GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

lysP, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
cadA lysine decarboxylase CA265_RS04075 CA265_RS10665
patA cadaverine aminotransferase CA265_RS15205 CA265_RS18530
patD 5-aminopentanal dehydrogenase CA265_RS14635 CA265_RS24850
davT 5-aminovalerate aminotransferase CA265_RS18530 CA265_RS15205
davD glutarate semialdehyde dehydrogenase CA265_RS14635 CA265_RS24850
gcdG succinyl-CoA:glutarate CoA-transferase CA265_RS08550
gcdH glutaryl-CoA dehydrogenase CA265_RS09630 CA265_RS14465
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CA265_RS20005 CA265_RS09125
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CA265_RS17590 CA265_RS07715
atoB acetyl-CoA C-acetyltransferase CA265_RS06590 CA265_RS17585
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) CA265_RS19780 CA265_RS14635
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit CA265_RS22715 CA265_RS02820
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit CA265_RS06305
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit CA265_RS06310
davA 5-aminovaleramidase CA265_RS08135 CA265_RS07705
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit CA265_RS08865
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit CA265_RS08870
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 CA265_RS10520 CA265_RS07485
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 CA265_RS14455
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CA265_RS19300
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase CA265_RS07515 CA265_RS18530
Slc7a1 L-lysine transporter Slc7a1 CA265_RS15000 CA265_RS17395
ydiJ (R)-2-hydroxyglutarate dehydrogenase CA265_RS09620

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