GapMind for catabolism of small carbon sources

 

lactose catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

lacA', lacC', lacB', klh, SSS-glucose, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit CA265_RS15345 CA265_RS16770
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit CA265_RS15340
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) CA265_RS15360 CA265_RS11590
klh periplasmic 3'-ketolactose hydrolase CA265_RS14585 CA265_RS02410
SSS-glucose Sodium/glucose cotransporter CA265_RS06755 CA265_RS19720
glk glucokinase CA265_RS15640 CA265_RS11300
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)
aglK' glucose ABC transporter, ATPase component (AglK) CA265_RS04345 CA265_RS15880
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase CA265_RS02050 CA265_RS19860
dgoD D-galactonate dehydratase CA265_RS15795 CA265_RS13665
dgoK 2-dehydro-3-deoxygalactonokinase
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CA265_RS19860 CA265_RS02050
edd phosphogluconate dehydratase
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) CA265_RS25055 CA265_RS13655
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) CA265_RS13660 CA265_RS15450
galE UDP-glucose 4-epimerase CA265_RS25430 CA265_RS25425
galK galactokinase (-1-phosphate forming) CA265_RS06125 CA265_RS09565
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase CA265_RS06120
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY)
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase CA265_RS06300 CA265_RS03100
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) CA265_RS15880 CA265_RS04175
gnl gluconolactonase CA265_RS25055 CA265_RS13655
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) CA265_RS04200 CA265_RS15880
kguD 2-keto-6-phosphogluconate reductase CA265_RS17230 CA265_RS12240
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
lacA galactose-6-phosphate isomerase, lacA subunit CA265_RS18380
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase CA265_RS02195 CA265_RS20980
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 CA265_RS04345 CA265_RS07485
lacL heteromeric lactase, large subunit CA265_RS04025
lacM heteromeric lactase, small subunit
lacP lactose permease LacP
lacS lactose permease LacS
lacY lactose:proton symporter LacY
lacZ lactase (homomeric) CA265_RS04025 CA265_RS08540
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily CA265_RS04675 CA265_RS08575
mglA glucose ABC transporter, ATP-binding component (MglA)
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase CA265_RS16425
pgmA alpha-phosphoglucomutase CA265_RS09660 CA265_RS13185
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase CA265_RS10795 CA265_RS01880

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