trehalose catabolism in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

trehalose catabolism in Dyella japonica UNC79MFTsu3.2

Best path

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).

all:

trehalose-3-dehydrogenase, klh and glucose-utilization
or treF and glucose-utilization
or trehalose-PTS, treC and glk
or trehalose-transport, treF and glk
or trehalose-PTS, trePP and pgmB
or trehalose-transport, treP, pgmB and glk
or trehalose-transport, PsTP, pgmA and glk
Comment: In the 3-ketotrehalose pathway, a periplasmic dehydrogenase forms 3-ketotrehalose, a periplasmic 3-ketoglycoside hydrolase (klh) forms glucose and 3-ketoglucose, and the glucose is taken up and utilized; the fate of the 3-ketoglucose is not well understood, but its utilization might not be necessary. In pathway VI, a periplasmic trehalase forms glucose, which is utilized. In pathway I, after uptake and phosphorylation by the PTS, trehalose 6-phosphate hydrolase (treC) forms D-glucose 6-phosphate and D-glucose, and glucokinase (glk) phosphorylates the glucose. In pathway II, a cytoplasmic trehalase cleaves trehalose to two glucose, followed by phosphorylation by glk. In pathway III, after uptake and phosphorylation by the PTS, trehalose-6-phosphate phosphorylase (trePP) forms beta-glucose-1-phosphate and glucose-6-phosphate, and beta-phosphoglucomutase converts glucose-1-phosphate to glucose-6-phosphate. In pathway IV, a secreted inverting trehalose phoshorylase (treP) forms beta-glucose 1-phosphate and glucose; the beta-D-glucose is consumed by beta-phosphoglucomutase. In pathway V, trehalose phosphorylase forms alpha-glucose-1-phosphate and glucose; these are converted to glucose-6-P by alpha-phosphoglucomutase (pgmA) and glk. (This is a fungal pathway and might not occur in prokaryotes.)

trehalose-3-dehydrogenase:

BT2158
or lacA, lacC and lacB

glucose-utilization:

glucose-transport and glk
or glucose-PTS
or gdh, gnl, gadh1, gadh2, gadh3, kguT, kguK, kguD, edd and eda
Comment: Glucose can be taken up and then phosphorylated to glucose 6-phosphate by the kinase glk. Or, both uptake and phosphorylation are catalyzed by a PTS system. Or, glucose is oxidized to glucono-1,5-lactone in the periplasm (by gdh), hydrolyzed to gluconate (by gnl), oxidized to 2-ketogluconate (by gadh123), taken up by kguT, phosphorylated to 2-dehydro-6-phosphogluconate (by kguK), reduced to gluconate 6-phosphate (by kguD), dehydrated by edd to 2-dehydro-3-deoxy-gluconate 6-phosphate, and cleaved by aldolase eda to pyruvate and D-glyceraldehyde 3-phosphate.

glucose-PTS:

ptsG-crr
or bglF
or ptsG and crr
or manX, manY and manZ

glucose-transport:

MFS-glucose
or SSS-glucose
or glcU'
or PAST-A
or SemiSWEET
or SWEET1
or mglA, mglB and mglC
or gtsA, gtsB, gtsC and gtsD
or glcS, glcT, glcU and glcV
or aglE', aglF', aglG' and aglK'
Comment: Transporters and PTS systems were analyzed uzing query: transporter:glucose:D-glucose:D-glucopyranose:ALPHA-GLUCOSE:GLC:CPD-15374

trehalose-transport:

thuE, thuF, thuG and thuK
or lpqY, thuF, thuG and thuK
or malE2, malF1, malG1 and thuK
or malF, malG, malK and malX
or treS, treT, treU and treV
or aglE, aglF, aglG and aglK
or TRET1
Comment: Transporters and PTS systems were identified using query: transporter:trehalose:D-trehalose

trehalose-PTS: treEIIA and treB

Comment: PTS systems form trehalose 6-phosphate. E. coli has EII-BC treB; crr is the EII-A. B. subtilis has EII-BC treP. PMC6148471 shows that ptsG is the predominant EII-A but gamP and ptsA also function. Listeria monocytogenes has EII-BC; the EII-A is not known. Pseudomonas simiae WCS417 and P. fluorescens FW300-N2E3 have similar systems but only EII-A is annotated. In FW300-N2E3, AO353_15980 (A0A0N9WDQ5) is the II-BC protein. In WCS417, PS417_23050 (A0A1N7UR85) is the II-BC protein. These are both similar to E. coli treB.

