GapMind for catabolism of small carbon sources

 

lactose catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit Echvi_1439 Echvi_1847
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit Echvi_1438 Echvi_1848
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) Echvi_1841
klh periplasmic 3'-ketolactose hydrolase Echvi_2156 Echvi_0491
MFS-glucose glucose transporter, MFS superfamily Echvi_3909 Echvi_2805
glk glucokinase Echvi_3894 Echvi_3892
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) Echvi_2123 Echvi_1022
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Echvi_3630 Echvi_3770
dgoD D-galactonate dehydratase Echvi_3769 Echvi_2055
dgoK 2-dehydro-3-deoxygalactonokinase Echvi_3631
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Echvi_3630 Echvi_3770
edd phosphogluconate dehydratase Echvi_2055
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit Echvi_1808
gadh3 gluconate 2-dehydrogenase subunit 3
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) Echvi_3728
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) Echvi_2940 Echvi_4610
galE UDP-glucose 4-epimerase Echvi_1472 Echvi_4409
galK galactokinase (-1-phosphate forming) Echvi_0696
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase Echvi_0695
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) Echvi_0155
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase Echvi_3019
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) Echvi_1022 Echvi_2123
gnl gluconolactonase Echvi_3728 Echvi_3767
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) Echvi_1022 Echvi_2123
kguD 2-keto-6-phosphogluconate reductase Echvi_2777
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
lacA galactose-6-phosphate isomerase, lacA subunit Echvi_1186
lacB galactose-6-phosphate isomerase, lacB subunit Echvi_2860 Echvi_1186
lacC D-tagatose-6-phosphate kinase Echvi_2325 Echvi_2380
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 Echvi_2123 Echvi_1022
lacL heteromeric lactase, large subunit Echvi_0485 Echvi_1698
lacM heteromeric lactase, small subunit
lacP lactose permease LacP
lacS lactose permease LacS
lacY lactose:proton symporter LacY
lacZ lactase (homomeric) Echvi_0485 Echvi_1669
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mglA glucose ABC transporter, ATP-binding component (MglA) Echvi_1282 Echvi_3112
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) Echvi_1280
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase Echvi_2982 Echvi_1178
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter Echvi_1871 Echvi_1880
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase Echvi_1196 Echvi_0337

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