GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pseudomonas fluorescens GW456-L13

Best path

argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB

Also see fitness data for the top candidates

Rules

Overview: Lysine degradation in GapMind is based on many metacyc pathways (link), including L-lysine degradation I via cadaverine (link), pathway IV via lysine monooxygenase (link), pathway V via D-lysine (link), pathway VI via lysine 6-aminotransferase (link), pathway VIII via lysine 6-dehydrogenase (link), and fermentation to acetate and butanoate (link). Pathway X (link) is similar to pathway I (with cadaverine and glutarate as intermediates), but glutarate is consumed via glutaryl-CoA (as in pathway IV); it does not introduce any new steps. Pathways II (L-pipecolate pathway) and III (via N6-acetyllysine) and VII (via 6-amino-2-oxohexanoate) and IX (similar to pathway IV) and XI (via saccharopine) are not thought to occur in prokaryotes and are not included in GapMind.

44 steps (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT PfGW456L13_4635 PfGW456L13_383
hisM L-lysine ABC transporter, permease component 1 (HisM) PfGW456L13_4637 PfGW456L13_385
hisQ L-lysine ABC transporter, permease component 2 (HisQ) PfGW456L13_4636 PfGW456L13_378
hisP L-lysine ABC transporter, ATPase component HisP PfGW456L13_376 PfGW456L13_4639
davB L-lysine 2-monooxygenase PfGW456L13_1171
davA 5-aminovaleramidase PfGW456L13_1170 PfGW456L13_4783
davT 5-aminovalerate aminotransferase PfGW456L13_494 PfGW456L13_4982
davD glutarate semialdehyde dehydrogenase PfGW456L13_495 PfGW456L13_3737
gcdG succinyl-CoA:glutarate CoA-transferase PfGW456L13_553 PfGW456L13_3635
gcdH glutaryl-CoA dehydrogenase PfGW456L13_554 PfGW456L13_2591
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PfGW456L13_2984 PfGW456L13_2434
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_3873
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
Alternative steps:
alr lysine racemase PfGW456L13_1233 PfGW456L13_814
amaA L-pipecolate oxidase PfGW456L13_126 PfGW456L13_3923
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) PfGW456L13_127 PfGW456L13_495
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit PfGW456L13_2983 PfGW456L13_2985
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase PfGW456L13_3336 PfGW456L13_3776
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
dpkA 1-piperideine-2-carboxylate reductase PfGW456L13_2974
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit PfGW456L13_2137
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit PfGW456L13_2136
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase PfGW456L13_4924
kamD L-beta-lysine 5,6-aminomutase, alpha subunit
kamE L-beta-lysine 5,6-aminomutase, beta subunit
kce (S)-5-amino-3-oxohexanoate cleavage enzyme PfGW456L13_1095
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase PfGW456L13_494 PfGW456L13_2301
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL PfGW456L13_1875 PfGW456L13_1876
lysN 2-aminoadipate transaminase PfGW456L13_4982 PfGW456L13_494
lysP L-lysine:H+ symporter LysP PfGW456L13_3211 PfGW456L13_4790
patA cadaverine aminotransferase PfGW456L13_4910 PfGW456L13_2301
patD 5-aminopentanal dehydrogenase PfGW456L13_4766 PfGW456L13_4760
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase PfGW456L13_944

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