GapMind for catabolism of small carbon sources

 

lactose catabolism in Chryseobacterium viscerum 687B-08

Best path

lacA', lacC', lacB', klh, MFS-glucose, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) C1634_RS07015 C1634_RS08180
klh periplasmic 3'-ketolactose hydrolase
MFS-glucose glucose transporter, MFS superfamily C1634_RS17265 C1634_RS24605
glk glucokinase C1634_RS03565 C1634_RS17380
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) C1634_RS05005 C1634_RS14760
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
dgoD D-galactonate dehydratase C1634_RS17575
dgoK 2-dehydro-3-deoxygalactonokinase
eda 2-keto-3-deoxygluconate 6-phosphate aldolase
edd phosphogluconate dehydratase C1634_RS17575
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) C1634_RS02835 C1634_RS15470
galE UDP-glucose 4-epimerase C1634_RS07580 C1634_RS11405
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 C1634_RS21225
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) C1634_RS05280 C1634_RS14760
gnl gluconolactonase
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) C1634_RS14760 C1634_RS05005
kguD 2-keto-6-phosphogluconate reductase C1634_RS11965
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
lacA galactose-6-phosphate isomerase, lacA subunit C1634_RS02900
lacB galactose-6-phosphate isomerase, lacB subunit C1634_RS02900
lacC D-tagatose-6-phosphate kinase C1634_RS09815
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 C1634_RS14760 C1634_RS05005
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) C1634_RS05265 C1634_RS08970
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mglA glucose ABC transporter, ATP-binding component (MglA) C1634_RS05280 C1634_RS11590
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 C1634_RS13990 C1634_RS03120
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET C1634_RS15260
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase C1634_RS17535 C1634_RS02890

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