GapMind for catabolism of small carbon sources

 

lactose catabolism in Haloglycomyces albus DSM 45210

Best path

lacP, lacZ, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) HALAL_RS0100400
galK galactokinase (-1-phosphate forming) HALAL_RS0102100
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase HALAL_RS0102095
galE UDP-glucose 4-epimerase HALAL_RS0107925 HALAL_RS0107320
pgmA alpha-phosphoglucomutase HALAL_RS0110755 HALAL_RS0101005
glk glucokinase HALAL_RS0115585
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) HALAL_RS0110970
aglF' glucose ABC transporter, permease component 1 (AglF) HALAL_RS0110975
aglG' glucose ABC transporter, permease component 2 (AglG) HALAL_RS0110980
aglK' glucose ABC transporter, ATPase component (AglK) HALAL_RS0103205 HALAL_RS0106690
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA HALAL_RS0104250
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase HALAL_RS0114520
dgoD D-galactonate dehydratase
dgoK 2-dehydro-3-deoxygalactonokinase HALAL_RS0114515
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HALAL_RS0114520
edd phosphogluconate dehydratase HALAL_RS0110680
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) HALAL_RS0102560 HALAL_RS0108330
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 HALAL_RS0114665 HALAL_RS0112240
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) HALAL_RS0110980
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) HALAL_RS0103205 HALAL_RS0104115
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) HALAL_RS0110975 HALAL_RS17205
gtsC glucose ABC transporter, permease component 2 (GtsC) HALAL_RS0110980 HALAL_RS0103045
gtsD glucose ABC transporter, ATPase component (GtsD) HALAL_RS0103205 HALAL_RS0110610
kguD 2-keto-6-phosphogluconate reductase HALAL_RS0113460 HALAL_RS0112245
kguK 2-ketogluconokinase HALAL_RS0114515
kguT 2-ketogluconate transporter
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit HALAL_RS0115635
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 HALAL_RS0100180
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 HALAL_RS0110975 HALAL_RS17205
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 HALAL_RS0103205 HALAL_RS0106690
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 HALAL_RS0113840
mglA glucose ABC transporter, ATP-binding component (MglA) HALAL_RS0102075 HALAL_RS0102115
mglB glucose ABC transporter, substrate-binding component HALAL_RS0102080
mglC glucose ABC transporter, permease component (MglC) HALAL_RS0102070 HALAL_RS0102110
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
ptsG glucose PTS, enzyme IICB HALAL_RS0104260
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) HALAL_RS0104260
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase HALAL_RS0115215 HALAL_RS0115220

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