GapMind for catabolism of small carbon sources

 

lactose catabolism in Pseudomonas putida KT2440

Best path

lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)
klh periplasmic 3'-ketolactose hydrolase
gtsA glucose ABC transporter, substrate-binding component (GtsA) PP_1015
gtsB glucose ABC transporter, permease component 1 (GtsB) PP_1016
gtsC glucose ABC transporter, permease component 2 (GtsC) PP_1017
gtsD glucose ABC transporter, ATPase component (GtsD) PP_1018 PP_0411
glk glucokinase PP_1011
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) PP_1017 PP_2263
aglK' glucose ABC transporter, ATPase component (AglK) PP_1018 PP_5179
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase PP_1024
dgoD D-galactonate dehydratase
dgoK 2-dehydro-3-deoxygalactonokinase
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PP_1024
edd phosphogluconate dehydratase PP_1010 PP_5128
gadh1 gluconate 2-dehydrogenase flavoprotein subunit PP_3383
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PP_3382 PP_3623
gadh3 gluconate 2-dehydrogenase subunit 3 PP_3384
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) PP_2021 PP_1170
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) PP_1817 PP_1946
galE UDP-glucose 4-epimerase PP_0501 PP_3129
galK galactokinase (-1-phosphate forming)
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) PP_4960
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase PP_1444 PP_3569
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) PP_0411 PP_5179
gnl gluconolactonase PP_2021 PP_3180
kguD 2-keto-6-phosphogluconate reductase PP_3376 PP_1261
kguK 2-ketogluconokinase PP_3378
kguT 2-ketogluconate transporter PP_3377 PP_3176
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase PP_0794
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
lacIICB lactose PTS system, fused EIIC and EIIB components
lacK lactose ABC transporter, ATPase component PP_1018 PP_0411
lacL heteromeric lactase, large subunit
lacM heteromeric lactase, small subunit
lacP lactose permease LacP
lacS lactose permease LacS
lacY lactose:proton symporter LacY
lacZ lactase (homomeric)
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) PP_2759 PP_2455
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) PP_2761 PP_2456
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase PP_3578 PP_5288
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
tpi triose-phosphate isomerase PP_4715 PP_4963

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