GapMind for catabolism of small carbon sources

 

trehalose catabolism in Phaeobacter inhibens BS107

Best path

treF, aglE', aglF', aglG', aglK', 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase PGA1_c07890
aglE' glucose ABC transporter, substrate-binding component (AglE) PGA1_c07860
aglF' glucose ABC transporter, permease component 1 (AglF) PGA1_c07870
aglG' glucose ABC transporter, permease component 2 (AglG) PGA1_c07880 PGA1_78p00180
aglK' glucose ABC transporter, ATPase component (AglK) PGA1_c07900 PGA1_c16680
glk glucokinase PGA1_c05420 PGA1_262p00420
Alternative steps:
aglE trehalose ABC transporter, substrate-binding component AglE PGA1_c07860
aglF trehalose ABC transporter, permease component 1 (AglF) PGA1_c07870 PGA1_c07410
aglG trehalose ABC transporter, permease component 2 (AglG) PGA1_c07880 PGA1_c19480
aglK trehalose ABC trehalose, ATPase component AglK PGA1_c07900 PGA1_c16680
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PGA1_c28010 PGA1_c07350
edd phosphogluconate dehydratase PGA1_c28000 PGA1_c07380
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase PGA1_c15880
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) PGA1_c02740 PGA1_c27320
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) PGA1_c19500 PGA1_78p00160
gtsB glucose ABC transporter, permease component 1 (GtsB) PGA1_c19490 PGA1_78p00170
gtsC glucose ABC transporter, permease component 2 (GtsC) PGA1_c19480 PGA1_78p00180
gtsD glucose ABC transporter, ATPase component (GtsD) PGA1_c19470 PGA1_c16680
kguD 2-keto-6-phosphogluconate reductase PGA1_c28260 PGA1_c24680
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) PGA1_c16690 PGA1_c07880
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK PGA1_c02740 PGA1_c07440
malX trehalose ABC transporter, substrate-binding component MalX
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) PGA1_262p00450 PGA1_c23060
mglB glucose ABC transporter, substrate-binding component PGA1_262p00430
mglC glucose ABC transporter, permease component (MglC) PGA1_262p00440 PGA1_c28050
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PGA1_c24340 PGA1_c06550
pgmB beta-phosphoglucomutase PGA1_c29250
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
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) PGA1_c16700 PGA1_c07410
thuG trehalose ABC transporter, permease component 2 (ThuG) PGA1_c16690 PGA1_c27350
thuK trehalose ABC transporter, ATPase component ThuK PGA1_c13180 PGA1_c02740
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase PGA1_c07890
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP)
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) PGA1_c16700
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU) PGA1_c16690 PGA1_c05190
treV trehalose ABC transporter, ATPase component TreV PGA1_c27970 PGA1_c13180

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 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