GapMind for catabolism of small carbon sources

 

lactose catabolism in Phaeobacter inhibens BS107

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) PGA1_c07330 PGA1_c07840
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) PGA1_c07370 PGA1_c23480
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) PGA1_c07340
dgoD D-galactonate dehydratase PGA1_c07380 PGA1_c04540
dgoK 2-dehydro-3-deoxygalactonokinase PGA1_c07360
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase PGA1_c07350 PGA1_c28010
glk glucokinase PGA1_c05420 PGA1_262p00420
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) PGA1_c07860
aglF' glucose ABC transporter, permease component 1 (AglF) PGA1_c07870
aglG' glucose ABC transporter, permease component 2 (AglG) PGA1_c07880 PGA1_78p00180
aglK' glucose ABC transporter, ATPase component (AglK) PGA1_c07900 PGA1_c16680
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PGA1_c28010 PGA1_c07350
edd phosphogluconate dehydratase PGA1_c28000 PGA1_c07380
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase PGA1_c34470 PGA1_65p00240
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) PGA1_c07220
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase PGA1_c15880
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) PGA1_c02740 PGA1_c27320
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) PGA1_c19500 PGA1_78p00160
gtsB glucose ABC transporter, permease component 1 (GtsB) PGA1_c19490 PGA1_78p00170
gtsC glucose ABC transporter, permease component 2 (GtsC) PGA1_c19480 PGA1_78p00180
gtsD glucose ABC transporter, ATPase component (GtsD) PGA1_c19470 PGA1_c16680
kguD 2-keto-6-phosphogluconate reductase PGA1_c28260 PGA1_c24680
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit PGA1_c10730
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit PGA1_c10730
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)
lacC D-tagatose-6-phosphate kinase
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 PGA1_c16700
lacG lactose ABC transporter, permease component 2 PGA1_c02730
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 PGA1_c07440 PGA1_c16680
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) PGA1_262p00450 PGA1_c23060
mglB glucose ABC transporter, substrate-binding component PGA1_262p00430
mglC glucose ABC transporter, permease component (MglC) PGA1_262p00440 PGA1_c28050
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase PGA1_c07840
pgmA alpha-phosphoglucomutase PGA1_c24340 PGA1_c06550
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 PGA1_c20650 PGA1_c17530

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