GapMind for catabolism of small carbon sources

 

lactose catabolism in Pseudomonas fluorescens FW300-N2E3

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 (38 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) AO353_23370 AO353_18090
klh periplasmic 3'-ketolactose hydrolase
gtsA glucose ABC transporter, substrate-binding component (GtsA) AO353_03395
gtsB glucose ABC transporter, permease component 1 (GtsB) AO353_03390
gtsC glucose ABC transporter, permease component 2 (GtsC) AO353_03385 AO353_25125
gtsD glucose ABC transporter, ATPase component (GtsD) AO353_03380 AO353_25130
glk glucokinase AO353_03415
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) AO353_03385
aglK' glucose ABC transporter, ATPase component (AglK) AO353_25895 AO353_25130
bglF glucose PTS, enzyme II (BCA components, BglF) AO353_15980
crr glucose PTS, enzyme IIA AO353_15995 AO353_04460
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase AO353_03350 AO353_01265
dgoD D-galactonate dehydratase AO353_03420
dgoK 2-dehydro-3-deoxygalactonokinase AO353_01270 AO353_21745
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO353_03350 AO353_01265
edd phosphogluconate dehydratase AO353_03420 AO353_08345
gadh1 gluconate 2-dehydrogenase flavoprotein subunit AO353_10795
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AO353_10800 AO353_27065
gadh3 gluconate 2-dehydrogenase subunit 3 AO353_10790
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) AO353_23650
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) AO353_01660 AO353_23170
galE UDP-glucose 4-epimerase AO353_06770 AO353_21135
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) AO353_07930
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase AO353_16045
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) AO353_07265 AO353_29310
gnl gluconolactonase AO353_23650
kguD 2-keto-6-phosphogluconate reductase AO353_04850 AO353_26885
kguK 2-ketogluconokinase AO353_26875
kguT 2-ketogluconate transporter AO353_26880 AO353_26910
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase AO353_05480
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 AO353_25895 AO353_25130
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 AO353_25100
mglA glucose ABC transporter, ATP-binding component (MglA) AO353_21385 AO353_20820
mglB glucose ABC transporter, substrate-binding component AO353_21380
mglC glucose ABC transporter, permease component (MglC) AO353_21390 AO353_20825
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase AO353_24665 AO353_09235
ptsG glucose PTS, enzyme IICB AO353_04465
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) AO353_04465
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase AO353_05590 AO353_07945

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