GapMind for catabolism of small carbon sources

 

trehalose catabolism in Sinorhizobium meliloti 1021

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase SMc03064 SMc01532
aglE' glucose ABC transporter, substrate-binding component (AglE) SMc03061
aglF' glucose ABC transporter, permease component 1 (AglF) SMc03062 SM_b20232
aglG' glucose ABC transporter, permease component 2 (AglG) SMc03063 SMc04257
aglK' glucose ABC transporter, ATPase component (AglK) SMc03065 SM_b21605
glk glucokinase SMc02835 SMc03109
Alternative steps:
aglE trehalose ABC transporter, substrate-binding component AglE SMc03061
aglF trehalose ABC transporter, permease component 1 (AglF) SMc03062 SM_b20232
aglG trehalose ABC transporter, permease component 2 (AglG) SMc03063 SMc04257
aglK trehalose ABC trehalose, ATPase component AglK SMc03065 SMc04140
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 SMc03153 SMc02043
edd phosphogluconate dehydratase SMc03068 SMc04045
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit SM_b20402 SMc00086
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase SMc00110 SMa0564
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) SM_b20419 SMc01608
gnl gluconolactonase SMa0196 SM_b20453
gtsA glucose ABC transporter, substrate-binding component (GtsA) SMc04396 SMc04259
gtsB glucose ABC transporter, permease component 1 (GtsB) SMc04395 SMc04258
gtsC glucose ABC transporter, permease component 2 (GtsC) SMc04394 SMc04257
gtsD glucose ABC transporter, ATPase component (GtsD) SM_b20661 SMc04393
kguD 2-keto-6-phosphogluconate reductase SMc01943 SMa2137
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) SMc01978
malF1 trehalose ABC transporter, permease component 1
malG trehalose ABC transporter, permease component 2 (MalG) SMc01979 SMc04137
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK SM_b21106 SM_b20661
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) SM_b20894 SM_b20904
mglB glucose ABC transporter, substrate-binding component SM_b20895 SM_b20902
mglC glucose ABC transporter, permease component (MglC) SM_b20893 SM_b20903
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase SMc03925 SM_b21081
pgmB beta-phosphoglucomutase SMc01502 SM_b21214
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 SM_b20325 SM_b21461
thuF trehalose ABC transporter, permease component 1 (ThuF) SM_b20326 SM_b21459
thuG trehalose ABC transporter, permease component 2 (ThuG) SM_b20327 SM_b21458
thuK trehalose ABC transporter, ATPase component ThuK SM_b20328 SMc02869
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase SMc01532 SMc03064
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) SMc02437
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) SM_b21220 SMa1339
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU) SM_b21219 SMc01979
treV trehalose ABC transporter, ATPase component TreV SM_b20630 SMc01499

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 preprint 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