GapMind for catabolism of small carbon sources

 

trehalose catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

treF, gtsA, gtsB, gtsC, gtsD, 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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
treF trehalase H281DRAFT_02853 H281DRAFT_02882
gtsA glucose ABC transporter, substrate-binding component (GtsA) H281DRAFT_00166 H281DRAFT_01454
gtsB glucose ABC transporter, permease component 1 (GtsB) H281DRAFT_00167 H281DRAFT_01453
gtsC glucose ABC transporter, permease component 2 (GtsC) H281DRAFT_00168 H281DRAFT_01452
gtsD glucose ABC transporter, ATPase component (GtsD) H281DRAFT_00169 H281DRAFT_03749
glk glucokinase H281DRAFT_00163
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) H281DRAFT_03232 H281DRAFT_02632
aglG' glucose ABC transporter, permease component 2 (AglG) H281DRAFT_00168 H281DRAFT_03232
aglK trehalose ABC trehalose, ATPase component AglK H281DRAFT_04155 H281DRAFT_03228
aglK' glucose ABC transporter, ATPase component (AglK) H281DRAFT_04155 H281DRAFT_03228
bglF glucose PTS, enzyme II (BCA components, BglF)
BT2158 periplasmic trehalose 3-dehydrogenase (BT2158)
crr glucose PTS, enzyme IIA H281DRAFT_01852 H281DRAFT_01977
eda 2-keto-3-deoxygluconate 6-phosphate aldolase H281DRAFT_04277 H281DRAFT_06295
edd phosphogluconate dehydratase H281DRAFT_04278 H281DRAFT_00127
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit H281DRAFT_04220 H281DRAFT_05401
gadh3 gluconate 2-dehydrogenase subunit 3
gdh quinoprotein glucose dehydrogenase H281DRAFT_03298 H281DRAFT_00328
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) H281DRAFT_01452 H281DRAFT_00168
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) H281DRAFT_05887 H281DRAFT_05405
gnl gluconolactonase H281DRAFT_00300 H281DRAFT_05949
kguD 2-keto-6-phosphogluconate reductase H281DRAFT_05213 H281DRAFT_04333
kguK 2-ketogluconokinase H281DRAFT_05211
kguT 2-ketogluconate transporter H281DRAFT_05212 H281DRAFT_00211
klh 3-ketotrehalose hydrolase
lacA periplasmic trehalose 3-dehydrogenase, LacA subunit
lacB periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) H281DRAFT_02148 H281DRAFT_00126
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 H281DRAFT_03749 H281DRAFT_04155
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) H281DRAFT_02712 H281DRAFT_00426
mglB glucose ABC transporter, substrate-binding component H281DRAFT_03877 H281DRAFT_02713
mglC glucose ABC transporter, permease component (MglC) H281DRAFT_02714 H281DRAFT_04148
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase H281DRAFT_00078 H281DRAFT_04410
pgmB beta-phosphoglucomutase H281DRAFT_04156
PsTP trehalose phosphorylase
ptsG glucose PTS, enzyme IICB H281DRAFT_01853 H281DRAFT_01976
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) H281DRAFT_01853 H281DRAFT_01976
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) H281DRAFT_05891 H281DRAFT_03746
thuG trehalose ABC transporter, permease component 2 (ThuG) H281DRAFT_05890 H281DRAFT_04157
thuK trehalose ABC transporter, ATPase component ThuK H281DRAFT_00169 H281DRAFT_03749
treB trehalose PTS system, EII-BC components TreB
treC trehalose-6-phosphate hydrolase H281DRAFT_02777 H281DRAFT_02776
treEIIA N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) H281DRAFT_01852 H281DRAFT_01977
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) H281DRAFT_05703
TRET1 facilitated trehalose transporter Tret1
treU trehalose ABC transporter, permease component 2 (TreU)
treV trehalose ABC transporter, ATPase component TreV H281DRAFT_04155 H281DRAFT_03749

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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