74 steps (39 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
treF	trehalase	N515DRAFT_3393	N515DRAFT_1888
MFS-glucose	glucose transporter, MFS superfamily	N515DRAFT_1228	N515DRAFT_0382
glk	glucokinase	N515DRAFT_4210	N515DRAFT_0393
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)	N515DRAFT_3134
aglF'	glucose ABC transporter, permease component 1 (AglF)	N515DRAFT_3134
aglG	trehalose ABC transporter, permease component 2 (AglG)	N515DRAFT_3133
aglG'	glucose ABC transporter, permease component 2 (AglG)	N515DRAFT_3133
aglK	trehalose ABC trehalose, ATPase component AglK	N515DRAFT_4212	N515DRAFT_1562
aglK'	glucose ABC transporter, ATPase component (AglK)	N515DRAFT_4212	N515DRAFT_1562
bglF	glucose PTS, enzyme II (BCA components, BglF)
BT2158	periplasmic trehalose 3-dehydrogenase (BT2158)	N515DRAFT_2427
crr	glucose PTS, enzyme IIA
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	N515DRAFT_3178	N515DRAFT_1232
edd	phosphogluconate dehydratase	N515DRAFT_3177
gadh1	gluconate 2-dehydrogenase flavoprotein subunit
gadh2	gluconate 2-dehydrogenase cytochrome c subunit	N515DRAFT_0703	N515DRAFT_2297
gadh3	gluconate 2-dehydrogenase subunit 3
gdh	quinoprotein glucose dehydrogenase	N515DRAFT_0461
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)	N515DRAFT_4212	N515DRAFT_1562
gnl	gluconolactonase	N515DRAFT_1229
gtsA	glucose ABC transporter, substrate-binding component (GtsA)
gtsB	glucose ABC transporter, permease component 1 (GtsB)
gtsC	glucose ABC transporter, permease component 2 (GtsC)	N515DRAFT_3133
gtsD	glucose ABC transporter, ATPase component (GtsD)	N515DRAFT_4212	N515DRAFT_1562
kguD	2-keto-6-phosphogluconate reductase	N515DRAFT_0108	N515DRAFT_3581
kguK	2-ketogluconokinase	N515DRAFT_0916
kguT	2-ketogluconate transporter	N515DRAFT_2085
klh	3-ketotrehalose hydrolase	N515DRAFT_1317
lacA	periplasmic trehalose 3-dehydrogenase, LacA subunit	N515DRAFT_1321
lacB	periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB)
lacC	periplasmic trehalose 3-dehydrogenase, LacC subunit	N515DRAFT_1320
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)	N515DRAFT_3133
malG1	trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK	trehalose ABC transporter, ATPase component MalK	N515DRAFT_4212	N515DRAFT_1562
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)	N515DRAFT_3232	N515DRAFT_2413
mglB	glucose ABC transporter, substrate-binding component	N515DRAFT_3231
mglC	glucose ABC transporter, permease component (MglC)	N515DRAFT_3233	N515DRAFT_2415
PAST-A	proton-associated sugar transporter A
pgmA	alpha-phosphoglucomutase	N515DRAFT_2990	N515DRAFT_1372
pgmB	beta-phosphoglucomutase	N515DRAFT_1906
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)	N515DRAFT_3134
thuG	trehalose ABC transporter, permease component 2 (ThuG)	N515DRAFT_3133
thuK	trehalose ABC transporter, ATPase component ThuK	N515DRAFT_4212	N515DRAFT_1562
treB	trehalose PTS system, EII-BC components TreB
treC	trehalose-6-phosphate hydrolase	N515DRAFT_3393	N515DRAFT_3391
treEIIA	N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP)	N515DRAFT_3957
treP	trehalose phosphorylase, inverting	N515DRAFT_1906
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	N515DRAFT_1228
treU	trehalose ABC transporter, permease component 2 (TreU)
treV	trehalose ABC transporter, ATPase component TreV	N515DRAFT_4212	N515DRAFT_1562

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources