GapMind for catabolism of small carbon sources

 

trehalose catabolism in Shewanella sp. ANA-3

Best path

treF, MFS-glucose, glk

Also see fitness data for the top candidates

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase Shewana3_2311
MFS-glucose glucose transporter, MFS superfamily Shewana3_2310 Shewana3_2696
glk glucokinase Shewana3_2790 Shewana3_2698
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 Shewana3_3096 Shewana3_3192
aglK' glucose ABC transporter, ATPase component (AglK) Shewana3_3096 Shewana3_3192
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA Shewana3_2258
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Shewana3_2148
edd phosphogluconate dehydratase Shewana3_2149 Shewana3_0358
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) Shewana3_3192 Shewana3_3096
gnl gluconolactonase Shewana3_2088
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) Shewana3_3096 Shewana3_3192
kguD 2-keto-6-phosphogluconate reductase Shewana3_3416 Shewana3_1476
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
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)
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK Shewana3_3096 Shewana3_3192
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) Shewana3_2074 Shewana3_3096
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) Shewana3_2076 Shewana3_2075
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Shewana3_2134 Shewana3_2707
pgmB beta-phosphoglucomutase Shewana3_2067
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB Shewana3_2822
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) Shewana3_2822
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)
thuG trehalose ABC transporter, permease component 2 (ThuG)
thuK trehalose ABC transporter, ATPase component ThuK Shewana3_3096 Shewana3_3192
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase Shewana3_2311
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) Shewana3_2258 Shewana3_3042
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
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV Shewana3_3192 Shewana3_3096

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:

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