GapMind for catabolism of small carbon sources

 

trehalose catabolism in Photobacterium jeanii R-40508

Best path

treEIIA, treB, treC, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) A3K86_RS12910 A3K86_RS02900
treB trehalose PTS system, EII-BC components TreB A3K86_RS14090 A3K86_RS20820
treC trehalose-6-phosphate hydrolase A3K86_RS14095
glk glucokinase A3K86_RS19100 A3K86_RS03930
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) A3K86_RS19490
aglG' glucose ABC transporter, permease component 2 (AglG) A3K86_RS19490
aglK trehalose ABC trehalose, ATPase component AglK A3K86_RS19475 A3K86_RS19360
aglK' glucose ABC transporter, ATPase component (AglK) A3K86_RS19475 A3K86_RS19360
bglF glucose PTS, enzyme II (BCA components, BglF) A3K86_RS20820
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA A3K86_RS12910
eda 2-keto-3-deoxygluconate 6-phosphate aldolase A3K86_RS14285 A3K86_RS16310
edd phosphogluconate dehydratase A3K86_RS17170
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) A3K86_RS19475 A3K86_RS02885
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) A3K86_RS02915
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) A3K86_RS19360 A3K86_RS19475
kguD 2-keto-6-phosphogluconate reductase A3K86_RS17455 A3K86_RS13295
kguK 2-ketogluconokinase A3K86_RS20825
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 A3K86_RS19480
malF trehalose ABC transporter, permease component 1 (MalF) A3K86_RS19485
malF1 trehalose ABC transporter, permease component 1
malG trehalose ABC transporter, permease component 2 (MalG) A3K86_RS19490
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK A3K86_RS19360 A3K86_RS19475
malX trehalose ABC transporter, substrate-binding component MalX
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC A3K86_RS16385
manZ glucose PTS, enzyme EIID A3K86_RS16380
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) A3K86_RS19615 A3K86_RS15085
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) A3K86_RS19610
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase A3K86_RS06355 A3K86_RS19410
pgmB beta-phosphoglucomutase
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB A3K86_RS05470 A3K86_RS02900
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) A3K86_RS02900 A3K86_RS05470
SemiSWEET Sugar transporter SemiSWEET
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) A3K86_RS19335 A3K86_RS19485
thuG trehalose ABC transporter, permease component 2 (ThuG) A3K86_RS19490 A3K86_RS19340
thuK trehalose ABC transporter, ATPase component ThuK A3K86_RS19360 A3K86_RS19475
treF trehalase A3K86_RS14095
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) A3K86_RS19485
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV A3K86_RS19475 A3K86_RS02885

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