GapMind for catabolism of small carbon sources

 

trehalose catabolism in Mucilaginibacter mallensis MP1X4

Best path

lacA, lacC, lacB, klh, SSS-glucose, 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
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit BLU33_RS12800 BLU33_RS20725
lacC periplasmic trehalose 3-dehydrogenase, LacC subunit BLU33_RS12795
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) BLU33_RS13320 BLU33_RS06140
klh 3-ketotrehalose hydrolase BLU33_RS13315 BLU33_RS08150
SSS-glucose Sodium/glucose cotransporter BLU33_RS02755 BLU33_RS02975
glk glucokinase BLU33_RS02715 BLU33_RS17875
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 BLU33_RS19840 BLU33_RS05275
aglK' glucose ABC transporter, ATPase component (AglK) BLU33_RS19840 BLU33_RS05275
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158) BLU33_RS09135
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BLU33_RS12875
edd phosphogluconate dehydratase BLU33_RS19300
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase BLU33_RS13310
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) BLU33_RS00530 BLU33_RS19840
gnl gluconolactonase BLU33_RS22265 BLU33_RS17565
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) BLU33_RS19840 BLU33_RS14325
kguD 2-keto-6-phosphogluconate reductase BLU33_RS10820 BLU33_RS17605
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 BLU33_RS19840 BLU33_RS14325
malX trehalose ABC transporter, substrate-binding component MalX
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC BLU33_RS11280
manZ glucose PTS, enzyme EIID BLU33_RS11280
MFS-glucose glucose transporter, MFS superfamily BLU33_RS04860 BLU33_RS04945
mglA glucose ABC transporter, ATP-binding component (MglA) BLU33_RS17430 BLU33_RS14325
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BLU33_RS13775 BLU33_RS08520
pgmB beta-phosphoglucomutase BLU33_RS16610 BLU33_RS07050
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET BLU33_RS05585
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 BLU33_RS19840 BLU33_RS00530
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) BLU33_RS11285
treF trehalase BLU33_RS16945 BLU33_RS12070
treP trehalose phosphorylase, inverting BLU33_RS22095 BLU33_RS16605
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 BLU33_RS04945 BLU33_RS04860
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV BLU33_RS19840 BLU33_RS19505

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