GapMind for catabolism of small carbon sources

 

lactose catabolism in Gallaecimonas xiamenensis 3-C-1

Best path

lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric)
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) B3C1_RS10890 B3C1_RS09380
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) B3C1_RS10855
dgoD D-galactonate dehydratase B3C1_RS10895
dgoK 2-dehydro-3-deoxygalactonokinase B3C1_RS16155
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase B3C1_RS03510 B3C1_RS16160
glk glucokinase B3C1_RS06795 B3C1_RS03115
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) B3C1_RS04305 B3C1_RS03280
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA B3C1_RS04845
eda 2-keto-3-deoxygluconate 6-phosphate aldolase B3C1_RS03510 B3C1_RS16160
edd phosphogluconate dehydratase B3C1_RS03505 B3C1_RS00895
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase B3C1_RS06810 B3C1_RS06805
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) B3C1_RS18205
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) B3C1_RS01950
gdh quinoprotein glucose dehydrogenase B3C1_RS03040
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) B3C1_RS03280 B3C1_RS04305
gnl gluconolactonase B3C1_RS10855
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) B3C1_RS04305 B3C1_RS03280
kguD 2-keto-6-phosphogluconate reductase B3C1_RS14495 B3C1_RS14645
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)
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
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 B3C1_RS04305 B3C1_RS03280
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 B3C1_RS00390 B3C1_RS00395
mglA glucose ABC transporter, ATP-binding component (MglA) B3C1_RS10870 B3C1_RS03280
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) B3C1_RS10860 B3C1_RS10865
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase B3C1_RS00785 B3C1_RS09430
ptsG glucose PTS, enzyme IICB B3C1_RS15380
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 B3C1_RS13285 B3C1_RS18200

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