GapMind for catabolism of small carbon sources

 

lactose catabolism in Sinorhizobium meliloti 1021

Best path

lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, 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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacE lactose ABC transporter, substrate-binding component SM_b21652
lacF lactose ABC transporter, permease component 1 SM_b21653 SM_b20232
lacG lactose ABC transporter, permease component 2 SM_b21654 SM_b20969
lacK lactose ABC transporter, ATPase component SM_b20002 SM_b21605
lacZ lactase (homomeric) SM_b21655 SM_b20966
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) SMc00588 SMc00880
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) SMc00883 SMa0717
dgoD D-galactonate dehydratase SM_b20510 SM_b20890
dgoK 2-dehydro-3-deoxygalactonokinase SMc00881 SMc01531
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase SMc00882 SMc02043
glk glucokinase SMc02835 SMc03109
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) SMc03061
aglF' glucose ABC transporter, permease component 1 (AglF) SMc03062 SM_b20232
aglG' glucose ABC transporter, permease component 2 (AglG) SMc03063 SMc04257
aglK' glucose ABC transporter, ATPase component (AglK) SMc03065 SM_b21605
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase SMc03153 SMc02043
edd phosphogluconate dehydratase SMc03068 SMc04045
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit SM_b20402 SMc00086
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase SMc02252 SM_b20942
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) SM_b21192 SM_b20199
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) SM_b21373
gdh quinoprotein glucose dehydrogenase SMc00110 SMa0564
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) SM_b20419 SMc01608
gnl gluconolactonase SMa0196 SM_b20453
gtsA glucose ABC transporter, substrate-binding component (GtsA) SMc04396 SMc04259
gtsB glucose ABC transporter, permease component 1 (GtsB) SMc04395 SMc04258
gtsC glucose ABC transporter, permease component 2 (GtsC) SMc04394 SMc04257
gtsD glucose ABC transporter, ATPase component (GtsD) SM_b20661 SMc04393
kguD 2-keto-6-phosphogluconate reductase SMc01943 SMa2137
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit SMc01613 SM_b20371
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit SM_b20371 SMc01613
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) SMa1487
lacC D-tagatose-6-phosphate kinase
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
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
lacL heteromeric lactase, large subunit
lacM heteromeric lactase, small subunit
lacP lactose permease LacP
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) SM_b20894 SM_b20904
mglB glucose ABC transporter, substrate-binding component SM_b20895 SM_b20902
mglC glucose ABC transporter, permease component (MglC) SM_b20893 SM_b20903
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase SMc03160
pgmA alpha-phosphoglucomutase SMc03925 SM_b21081
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 SMc01023 SMc01614

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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