GapMind for catabolism of small carbon sources

 

trehalose catabolism in Klebsiella michiganensis M5al

Best path

treF, mglA, mglB, mglC, 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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase BWI76_RS26700 BWI76_RS17700
mglA glucose ABC transporter, ATP-binding component (MglA) BWI76_RS19640 BWI76_RS07240
mglB glucose ABC transporter, substrate-binding component BWI76_RS19645 BWI76_RS27030
mglC glucose ABC transporter, permease component (MglC) BWI76_RS19635 BWI76_RS14865
glk glucokinase BWI76_RS20510 BWI76_RS22415
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) BWI76_RS03135
aglF' glucose ABC transporter, permease component 1 (AglF) BWI76_RS03135
aglG trehalose ABC transporter, permease component 2 (AglG) BWI76_RS17835 BWI76_RS06705
aglG' glucose ABC transporter, permease component 2 (AglG) BWI76_RS01820
aglK trehalose ABC trehalose, ATPase component AglK BWI76_RS01840 BWI76_RS06690
aglK' glucose ABC transporter, ATPase component (AglK) BWI76_RS01840 BWI76_RS06690
bglF glucose PTS, enzyme II (BCA components, BglF) BWI76_RS19555 BWI76_RS07290
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA BWI76_RS20655 BWI76_RS08220
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BWI76_RS18095 BWI76_RS27940
edd phosphogluconate dehydratase BWI76_RS18100 BWI76_RS00975
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase BWI76_RS04950 BWI76_RS13270
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) BWI76_RS09465 BWI76_RS06035
gnl gluconolactonase BWI76_RS23720 BWI76_RS21470
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) BWI76_RS23380
gtsC glucose ABC transporter, permease component 2 (GtsC) BWI76_RS17835 BWI76_RS06705
gtsD glucose ABC transporter, ATPase component (GtsD) BWI76_RS03270 BWI76_RS06690
kguD 2-keto-6-phosphogluconate reductase BWI76_RS26960 BWI76_RS27925
kguK 2-ketogluconokinase BWI76_RS26950 BWI76_RS07325
kguT 2-ketogluconate transporter BWI76_RS26955 BWI76_RS06145
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 BWI76_RS01830 BWI76_RS06695
malF trehalose ABC transporter, permease component 1 (MalF) BWI76_RS03245 BWI76_RS06700
malF1 trehalose ABC transporter, permease component 1 BWI76_RS01825
malG trehalose ABC transporter, permease component 2 (MalG) BWI76_RS03240 BWI76_RS06705
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK BWI76_RS03270 BWI76_RS23390
malX trehalose ABC transporter, substrate-binding component MalX
manX glucose PTS, enzyme EIIAB BWI76_RS17890 BWI76_RS01735
manY glucose PTS, enzyme EIIC BWI76_RS17895 BWI76_RS01730
manZ glucose PTS, enzyme EIID BWI76_RS17900 BWI76_RS01725
MFS-glucose glucose transporter, MFS superfamily BWI76_RS24055 BWI76_RS17580
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BWI76_RS08290 BWI76_RS25130
pgmB beta-phosphoglucomutase BWI76_RS11780
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB BWI76_RS11130 BWI76_RS08220
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BWI76_RS11130 BWI76_RS08220
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) BWI76_RS23380 BWI76_RS17840
thuG trehalose ABC transporter, permease component 2 (ThuG) BWI76_RS03240 BWI76_RS01820
thuK trehalose ABC transporter, ATPase component ThuK BWI76_RS03270 BWI76_RS23390
treB trehalose PTS system, EII-BC components TreB BWI76_RS02965 BWI76_RS07315
treC trehalose-6-phosphate hydrolase BWI76_RS02960 BWI76_RS16585
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) BWI76_RS20655 BWI76_RS08220
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) BWI76_RS26300
TRET1 facilitated trehalose transporter Tret1 BWI76_RS24055 BWI76_RS23425
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV BWI76_RS06690 BWI76_RS26290

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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