GapMind for catabolism of small carbon sources

 

lactose catabolism in Pseudomonas simiae WCS417

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) PS417_06840
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) PS417_21340 PS417_11045
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) PS417_15140 PS417_17365
dgoD D-galactonate dehydratase PS417_00165 PS417_11000
dgoK 2-dehydro-3-deoxygalactonokinase PS417_00155 PS417_12130
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase PS417_22100 PS417_00160
glk glucokinase PS417_22685
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) PS417_22135 PS417_16225
aglK' glucose ABC transporter, ATPase component (AglK) PS417_12700 PS417_22130
bglF glucose PTS, enzyme II (BCA components, BglF) PS417_23050
crr glucose PTS, enzyme IIA PS417_23035 PS417_22995
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PS417_22100 PS417_00160
edd phosphogluconate dehydratase PS417_22690 PS417_26890
gadh1 gluconate 2-dehydrogenase flavoprotein subunit PS417_00265
gadh2 gluconate 2-dehydrogenase cytochrome c subunit PS417_00270 PS417_10880
gadh3 gluconate 2-dehydrogenase subunit 3 PS417_00260
galE UDP-glucose 4-epimerase PS417_02315 PS417_01385
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) PS417_26415
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase PS417_05300 PS417_10960
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) PS417_27115 PS417_25760
gnl gluconolactonase PS417_15140 PS417_14855
gtsA glucose ABC transporter, substrate-binding component (GtsA) PS417_22145
gtsB glucose ABC transporter, permease component 1 (GtsB) PS417_22140
gtsC glucose ABC transporter, permease component 2 (GtsC) PS417_22135
gtsD glucose ABC transporter, ATPase component (GtsD) PS417_22130 PS417_12700
kguD 2-keto-6-phosphogluconate reductase PS417_04730 PS417_12555
kguK 2-ketogluconokinase PS417_12565
kguT 2-ketogluconate transporter PS417_12560 PS417_10835
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit PS417_12070
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit PS417_12070
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) PS417_23305
lacC D-tagatose-6-phosphate kinase PS417_03970
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 PS417_12700 PS417_22130
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 PS417_04925
mglA glucose ABC transporter, ATP-binding component (MglA) PS417_11890 PS417_13635
mglB glucose ABC transporter, substrate-binding component PS417_10940 PS417_11885
mglC glucose ABC transporter, permease component (MglC) PS417_10930 PS417_12060
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase PS417_13395 PS417_27785
ptsG glucose PTS, enzyme IICB PS417_23000
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) PS417_23000
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase PS417_24000 PS417_26430

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