GapMind for catabolism of small carbon sources

 

lactose catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric)
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Pf1N1B4_412 Pf1N1B4_512
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Pf1N1B4_4626 Pf1N1B4_413
dgoD D-galactonate dehydratase Pf1N1B4_398 Pf1N1B4_4621
dgoK 2-dehydro-3-deoxygalactonokinase Pf1N1B4_400 Pf1N1B4_5638
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Pf1N1B4_587 Pf1N1B4_399
glk glucokinase Pf1N1B4_600
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) Pf1N1B4_4011 Pf1N1B4_594
aglK' glucose ABC transporter, ATPase component (AglK) Pf1N1B4_4847 Pf1N1B4_5115
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA Pf1N1B4_833
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf1N1B4_587 Pf1N1B4_399
edd phosphogluconate dehydratase Pf1N1B4_601 Pf1N1B4_2303
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase Pf1N1B4_2638 Pf1N1B4_3585
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) Pf1N1B4_2402
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase Pf1N1B4_821 Pf1N1B4_5582
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) Pf1N1B4_594
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) Pf1N1B4_2538 Pf1N1B4_4352
gnl gluconolactonase Pf1N1B4_4626 Pf1N1B4_4510
gtsA glucose ABC transporter, substrate-binding component (GtsA) Pf1N1B4_596
gtsB glucose ABC transporter, permease component 1 (GtsB) Pf1N1B4_595
gtsC glucose ABC transporter, permease component 2 (GtsC) Pf1N1B4_594 Pf1N1B4_5114
gtsD glucose ABC transporter, ATPase component (GtsD) Pf1N1B4_593 Pf1N1B4_5115
kguD 2-keto-6-phosphogluconate reductase Pf1N1B4_1004 Pf1N1B4_4763
kguK 2-ketogluconokinase Pf1N1B4_4765
kguT 2-ketogluconate transporter Pf1N1B4_4764 Pf1N1B4_5000
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) Pf1N1B4_4109
lacC D-tagatose-6-phosphate kinase Pf1N1B4_1145
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
lacIICB lactose PTS system, fused EIIC and EIIB components
lacK lactose ABC transporter, ATPase component Pf1N1B4_4847 Pf1N1B4_5115
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
mglA glucose ABC transporter, ATP-binding component (MglA) Pf1N1B4_4286 Pf1N1B4_410
mglB glucose ABC transporter, substrate-binding component Pf1N1B4_4386
mglC glucose ABC transporter, permease component (MglC) Pf1N1B4_4287 Pf1N1B4_409
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase Pf1N1B4_4886 Pf1N1B4_2122
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 Pf1N1B4_1164 Pf1N1B4_2399

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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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