GapMind for catabolism of small carbon sources

 

lactose catabolism in Rhizorhabdus wittichii RW1

Best path

lacA', lacC', lacB', klh, ptsG-crr

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
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit SWIT_RS08250 SWIT_RS09565
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit SWIT_RS09570
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) SWIT_RS12205
klh periplasmic 3'-ketolactose hydrolase SWIT_RS08240
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
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) SWIT_RS01355 SWIT_RS00630
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase SWIT_RS08220 SWIT_RS09510
dgoD D-galactonate dehydratase SWIT_RS16515 SWIT_RS08390
dgoK 2-dehydro-3-deoxygalactonokinase SWIT_RS09545 SWIT_RS08585
eda 2-keto-3-deoxygluconate 6-phosphate aldolase SWIT_RS08220 SWIT_RS09510
edd phosphogluconate dehydratase SWIT_RS08210 SWIT_RS08725
gadh1 gluconate 2-dehydrogenase flavoprotein subunit SWIT_RS03715
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) SWIT_RS01395 SWIT_RS21370
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) SWIT_RS01525 SWIT_RS16600
galE UDP-glucose 4-epimerase SWIT_RS15065 SWIT_RS06115
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 SWIT_RS05365 SWIT_RS10225
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) SWIT_RS01355 SWIT_RS00070
glk glucokinase SWIT_RS08215 SWIT_RS05865
gnl gluconolactonase SWIT_RS21370 SWIT_RS01395
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) SWIT_RS04010 SWIT_RS13320
kguD 2-keto-6-phosphogluconate reductase SWIT_RS09455 SWIT_RS23135
kguK 2-ketogluconokinase SWIT_RS08585
kguT 2-ketogluconate transporter
lacA galactose-6-phosphate isomerase, lacA subunit SWIT_RS05760
lacB galactose-6-phosphate isomerase, lacB subunit SWIT_RS05760
lacC D-tagatose-6-phosphate kinase SWIT_RS15245
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 SWIT_RS13320 SWIT_RS04010
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)
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) SWIT_RS01285 SWIT_RS03290
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 SWIT_RS14130 SWIT_RS02730
ptsG glucose PTS, enzyme IICB
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase SWIT_RS11890 SWIT_RS13230

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 Apr 09 2024. 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