GapMind for catabolism of small carbon sources

 

lactose catabolism in Sphingomonas koreensis DSMZ 15582

Best path

lacA', lacC', lacB', klh, MFS-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 Ga0059261_0546
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit Ga0059261_0548
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) Ga0059261_0551
klh periplasmic 3'-ketolactose hydrolase
MFS-glucose glucose transporter, MFS superfamily Ga0059261_1891 Ga0059261_0767
glk glucokinase Ga0059261_0355 Ga0059261_1776
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) Ga0059261_3668 Ga0059261_0562
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA Ga0059261_1646
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Ga0059261_1625 Ga0059261_0356
dgoD D-galactonate dehydratase Ga0059261_2649 Ga0059261_4216
dgoK 2-dehydro-3-deoxygalactonokinase Ga0059261_2965 Ga0059261_1624
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Ga0059261_0356 Ga0059261_1625
edd phosphogluconate dehydratase Ga0059261_0354 Ga0059261_4216
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) Ga0059261_1893
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Ga0059261_1621 Ga0059261_1894
galE UDP-glucose 4-epimerase Ga0059261_1305 Ga0059261_3099
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)
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
glcV glucose ABC transporter, ATPase component (GclV) Ga0059261_3874 Ga0059261_1321
gnl gluconolactonase Ga0059261_1893
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) Ga0059261_3668 Ga0059261_3874
kguD 2-keto-6-phosphogluconate reductase Ga0059261_2669 Ga0059261_2264
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
lacA galactose-6-phosphate isomerase, lacA subunit Ga0059261_1987
lacB galactose-6-phosphate isomerase, lacB subunit Ga0059261_1987
lacC D-tagatose-6-phosphate kinase
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 Ga0059261_3668 Ga0059261_0562
lacL heteromeric lactase, large subunit
lacM heteromeric lactase, small subunit
lacP lactose permease LacP
lacS lactose permease LacS
lacY lactose:proton symporter LacY
lacZ lactase (homomeric) Ga0059261_2643 Ga0059261_2642
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mglA glucose ABC transporter, ATP-binding component (MglA) Ga0059261_2542 Ga0059261_3276
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
pgmA alpha-phosphoglucomutase Ga0059261_2456 Ga0059261_1954
ptsG glucose PTS, enzyme IICB Ga0059261_1647
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) Ga0059261_1647
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter Ga0059261_1623
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase Ga0059261_0254 Ga0059261_0728

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