GapMind for catabolism of small carbon sources

 

lactose catabolism in Shewanella loihica PV-4

Best path

lacP, lacZ, galK, galT, galE, pgmA, glk

Also see fitness data for the top candidates

Rules

Overview: Lactose utilization in GapMind is based on MetaCyc pathway lactose degradation II via 3'-ketolactose (link), pathway III via beta-galactosidase (link), or uptake by a PTS system followed by hydrolysis of lactose 6'-phosphate. (There is no pathway I.)

74 steps (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) Shew_3269
galK galactokinase (-1-phosphate forming) Shew_3271 Shew_2287
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase Shew_2288
galE UDP-glucose 4-epimerase Shew_1433 Shew_2285
pgmA alpha-phosphoglucomutase Shew_1922 Shew_2544
glk glucokinase Shew_1428
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG' glucose ABC transporter, permease component 2 (AglG)
aglK' glucose ABC transporter, ATPase component (AglK) Shew_0974 Shew_0863
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA Shew_1864
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Shew_2045
dgoD D-galactonate dehydratase Shew_2046 Shew_0292
dgoK 2-dehydro-3-deoxygalactonokinase
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Shew_2045
edd phosphogluconate dehydratase Shew_2046 Shew_0292
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone)
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Shew_2863 Shew_2862
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) Shew_0755
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase
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) Shew_0974 Shew_0863
gnl gluconolactonase
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) Shew_0974 Shew_0863
kguD 2-keto-6-phosphogluconate reductase Shew_3196 Shew_2309
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)
lacC D-tagatose-6-phosphate kinase
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacE lactose ABC transporter, substrate-binding component
lacF lactose ABC transporter, permease component 1
lacG lactose ABC transporter, permease component 2
lacIIA lactose PTS system, EIIA component
lacIIB lactose PTS system, EIIB component
lacIIC lactose PTS system, EIIC component Shew_0919
lacIICB lactose PTS system, fused EIIC and EIIB components
lacK lactose ABC transporter, ATPase component Shew_0974 Shew_0863
lacL heteromeric lactase, large subunit Shew_3269
lacM heteromeric lactase, small subunit
lacS lactose permease LacS
lacY lactose:proton symporter LacY
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily Shew_1890 Shew_1119
mglA glucose ABC transporter, ATP-binding component (MglA) Shew_0974 Shew_3087
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
ptsG glucose PTS, enzyme IICB Shew_2641
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) Shew_2641
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter Shew_2286 Shew_3270
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase Shew_2831 Shew_0754

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