GapMind for catabolism of small carbon sources

 

trehalose catabolism in Sinorhizobium fredii NGR234

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase NGR_RS12930 NGR_RS23020
gtsA glucose ABC transporter, substrate-binding component (GtsA) NGR_RS27655 NGR_RS07700
gtsB glucose ABC transporter, permease component 1 (GtsB) NGR_RS27660 NGR_RS07695
gtsC glucose ABC transporter, permease component 2 (GtsC) NGR_RS07690 NGR_RS27665
gtsD glucose ABC transporter, ATPase component (GtsD) NGR_RS07685 NGR_RS05625
glk glucokinase NGR_RS28545 NGR_RS26390
Alternative steps:
aglE trehalose ABC transporter, substrate-binding component AglE NGR_RS12915
aglE' glucose ABC transporter, substrate-binding component (AglE) NGR_RS12915
aglF trehalose ABC transporter, permease component 1 (AglF) NGR_RS12920 NGR_RS01320
aglF' glucose ABC transporter, permease component 1 (AglF) NGR_RS12920 NGR_RS30985
aglG trehalose ABC transporter, permease component 2 (AglG) NGR_RS12925 NGR_RS20150
aglG' glucose ABC transporter, permease component 2 (AglG) NGR_RS12925 NGR_RS20150
aglK trehalose ABC trehalose, ATPase component AglK NGR_RS12935 NGR_RS08670
aglK' glucose ABC transporter, ATPase component (AglK) NGR_RS12935 NGR_RS01305
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 NGR_RS25805 NGR_RS13545
edd phosphogluconate dehydratase NGR_RS12950 NGR_RS24345
gadh1 gluconate 2-dehydrogenase flavoprotein subunit NGR_RS00555
gadh2 gluconate 2-dehydrogenase cytochrome c subunit NGR_RS15000
gadh3 gluconate 2-dehydrogenase subunit 3 NGR_RS00550 NGR_RS00545
gdh quinoprotein glucose dehydrogenase NGR_RS15020 NGR_RS22565
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) NGR_RS09940 NGR_RS01050
gnl gluconolactonase NGR_RS10695 NGR_RS02200
kguD 2-keto-6-phosphogluconate reductase NGR_RS25005 NGR_RS25725
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter NGR_RS09750
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit NGR_RS00540
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
malF trehalose ABC transporter, permease component 1 (MalF)
malF1 trehalose ABC transporter, permease component 1
malG trehalose ABC transporter, permease component 2 (MalG) NGR_RS23885 NGR_RS11130
malG1 trehalose ABC transporter, permease component 2 (MalG1/MalG2)
malK trehalose ABC transporter, ATPase component MalK NGR_RS05345 NGR_RS30975
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) NGR_RS23220 NGR_RS00525
mglB glucose ABC transporter, substrate-binding component NGR_RS23225 NGR_RS23260
mglC glucose ABC transporter, permease component (MglC) NGR_RS23215 NGR_RS23265
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase NGR_RS25635 NGR_RS06645
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
SWEET1 bidirectional sugar transporter SWEET1
thuE trehalose ABC transporter, substrate-binding component ThuE NGR_RS11140 NGR_RS05650
thuF trehalose ABC transporter, permease component 1 (ThuF) NGR_RS11135 NGR_RS09950
thuG trehalose ABC transporter, permease component 2 (ThuG) NGR_RS11130 NGR_RS23885
thuK trehalose ABC transporter, ATPase component ThuK NGR_RS11125 NGR_RS28730
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase NGR_RS12930 NGR_RS23020
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) NGR_RS02015
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) NGR_RS05645
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU) NGR_RS05640 NGR_RS23885
treV trehalose ABC transporter, ATPase component TreV NGR_RS23510 NGR_RS08900

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