GapMind for catabolism of small carbon sources

 

trehalose catabolism in Nocardiopsis gilva YIM 90087

Best path

treF, MFS-glucose, glk

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase CDO52_RS09975 CDO52_RS13800
MFS-glucose glucose transporter, MFS superfamily CDO52_RS15385 CDO52_RS07205
glk glucokinase CDO52_RS11555 CDO52_RS05395
Alternative steps:
aglE trehalose ABC transporter, substrate-binding component AglE CDO52_RS08520
aglE' glucose ABC transporter, substrate-binding component (AglE) CDO52_RS08520
aglF trehalose ABC transporter, permease component 1 (AglF) CDO52_RS08515 CDO52_RS10155
aglF' glucose ABC transporter, permease component 1 (AglF) CDO52_RS08515 CDO52_RS22265
aglG trehalose ABC transporter, permease component 2 (AglG) CDO52_RS13840 CDO52_RS08510
aglG' glucose ABC transporter, permease component 2 (AglG) CDO52_RS13840 CDO52_RS08510
aglK trehalose ABC trehalose, ATPase component AglK CDO52_RS13825 CDO52_RS13845
aglK' glucose ABC transporter, ATPase component (AglK) CDO52_RS13825 CDO52_RS13845
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA CDO52_RS24075
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CDO52_RS15330
edd phosphogluconate dehydratase CDO52_RS15320 CDO52_RS20460
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase CDO52_RS22395
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) CDO52_RS13845 CDO52_RS13825
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) CDO52_RS10155
gtsC glucose ABC transporter, permease component 2 (GtsC) CDO52_RS13840 CDO52_RS22270
gtsD glucose ABC transporter, ATPase component (GtsD) CDO52_RS13845 CDO52_RS13825
kguD 2-keto-6-phosphogluconate reductase CDO52_RS22540 CDO52_RS20985
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 CDO52_RS11090
malE2 trehalose ABC transporter, substrate-binding component MalE2
malF trehalose ABC transporter, permease component 1 (MalF) CDO52_RS16290
malF1 trehalose ABC transporter, permease component 1
malG trehalose ABC transporter, permease component 2 (MalG) CDO52_RS20665 CDO52_RS16285
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK CDO52_RS13845 CDO52_RS13825
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) CDO52_RS18110 CDO52_RS22210
mglB glucose ABC transporter, substrate-binding component CDO52_RS18115
mglC glucose ABC transporter, permease component (MglC) CDO52_RS22215
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase CDO52_RS24225 CDO52_RS21155
pgmB beta-phosphoglucomutase CDO52_RS14830 CDO52_RS24070
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB CDO52_RS24095
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) CDO52_RS24095
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
thuE trehalose ABC transporter, substrate-binding component ThuE CDO52_RS11090
thuF trehalose ABC transporter, permease component 1 (ThuF) CDO52_RS16290 CDO52_RS20920
thuG trehalose ABC transporter, permease component 2 (ThuG) CDO52_RS11100 CDO52_RS10160
thuK trehalose ABC transporter, ATPase component ThuK CDO52_RS13825 CDO52_RS13845
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase CDO52_RS09975 CDO52_RS13800
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) CDO52_RS24060 CDO52_RS24095
treP trehalose phosphorylase, inverting
trePP trehalose-6-phosphate phosphorylase CDO52_RS14825
treS trehalose ABC transporter, substrate-binding comopnent TreS
treT trehalose ABC transporter, permease component 1 (TreT) CDO52_RS10155
TRET1 facilitated trehalose transporter Tret1 CDO52_RS15385
treU trehalose ABC transporter, permease component 2 (TreU) CDO52_RS20070 CDO52_RS16285
treV trehalose ABC transporter, ATPase component TreV CDO52_RS13825 CDO52_RS13845

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 24 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