GapMind for catabolism of small carbon sources

 

lactose catabolism in Pseudomonas fluorescens FW300-N2E2

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) Pf6N2E2_2809
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Pf6N2E2_5967 Pf6N2E2_1441
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Pf6N2E2_614 Pf6N2E2_5966
dgoD D-galactonate dehydratase Pf6N2E2_5977 Pf6N2E2_609
dgoK 2-dehydro-3-deoxygalactonokinase Pf6N2E2_5975 Pf6N2E2_2046
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Pf6N2E2_2883 Pf6N2E2_5976
glk glucokinase Pf6N2E2_2897
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) Pf6N2E2_2890 Pf6N2E2_106
aglK' glucose ABC transporter, ATPase component (AglK) Pf6N2E2_807 Pf6N2E2_1960
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf6N2E2_2883 Pf6N2E2_5976
edd phosphogluconate dehydratase Pf6N2E2_2898 Pf6N2E2_1668
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Pf6N2E2_1903 Pf6N2E2_4408
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase Pf6N2E2_4908 Pf6N2E2_2512
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) Pf6N2E2_4660
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase Pf6N2E2_5442 Pf6N2E2_1939
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) Pf6N2E2_4815 Pf6N2E2_4515
gnl gluconolactonase Pf6N2E2_614 Pf6N2E2_318
gtsA glucose ABC transporter, substrate-binding component (GtsA) Pf6N2E2_2892
gtsB glucose ABC transporter, permease component 1 (GtsB) Pf6N2E2_2891
gtsC glucose ABC transporter, permease component 2 (GtsC) Pf6N2E2_2890 Pf6N2E2_1648
gtsD glucose ABC transporter, ATPase component (GtsD) Pf6N2E2_2889 Pf6N2E2_807
kguD 2-keto-6-phosphogluconate reductase Pf6N2E2_5310 Pf6N2E2_627
kguK 2-ketogluconokinase Pf6N2E2_629
kguT 2-ketogluconate transporter Pf6N2E2_628 Pf6N2E2_1312
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 Pf6N2E2_3338
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 Pf6N2E2_807 Pf6N2E2_1960
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 Pf6N2E2_883 Pf6N2E2_1003
mglA glucose ABC transporter, ATP-binding component (MglA) Pf6N2E2_523 Pf6N2E2_1456
mglB glucose ABC transporter, substrate-binding component Pf6N2E2_1455 Pf6N2E2_1015
mglC glucose ABC transporter, permease component (MglC) Pf6N2E2_524 Pf6N2E2_1457
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase Pf6N2E2_1059 Pf6N2E2_4374
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 Pf6N2E2_3356 Pf6N2E2_4657

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, 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