GapMind for catabolism of small carbon sources

 

lactose catabolism in Lactobacillus shenzhenensis LY-73

Best path

lacE, lacF, lacG, lacK, lacL, lacM, galK, galT, galE, pgmA, glk

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacE lactose ABC transporter, substrate-binding component L248_RS09255
lacF lactose ABC transporter, permease component 1 L248_RS09250 L248_RS03135
lacG lactose ABC transporter, permease component 2 L248_RS09245 L248_RS14290
lacK lactose ABC transporter, ATPase component L248_RS10935 L248_RS05360
lacL heteromeric lactase, large subunit L248_RS02125
lacM heteromeric lactase, small subunit L248_RS02130
galK galactokinase (-1-phosphate forming) L248_RS14735
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase L248_RS14745 L248_RS10050
galE UDP-glucose 4-epimerase L248_RS14740 L248_RS03805
pgmA alpha-phosphoglucomutase L248_RS03010 L248_RS03240
glk glucokinase L248_RS05860 L248_RS08620
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) L248_RS12535
aglK' glucose ABC transporter, ATPase component (AglK) L248_RS10935 L248_RS03710
bglF glucose PTS, enzyme II (BCA components, BglF) L248_RS02405 L248_RS07540
crr glucose PTS, enzyme IIA L248_RS07540 L248_RS02405
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase L248_RS07580
dgoD D-galactonate dehydratase
dgoK 2-dehydro-3-deoxygalactonokinase L248_RS06890
eda 2-keto-3-deoxygluconate 6-phosphate aldolase L248_RS07580
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)
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) L248_RS03880 L248_RS07685
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
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 L248_RS06975
glcV glucose ABC transporter, ATPase component (GclV) L248_RS08300 L248_RS03205
gnl gluconolactonase L248_RS02800
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) L248_RS09035
gtsC glucose ABC transporter, permease component 2 (GtsC) L248_RS12535 L248_RS14290
gtsD glucose ABC transporter, ATPase component (GtsD) L248_RS10935 L248_RS05360
kguD 2-keto-6-phosphogluconate reductase L248_RS00245 L248_RS02355
kguK 2-ketogluconokinase L248_RS07595 L248_RS06890
kguT 2-ketogluconate transporter
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 L248_RS01080 L248_RS08245
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric) L248_RS07555 L248_RS00270
lacIIA lactose PTS system, EIIA component L248_RS12015
lacIIB lactose PTS system, EIIB component L248_RS03500
lacIIC lactose PTS system, EIIC component L248_RS09740 L248_RS12020
lacIICB lactose PTS system, fused EIIC and EIIB components L248_RS07875 L248_RS07850
lacP lactose permease LacP
lacS lactose permease LacS L248_RS11455
lacY lactose:proton symporter LacY
lacZ lactase (homomeric) L248_RS08260 L248_RS09345
manX glucose PTS, enzyme EIIAB L248_RS06630 L248_RS05510
manY glucose PTS, enzyme EIIC L248_RS06625
manZ glucose PTS, enzyme EIID L248_RS05520 L248_RS07725
MFS-glucose glucose transporter, MFS superfamily L248_RS09215 L248_RS09595
mglA glucose ABC transporter, ATP-binding component (MglA) L248_RS00360 L248_RS11555
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) L248_RS00365 L248_RS11550
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase L248_RS13935 L248_RS02410
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 L248_RS03080 L248_RS03075

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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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