GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Dyella japonica UNC79MFTsu3.2

Best path

lysP, lat, amaB, lysN, hglS, ydiJ

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP N515DRAFT_2630 N515DRAFT_3653
lat L-lysine 6-aminotransferase N515DRAFT_3630 N515DRAFT_3308
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) N515DRAFT_0465 N515DRAFT_3729
lysN 2-aminoadipate transaminase N515DRAFT_0006 N515DRAFT_3308
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase N515DRAFT_3582 N515DRAFT_1999
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
atoB acetyl-CoA C-acetyltransferase N515DRAFT_0938 N515DRAFT_2688
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit N515DRAFT_0492 N515DRAFT_0941
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase N515DRAFT_2779
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit N515DRAFT_1736
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit N515DRAFT_1736
davA 5-aminovaleramidase N515DRAFT_1536 N515DRAFT_1894
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
davT 5-aminovalerate aminotransferase N515DRAFT_3308 N515DRAFT_1751
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase N515DRAFT_1164 N515DRAFT_0416
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit N515DRAFT_4319
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit N515DRAFT_4320
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase N515DRAFT_2687 N515DRAFT_0416
gcdG succinyl-CoA:glutarate CoA-transferase N515DRAFT_3223
gcdH glutaryl-CoA dehydrogenase N515DRAFT_0484 N515DRAFT_0492
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hisM L-lysine ABC transporter, permease component 1 (HisM)
hisP L-lysine ABC transporter, ATPase component HisP N515DRAFT_1085 N515DRAFT_1562
hisQ L-lysine ABC transporter, permease component 2 (HisQ)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase N515DRAFT_3749
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
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
patA cadaverine aminotransferase N515DRAFT_3308 N515DRAFT_1751
patD 5-aminopentanal dehydrogenase N515DRAFT_3729 N515DRAFT_0379
Slc7a1 L-lysine transporter Slc7a1 N515DRAFT_2925 N515DRAFT_2924

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