GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Escherichia coli BW25113

Best path

argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, glaH, lhgD

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT b2310 b2309
hisM L-lysine ABC transporter, permease component 1 (HisM) b2307 b0861
hisQ L-lysine ABC transporter, permease component 2 (HisQ) b2308 b0862
hisP L-lysine ABC transporter, ATPase component HisP b2306 b3271
cadA lysine decarboxylase b0186 b4131
patA cadaverine aminotransferase b3073 b1302
patD 5-aminopentanal dehydrogenase b1444 b0312
davT 5-aminovalerate aminotransferase b2662 b1302
davD glutarate semialdehyde dehydrogenase b2661 b1415
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) b2659
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) b2660
Alternative steps:
alr lysine racemase b3958 b4053
amaA L-pipecolate oxidase b1301
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) b2661 b1415
amaD D-lysine oxidase
atoB acetyl-CoA C-acetyltransferase b2224 b2844
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit b1695 b0039
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit b2221
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit b2222
davA 5-aminovaleramidase b0219
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase b0801 b0517
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase b1393 b3846
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit b1698 b0042
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase b3846 b2341
gcdG succinyl-CoA:glutarate CoA-transferase b2371 b2374
gcdH glutaryl-CoA dehydrogenase
hglS D-2-hydroxyglutarate synthase b1423
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase b4146
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 b1302 b2662
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL b1605
lysN 2-aminoadipate transaminase b2662 b1302
lysP L-lysine:H+ symporter LysP b2156 b0260
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase b1687

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