GapMind for catabolism of small carbon sources

 

lactose catabolism in Shewanella sp. ANA-3

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)
galK galactokinase (-1-phosphate forming) Shewana3_3578
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galE UDP-glucose 4-epimerase Shewana3_2783 Shewana3_1302
pgmA alpha-phosphoglucomutase Shewana3_2134 Shewana3_2707
glk glucokinase Shewana3_2790 Shewana3_2698
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) Shewana3_3096 Shewana3_3192
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA Shewana3_2258
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Shewana3_2148
dgoD D-galactonate dehydratase Shewana3_2070 Shewana3_2149
dgoK 2-dehydro-3-deoxygalactonokinase
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Shewana3_2148
edd phosphogluconate dehydratase Shewana3_2149 Shewana3_0358
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) Shewana3_2088
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Shewana3_2071 Shewana3_2690
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) Shewana3_3350
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) Shewana3_2700
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) Shewana3_3192 Shewana3_3096
gnl gluconolactonase Shewana3_2088
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) Shewana3_3096 Shewana3_3192
kguD 2-keto-6-phosphogluconate reductase Shewana3_3416 Shewana3_1476
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 Shewana3_3357
lacIICB lactose PTS system, fused EIIC and EIIB components
lacK lactose ABC transporter, ATPase component Shewana3_3096 Shewana3_3192
lacL heteromeric lactase, large subunit
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 Shewana3_2310 Shewana3_2696
mglA glucose ABC transporter, ATP-binding component (MglA) Shewana3_2074 Shewana3_3096
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) Shewana3_2076 Shewana3_2075
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
ptsG glucose PTS, enzyme IICB Shewana3_2822
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) Shewana3_2822
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase Shewana3_1026 Shewana3_3351

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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