GapMind for catabolism of small carbon sources

 

lactose catabolism in Photobacterium jeanii R-40508

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) A3K86_RS04880 A3K86_RS20840
galK galactokinase (-1-phosphate forming) A3K86_RS04815
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase A3K86_RS04820
galE UDP-glucose 4-epimerase A3K86_RS04825 A3K86_RS22330
pgmA alpha-phosphoglucomutase A3K86_RS06355 A3K86_RS19410
glk glucokinase A3K86_RS19100 A3K86_RS03930
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) A3K86_RS19490
aglK' glucose ABC transporter, ATPase component (AglK) A3K86_RS19475 A3K86_RS19360
bglF glucose PTS, enzyme II (BCA components, BglF) A3K86_RS20820
crr glucose PTS, enzyme IIA A3K86_RS12910
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase A3K86_RS14285 A3K86_RS16310
dgoD D-galactonate dehydratase A3K86_RS18020
dgoK 2-dehydro-3-deoxygalactonokinase A3K86_RS14280 A3K86_RS16315
eda 2-keto-3-deoxygluconate 6-phosphate aldolase A3K86_RS14285 A3K86_RS16310
edd phosphogluconate dehydratase A3K86_RS17170
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) A3K86_RS16360 A3K86_RS19560
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) A3K86_RS16320
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) A3K86_RS16400
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) A3K86_RS19475 A3K86_RS02885
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) A3K86_RS02915
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) A3K86_RS19360 A3K86_RS19475
kguD 2-keto-6-phosphogluconate reductase A3K86_RS17455 A3K86_RS13295
kguK 2-ketogluconokinase A3K86_RS20825
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 A3K86_RS08810 A3K86_RS02150
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 A3K86_RS19335
lacG lactose ABC transporter, permease component 2
lacIIA lactose PTS system, EIIA component A3K86_RS01475 A3K86_RS15445
lacIIB lactose PTS system, EIIB component A3K86_RS15455 A3K86_RS01465
lacIIC lactose PTS system, EIIC component
lacIICB lactose PTS system, fused EIIC and EIIB components A3K86_RS01470 A3K86_RS15450
lacK lactose ABC transporter, ATPase component A3K86_RS19475 A3K86_RS19360
lacL heteromeric lactase, large subunit A3K86_RS04880
lacM heteromeric lactase, small subunit
lacS lactose permease LacS
lacY lactose:proton symporter LacY
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC A3K86_RS16385
manZ glucose PTS, enzyme EIID A3K86_RS16380
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) A3K86_RS19615 A3K86_RS15085
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) A3K86_RS19610
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase A3K86_RS20840
ptsG glucose PTS, enzyme IICB A3K86_RS05470 A3K86_RS02900
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) A3K86_RS02900 A3K86_RS05470
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase A3K86_RS08815 A3K86_RS17420

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