GapMind for catabolism of small carbon sources

 

trehalose catabolism in Brucella inopinata BO1

Best path

thuE, thuF, thuG, thuK, PsTP, pgmA, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
thuE trehalose ABC transporter, substrate-binding component ThuE BIBO1_RS16185
thuF trehalose ABC transporter, permease component 1 (ThuF) BIBO1_RS16190 BIBO1_RS17960
thuG trehalose ABC transporter, permease component 2 (ThuG) BIBO1_RS16195 BIBO1_RS17965
thuK trehalose ABC transporter, ATPase component ThuK BIBO1_RS16200 BIBO1_RS12775
PsTP trehalose phosphorylase
pgmA alpha-phosphoglucomutase BIBO1_RS19955 BIBO1_RS11825
glk glucokinase BIBO1_RS19405 BIBO1_RS14955
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)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG trehalose ABC transporter, permease component 2 (AglG) BIBO1_RS16195 BIBO1_RS17480
aglG' glucose ABC transporter, permease component 2 (AglG) BIBO1_RS17480 BIBO1_RS16195
aglK trehalose ABC trehalose, ATPase component AglK BIBO1_RS16720 BIBO1_RS17490
aglK' glucose ABC transporter, ATPase component (AglK) BIBO1_RS12775 BIBO1_RS16720
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 BIBO1_RS15530 BIBO1_RS18915
edd phosphogluconate dehydratase BIBO1_RS18110 BIBO1_RS18925
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase
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) BIBO1_RS16955 BIBO1_RS11500
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) BIBO1_RS14920 BIBO1_RS17475
gtsC glucose ABC transporter, permease component 2 (GtsC) BIBO1_RS16195 BIBO1_RS17965
gtsD glucose ABC transporter, ATPase component (GtsD) BIBO1_RS12775 BIBO1_RS16720
kguD 2-keto-6-phosphogluconate reductase BIBO1_RS11805 BIBO1_RS06720
kguK 2-ketogluconokinase BIBO1_RS16980
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) BIBO1_RS16195
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK BIBO1_RS12775 BIBO1_RS16720
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 BIBO1_RS15725
mglA glucose ABC transporter, ATP-binding component (MglA) BIBO1_RS18905 BIBO1_RS14060
mglB glucose ABC transporter, substrate-binding component BIBO1_RS18910 BIBO1_RS15350
mglC glucose ABC transporter, permease component (MglC) BIBO1_RS18900 BIBO1_RS11585
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase
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
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) BIBO1_RS12560
treF trehalase
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)
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV BIBO1_RS16720 BIBO1_RS17945

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