GapMind for catabolism of small carbon sources

 

lactose catabolism in Chromobacterium vaccinii MWU205

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric)
galK galactokinase (-1-phosphate forming)
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galE UDP-glucose 4-epimerase VL52_RS06655 VL52_RS05985
pgmA alpha-phosphoglucomutase VL52_RS03735 VL52_RS02510
glk glucokinase VL52_RS05495 VL52_RS08435
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF) VL52_RS08420
aglG' glucose ABC transporter, permease component 2 (AglG) VL52_RS08415
aglK' glucose ABC transporter, ATPase component (AglK) VL52_RS04920 VL52_RS12740
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA VL52_RS01610 VL52_RS06575
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase VL52_RS05515
dgoD D-galactonate dehydratase
dgoK 2-dehydro-3-deoxygalactonokinase
eda 2-keto-3-deoxygluconate 6-phosphate aldolase VL52_RS05515
edd phosphogluconate dehydratase VL52_RS05510 VL52_RS11430
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit VL52_RS18000
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) VL52_RS17095 VL52_RS01235
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) VL52_RS05280
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) VL52_RS09435 VL52_RS12740
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) VL52_RS08420
gtsC glucose ABC transporter, permease component 2 (GtsC) VL52_RS08415 VL52_RS04910
gtsD glucose ABC transporter, ATPase component (GtsD) VL52_RS12740 VL52_RS04920
kguD 2-keto-6-phosphogluconate reductase VL52_RS02475 VL52_RS16495
kguK 2-ketogluconokinase
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) VL52_RS05340
lacC D-tagatose-6-phosphate kinase
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 VL52_RS04905 VL52_RS08420
lacG lactose ABC transporter, permease component 2 VL52_RS04910 VL52_RS08415
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 VL52_RS04920 VL52_RS12740
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 VL52_RS04135
mglA glucose ABC transporter, ATP-binding component (MglA) VL52_RS18715 VL52_RS07675
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) VL52_RS18720
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
ptsG glucose PTS, enzyme IICB VL52_RS01615 VL52_RS06570
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) VL52_RS01615 VL52_RS06570
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase VL52_RS01810 VL52_RS05270

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