GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pseudomonas stutzeri RCH2

Best path

argT, hisM, hisQ, hisP, cadA, patA, patD, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT Psest_0138
hisM L-lysine ABC transporter, permease component 1 (HisM) Psest_0136 Psest_0018
hisQ L-lysine ABC transporter, permease component 2 (HisQ) Psest_0137 Psest_0018
hisP L-lysine ABC transporter, ATPase component HisP Psest_0139 Psest_0016
cadA lysine decarboxylase Psest_2075 Psest_0649
patA cadaverine aminotransferase Psest_2719 Psest_4306
patD 5-aminopentanal dehydrogenase Psest_0905 Psest_2634
davT 5-aminovalerate aminotransferase Psest_3653 Psest_2719
davD glutarate semialdehyde dehydrogenase Psest_4237 Psest_3654
gcdG succinyl-CoA:glutarate CoA-transferase Psest_3829 Psest_2660
gcdH glutaryl-CoA dehydrogenase Psest_3830 Psest_2440
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Psest_2437 Psest_3109
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Psest_2654 Psest_4235
atoB acetyl-CoA C-acetyltransferase Psest_1076 Psest_2446
Alternative steps:
alr lysine racemase Psest_3639 Psest_0699
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Psest_4237 Psest_0375
amaD D-lysine oxidase Psest_3368
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Psest_2445 Psest_2440
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Psest_1078
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Psest_1077
davA 5-aminovaleramidase Psest_1269 Psest_3321
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Psest_1706
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Psest_1705
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
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
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase Psest_3653 Psest_4285
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Psest_0232
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL Psest_0273
lysN 2-aminoadipate transaminase Psest_3653 Psest_1990
lysP L-lysine:H+ symporter LysP Psest_1697
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Psest_3872

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, 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