS04720 ON01_RS09150
aglK' glucose ABC transporter, ATPase component (AglK) ON01_RS04720 ON01_RS09150
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA ON01_RS14400 ON01_RS04420
eda 2-keto-3-deoxygluconate 6-phosphate aldolase ON01_RS05400 ON01_RS08095
edd phosphogluconate dehydratase ON01_RS15945
gadh1 gluconate 2-dehydrogenase flavoprotein subunit ON01_RS04135 ON01_RS08085
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3 ON01_RS04140 ON01_RS08090
gdh quinoprotein glucose dehydrogenase ON01_RS02880
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) ON01_RS04720 ON01_RS16935
gnl gluconolactonase
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) ON01_RS04720 ON01_RS03245
kguD 2-keto-6-phosphogluconate reductase ON01_RS16130 ON01_RS17320
kguK 2-ketogluconokinase ON01_RS05395
kguT 2-ketogluconate transporter
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit ON01_RS08085
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB)
lacC periplasmic trehalose 3-dehydrogenase, LacC subunit
lpqY trehalose ABC transporter, substrate-binding lipoprotein component LpqY
malE2 trehalose ABC transporter, substrate-binding component MalE2
malF trehalose ABC transporter, permease component 1 (MalF)
malF1 trehalose ABC transporter, permease component 1
malG trehalose ABC transporter, permease component 2 (MalG) ON01_RS16345
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK ON01_RS04720 ON01_RS03245
malX trehalose ABC transporter, substrate-binding component MalX
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mglA glucose ABC transporter, ATP-binding component (MglA) ON01_RS16055 ON01_RS08915
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) ON01_RS16060
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase ON01_RS13145 ON01_RS00825
pgmB beta-phosphoglucomutase
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB ON01_RS04430 ON01_RS14380
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) ON01_RS04430 ON01_RS14380
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
thuE trehalose ABC transporter, substrate-binding component ThuE
thuF trehalose ABC transporter, permease component 1 (ThuF) ON01_RS16340
thuG trehalose ABC transporter, permease component 2 (ThuG) ON01_RS16345
thuK trehalose ABC transporter, ATPase component ThuK ON01_RS04720 ON01_RS03245
treB trehalose PTS system, EII-BC components TreB ON01_RS15075
treC trehalose-6-phosphate hydrolase ON01_RS02165
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) ON01_RS14400 ON01_RS04420
treP trehalose phosphorylase, inverting
trePP trehalose-6-phosphate phosphorylase
treS trehalose ABC transporter, substrate-binding comopnent TreS
treT trehalose ABC transporter, permease component 1 (TreT)
TRET1 facilitated trehalose transporter Tret1 ON01_RS14040
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV ON01_RS04720 ON01_RS09150

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