GapMind for catabolism of small carbon sources

 

trehalose catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

lacA, lacC, lacB, klh, MFS-glucose, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit Echvi_1847 Echvi_1439
lacC periplasmic trehalose 3-dehydrogenase, LacC subunit Echvi_1848 Echvi_1438
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) Echvi_1841
klh 3-ketotrehalose hydrolase Echvi_2921 Echvi_1840
MFS-glucose glucose transporter, MFS superfamily Echvi_3909 Echvi_2805
glk glucokinase Echvi_3894 Echvi_3892
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)
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK trehalose ABC trehalose, ATPase component AglK Echvi_1022 Echvi_2123
aglK' glucose ABC transporter, ATPase component (AglK) Echvi_2123 Echvi_1022
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158) Echvi_2281 Echvi_0565
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Echvi_3630 Echvi_3770
edd phosphogluconate dehydratase Echvi_2055
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Echvi_1808
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase Echvi_3019
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) Echvi_1022 Echvi_2123
gnl gluconolactonase Echvi_3728 Echvi_3767
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) Echvi_1022 Echvi_2123
kguD 2-keto-6-phosphogluconate reductase Echvi_2777
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
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 Echvi_1022 Echvi_2123
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) Echvi_1282 Echvi_3112
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) Echvi_1280
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase Echvi_2982 Echvi_1178
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 Echvi_1871 Echvi_1880
SWEET1 bidirectional sugar transporter SWEET1
thuE trehalose ABC transporter, substrate-binding component ThuE
thuF trehalose ABC transporter, permease component 1 (ThuF)
thuG trehalose ABC transporter, permease component 2 (ThuG)
thuK trehalose ABC transporter, ATPase component ThuK Echvi_1022 Echvi_2123
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase Echvi_2850
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP)
treF trehalase Echvi_2045 Echvi_2850
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 Echvi_2805
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV Echvi_1022 Echvi_2123

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