GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Shewanella sp. ANA-3

Best path

lysP, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase Shewana3_3642
davT 5-aminovalerate aminotransferase Shewana3_3091 Shewana3_0610
davD glutarate semialdehyde dehydrogenase Shewana3_3092 Shewana3_3105
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Shewana3_1672 Shewana3_2769
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shewana3_2768 Shewana3_0024
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shewana3_0024 Shewana3_1461
atoB acetyl-CoA C-acetyltransferase Shewana3_2771 Shewana3_0023
Alternative steps:
alr lysine racemase Shewana3_3905 Shewana3_0714
amaA L-pipecolate oxidase Shewana3_3093
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Shewana3_3092 Shewana3_0612
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT Shewana3_0882
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Shewana3_1672 Shewana3_2769
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase Shewana3_3682 Shewana3_3871
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Shewana3_1667 Shewana3_3467
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Shewana3_3468 Shewana3_1666
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Shewana3_1406
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Shewana3_1405
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) Shewana3_0881
hisP L-lysine ABC transporter, ATPase component HisP Shewana3_0880 Shewana3_3260
hisQ L-lysine ABC transporter, permease component 2 (HisQ) Shewana3_0881
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 Shewana3_3091 Shewana3_0610
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase Shewana3_3091 Shewana3_0610
patA cadaverine aminotransferase Shewana3_0610 Shewana3_3091
patD 5-aminopentanal dehydrogenase Shewana3_0250 Shewana3_3092
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Shewana3_1737

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