GapMind for catabolism of small carbon sources

 

lactose catabolism in Caulobacter crescentus NA1000

Best path

lacA', lacC', lacB', klh, MFS-glucose, glk

Also see fitness data for the top candidates

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit CCNA_01706
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit CCNA_01707
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) CCNA_01704 CCNA_01268
klh periplasmic 3'-ketolactose hydrolase CCNA_01705
MFS-glucose glucose transporter, MFS superfamily CCNA_00857 CCNA_01159
glk glucokinase CCNA_02133 CCNA_02549
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) CCNA_03235 CCNA_01670
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA CCNA_00571 CCNA_00457
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase CCNA_00825 CCNA_01562
dgoD D-galactonate dehydratase CCNA_01488 CCNA_00862
dgoK 2-dehydro-3-deoxygalactonokinase CCNA_00826 CCNA_01563
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CCNA_01562 CCNA_00825
edd phosphogluconate dehydratase CCNA_02134 CCNA_00862
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) CCNA_00863 CCNA_01882
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) CCNA_01018 CCNA_00864
galE UDP-glucose 4-epimerase CCNA_00233 CCNA_02466
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) CCNA_03360
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase CCNA_01575
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) CCNA_03235 CCNA_01670
gnl gluconolactonase CCNA_01282 CCNA_01882
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) CCNA_03235 CCNA_01670
kguD 2-keto-6-phosphogluconate reductase CCNA_03838 CCNA_02230
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase
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 CCNA_03235 CCNA_01670
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) CCNA_00830 CCNA_02220
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mglA glucose ABC transporter, ATP-binding component (MglA) CCNA_00903 CCNA_02751
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) CCNA_00904
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase CCNA_02220
pgmA alpha-phosphoglucomutase CCNA_00083 CCNA_02347
ptsG glucose PTS, enzyme IICB CCNA_00572 CCNA_00458
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) CCNA_00572 CCNA_00458
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase CCNA_01970 CCNA_03359

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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