GapMind for catabolism of small carbon sources

 

trehalose catabolism in Acidovorax sp. GW101-3H11

Best path

treF, gtsA, gtsB, gtsC, gtsD, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase
gtsA glucose ABC transporter, substrate-binding component (GtsA) Ac3H11_2062
gtsB glucose ABC transporter, permease component 1 (GtsB) Ac3H11_2064
gtsC glucose ABC transporter, permease component 2 (GtsC) Ac3H11_2065
gtsD glucose ABC transporter, ATPase component (GtsD) Ac3H11_2066 Ac3H11_4785
glk glucokinase Ac3H11_2067 Ac3H11_2882
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) Ac3H11_2065 Ac3H11_794
aglG' glucose ABC transporter, permease component 2 (AglG) Ac3H11_2065
aglK trehalose ABC trehalose, ATPase component AglK Ac3H11_2941 Ac3H11_4785
aglK' glucose ABC transporter, ATPase component (AglK) Ac3H11_2941 Ac3H11_2066
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 Ac3H11_2083 Ac3H11_601
edd phosphogluconate dehydratase Ac3H11_2082 Ac3H11_954
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Ac3H11_2872 Ac3H11_3427
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Ac3H11_2201
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) Ac3H11_2065
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) Ac3H11_2066 Ac3H11_4785
gnl gluconolactonase Ac3H11_615 Ac3H11_2081
kguD 2-keto-6-phosphogluconate reductase Ac3H11_2599 Ac3H11_2341
kguK 2-ketogluconokinase Ac3H11_700
kguT 2-ketogluconate transporter
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) Ac3H11_952
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)
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK Ac3H11_2941 Ac3H11_2066
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) Ac3H11_609 Ac3H11_2881
mglB glucose ABC transporter, substrate-binding component Ac3H11_610
mglC glucose ABC transporter, permease component (MglC) Ac3H11_608 Ac3H11_1841
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Ac3H11_2215 Ac3H11_444
pgmB beta-phosphoglucomutase Ac3H11_2632
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET Ac3H11_671
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) Ac3H11_793
thuG trehalose ABC transporter, permease component 2 (ThuG) Ac3H11_794 Ac3H11_2942
thuK trehalose ABC transporter, ATPase component ThuK Ac3H11_2941 Ac3H11_4785
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) Ac3H11_2115
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 Ac3H11_2941 Ac3H11_4785

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:

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