GapMind for catabolism of small carbon sources

 

lactose catabolism in Pseudomonas fluorescens FW300-N2C3

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) AO356_04805
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) AO356_20240 AO356_28440
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) AO356_24610 AO356_20235
dgoD D-galactonate dehydratase AO356_20290 AO356_24585
dgoK 2-dehydro-3-deoxygalactonokinase AO356_20280 AO356_28555
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase AO356_05150 AO356_20285
glk glucokinase AO356_05215
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) AO356_05185 AO356_21625
aglK' glucose ABC transporter, ATPase component (AglK) AO356_27685 AO356_00010
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA AO356_17540
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO356_05150 AO356_20285
edd phosphogluconate dehydratase AO356_05220 AO356_28760
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AO356_30205
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase AO356_14875 AO356_10040
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) AO356_13705
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase AO356_17600 AO356_30385
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) AO356_14385 AO356_13165
gnl gluconolactonase AO356_24610 AO356_23060
gtsA glucose ABC transporter, substrate-binding component (GtsA) AO356_05195
gtsB glucose ABC transporter, permease component 1 (GtsB) AO356_05190
gtsC glucose ABC transporter, permease component 2 (GtsC) AO356_05185 AO356_28580
gtsD glucose ABC transporter, ATPase component (GtsD) AO356_05180 AO356_28585
kguD 2-keto-6-phosphogluconate reductase AO356_16925 AO356_24675
kguK 2-ketogluconokinase AO356_24685
kguT 2-ketogluconate transporter AO356_24680 AO356_22860
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 AO356_07330
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 AO356_27685 AO356_00010
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 AO356_27270
mglA glucose ABC transporter, ATP-binding component (MglA) AO356_23205 AO356_28510
mglB glucose ABC transporter, substrate-binding component AO356_28505 AO356_23200
mglC glucose ABC transporter, permease component (MglC) AO356_23210 AO356_28515
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase AO356_27065 AO356_12530
ptsG glucose PTS, enzyme IICB AO356_17535
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AO356_17535
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase AO356_07440 AO356_13690

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