GapMind for catabolism of small carbon sources

 

lactose catabolism in Ruegeria conchae TW15

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) G7G_RS0111330 G7G_RS0120470
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) G7G_RS0111310 G7G_RS0103500
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) G7G_RS0100425 G7G_RS0111325
dgoD D-galactonate dehydratase G7G_RS0111305 G7G_RS0100630
dgoK 2-dehydro-3-deoxygalactonokinase G7G_RS0100465 G7G_RS0117160
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase G7G_RS0111320 G7G_RS0100470
glk glucokinase G7G_RS23700 G7G_RS0115580
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) G7G_RS0120460
aglF' glucose ABC transporter, permease component 1 (AglF) G7G_RS0120455
aglG' glucose ABC transporter, permease component 2 (AglG) G7G_RS0120450 G7G_RS0117195
aglK' glucose ABC transporter, ATPase component (AglK) G7G_RS0120440 G7G_RS0115470
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase G7G_RS0112140 G7G_RS0100605
edd phosphogluconate dehydratase G7G_RS0112135 G7G_RS0117165
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit G7G_RS0100695
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase G7G_RS0114775 G7G_RS0118490
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) G7G_RS0103280
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase G7G_RS0107420
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) G7G_RS0114935 G7G_RS0115525
gnl gluconolactonase G7G_RS0100425
gtsA glucose ABC transporter, substrate-binding component (GtsA) G7G_RS0103670 G7G_RS0117185
gtsB glucose ABC transporter, permease component 1 (GtsB) G7G_RS0103675 G7G_RS0117190
gtsC glucose ABC transporter, permease component 2 (GtsC) G7G_RS0103680 G7G_RS0117195
gtsD glucose ABC transporter, ATPase component (GtsD) G7G_RS0103685 G7G_RS0110555
kguD 2-keto-6-phosphogluconate reductase G7G_RS0120600 G7G_RS0120345
kguK 2-ketogluconokinase G7G_RS0119975 G7G_RS22610
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 G7G_RS0120455
lacG lactose ABC transporter, permease component 2 G7G_RS0121180
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 G7G_RS0111275 G7G_RS0115470
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
mglA glucose ABC transporter, ATP-binding component (MglA) G7G_RS0115595 G7G_RS0100415
mglB glucose ABC transporter, substrate-binding component G7G_RS0115585
mglC glucose ABC transporter, permease component (MglC) G7G_RS0115590 G7G_RS0100410
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase G7G_RS0120470
pgmA alpha-phosphoglucomutase G7G_RS0112845 G7G_RS0105430
ptsG glucose PTS, enzyme IICB
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 G7G_RS0106540 G7G_RS0114345

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