GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pseudomonas putida KT2440

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT PP_3593 PP_0282
hisM L-lysine ABC transporter, permease component 1 (HisM) PP_3595 PP_0280
hisQ L-lysine ABC transporter, permease component 2 (HisQ) PP_3594 PP_0281
hisP L-lysine ABC transporter, ATPase component HisP PP_3597 PP_0283
davB L-lysine 2-monooxygenase PP_0383
davA 5-aminovaleramidase PP_0382 PP_3846
davT 5-aminovalerate aminotransferase PP_0214 PP_4108
davD glutarate semialdehyde dehydrogenase PP_0213 PP_4422
gcdG succinyl-CoA:glutarate CoA-transferase PP_0159 PP_3001
gcdH glutaryl-CoA dehydrogenase PP_0158 PP_4064
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PP_2217 PP_3284
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PP_2136 PP_3755
atoB acetyl-CoA C-acetyltransferase PP_2215 PP_4636
Alternative steps:
alr lysine racemase PP_3722 PP_0432
amaA L-pipecolate oxidase PP_5257
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) PP_5258 PP_2694
amaD D-lysine oxidase PP_3596
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit PP_2216 PP_3492
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase PP_4140 PP_4871
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit PP_3951 PP_3122
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit PP_3123 PP_3952
dpkA 1-piperideine-2-carboxylate reductase PP_3591 PP_4431
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit PP_4201
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit PP_4202
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) PP_2909
hglS D-2-hydroxyglutarate synthase PP_5260
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase
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 PP_0303
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase PP_0214 PP_4223
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) PP_2910
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL PP_1002 PP_1003
lysN 2-aminoadipate transaminase PP_4108 PP_0214
lysP L-lysine:H+ symporter LysP PP_3727 PP_0660
patA cadaverine aminotransferase PP_4223 PP_4481
patD 5-aminopentanal dehydrogenase PP_1481 PP_2801
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase PP_4493 PP_5154

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