GapMind for catabolism of small carbon sources

 

trehalose catabolism in Polaromonas naphthalenivorans CJ2

Best path

treF, gtsA, gtsB, gtsC, gtsD, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase PNAP_RS02610
gtsA glucose ABC transporter, substrate-binding component (GtsA) PNAP_RS18440 PNAP_RS02600
gtsB glucose ABC transporter, permease component 1 (GtsB) PNAP_RS18450
gtsC glucose ABC transporter, permease component 2 (GtsC) PNAP_RS18455 PNAP_RS01130
gtsD glucose ABC transporter, ATPase component (GtsD) PNAP_RS18460 PNAP_RS01135
glk glucokinase PNAP_RS18470
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) PNAP_RS18450
aglF' glucose ABC transporter, permease component 1 (AglF) PNAP_RS18450
aglG trehalose ABC transporter, permease component 2 (AglG) PNAP_RS18455
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK trehalose ABC trehalose, ATPase component AglK PNAP_RS01135 PNAP_RS18460
aglK' glucose ABC transporter, ATPase component (AglK) PNAP_RS01135 PNAP_RS18460
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 PNAP_RS14930
edd phosphogluconate dehydratase PNAP_RS14935 PNAP_RS08485
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PNAP_RS06420 PNAP_RS10510
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase PNAP_RS08950
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) PNAP_RS18460 PNAP_RS14290
gnl gluconolactonase PNAP_RS07950
kguD 2-keto-6-phosphogluconate reductase PNAP_RS07420 PNAP_RS08100
kguK 2-ketogluconokinase PNAP_RS10375 PNAP_RS07425
kguT 2-ketogluconate transporter
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) PNAP_RS14375
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 PNAP_RS01135 PNAP_RS18460
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) PNAP_RS20195 PNAP_RS13010
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) PNAP_RS20205 PNAP_RS13005
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase PNAP_RS22340 PNAP_RS05550
pgmB beta-phosphoglucomutase
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET PNAP_RS18475
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) PNAP_RS01125
thuG trehalose ABC transporter, permease component 2 (ThuG) PNAP_RS01130
thuK trehalose ABC transporter, ATPase component ThuK PNAP_RS01135 PNAP_RS18460
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) PNAP_RS01175
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 PNAP_RS01135 PNAP_RS18460

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 Apr 09 2024. 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