GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Shewanella amazonensis SB2B

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 Sama_0473
davT 5-aminovalerate aminotransferase Sama_2636 Sama_1628
davD glutarate semialdehyde dehydrogenase Sama_2637 Sama_2648
gcdG succinyl-CoA:glutarate CoA-transferase Sama_3300
gcdH glutaryl-CoA dehydrogenase Sama_2796 Sama_1362
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Sama_1378 Sama_0032
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Sama_0032 Sama_2167
atoB acetyl-CoA C-acetyltransferase Sama_1375 Sama_0031
Alternative steps:
alr lysine racemase Sama_0256 Sama_3057
amaA L-pipecolate oxidase Sama_2638
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Sama_2637 Sama_2650
amaD D-lysine oxidase Sama_1533
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Sama_1362 Sama_1377
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase Sama_0410 Sama_3334
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Sama_1357 Sama_0518
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Sama_0519 Sama_1356
dpkA 1-piperideine-2-carboxylate reductase Sama_2610
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Sama_1170
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Sama_1169
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM)
hisP L-lysine ABC transporter, ATPase component HisP Sama_2864 Sama_1468
hisQ L-lysine ABC transporter, permease component 2 (HisQ)
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 Sama_2636 Sama_2643
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 Sama_2636 Sama_1628
patA cadaverine aminotransferase Sama_3011 Sama_2636
patD 5-aminopentanal dehydrogenase Sama_3435 Sama_2648
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Sama_2071

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