GapMind for catabolism of small carbon sources

 

trehalose catabolism in Azospirillum brasilense Sp245

Best path

treF, mglA, mglB, mglC, 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 AZOBR_RS25735 AZOBR_RS22875
mglA glucose ABC transporter, ATP-binding component (MglA) AZOBR_RS31245 AZOBR_RS31210
mglB glucose ABC transporter, substrate-binding component AZOBR_RS31240
mglC glucose ABC transporter, permease component (MglC) AZOBR_RS31250 AZOBR_RS31200
glk glucokinase AZOBR_RS05405 AZOBR_RS11685
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) AZOBR_RS18175
aglF' glucose ABC transporter, permease component 1 (AglF) AZOBR_RS18175
aglG trehalose ABC transporter, permease component 2 (AglG) AZOBR_RS18180 AZOBR_RS25890
aglG' glucose ABC transporter, permease component 2 (AglG) AZOBR_RS25890
aglK trehalose ABC trehalose, ATPase component AglK AZOBR_RS25595 AZOBR_RS00060
aglK' glucose ABC transporter, ATPase component (AglK) AZOBR_RS25595 AZOBR_RS00060
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 AZOBR_RS29850 AZOBR_RS22730
edd phosphogluconate dehydratase AZOBR_RS31260 AZOBR_RS15015
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AZOBR_RS04080
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase AZOBR_RS31355
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) AZOBR_RS30790 AZOBR_RS15495
gnl gluconolactonase AZOBR_RS31230
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) AZOBR_RS25590 AZOBR_RS27985
gtsD glucose ABC transporter, ATPase component (GtsD) AZOBR_RS25595 AZOBR_RS00060
kguD 2-keto-6-phosphogluconate reductase AZOBR_RS01325 AZOBR_RS15695
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit AZOBR_RS31645
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) AZOBR_RS25590 AZOBR_RS18180
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK AZOBR_RS00060 AZOBR_RS27980
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
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase AZOBR_RS02670 AZOBR_RS33725
pgmB beta-phosphoglucomutase
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 AZOBR_RS25580
thuF trehalose ABC transporter, permease component 1 (ThuF) AZOBR_RS25585 AZOBR_RS18175
thuG trehalose ABC transporter, permease component 2 (ThuG) AZOBR_RS25590 AZOBR_RS18180
thuK trehalose ABC transporter, ATPase component ThuK AZOBR_RS25595 AZOBR_RS00060
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase AZOBR_RS25735 AZOBR_RS04510
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) AZOBR_RS32325 AZOBR_RS30470
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) AZOBR_RS25585
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU) AZOBR_RS27985 AZOBR_RS25325
treV trehalose ABC transporter, ATPase component TreV AZOBR_RS00060 AZOBR_RS27980

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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