GapMind for catabolism of small carbon sources


L-lysine catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB

Also see fitness data for the top candidates


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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT Pf1N1B4_3179 Pf1N1B4_1641
hisM L-lysine ABC transporter, permease component 1 (HisM) Pf1N1B4_3177 Pf1N1B4_1643
hisQ L-lysine ABC transporter, permease component 2 (HisQ) Pf1N1B4_3178 Pf1N1B4_1642
hisP L-lysine ABC transporter, ATPase component HisP Pf1N1B4_1640 Pf1N1B4_3175
davB L-lysine 2-monooxygenase Pf1N1B4_2505
davA 5-aminovaleramidase Pf1N1B4_2504 Pf1N1B4_4326
davT 5-aminovalerate aminotransferase Pf1N1B4_1733 Pf1N1B4_4910
davD glutarate semialdehyde dehydrogenase Pf1N1B4_1734 Pf1N1B4_4931
gcdG succinyl-CoA:glutarate CoA-transferase Pf1N1B4_1815 Pf1N1B4_5611
gcdH glutaryl-CoA dehydrogenase Pf1N1B4_1816 Pf1N1B4_3987
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf1N1B4_4788 Pf1N1B4_3903
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf1N1B4_3903 Pf1N1B4_5134
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
Alternative steps:
alr lysine racemase Pf1N1B4_2559 Pf1N1B4_2146
amaA L-pipecolate oxidase Pf1N1B4_1383 Pf1N1B4_4356
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Pf1N1B4_1384 Pf1N1B4_1734
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Pf1N1B4_4787 Pf1N1B4_4789
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) Pf1N1B4_4805
cadA lysine decarboxylase Pf1N1B4_4600 Pf1N1B4_1389
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Pf1N1B4_5833
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Pf1N1B4_5834
dpkA 1-piperideine-2-carboxylate reductase Pf1N1B4_5979 Pf1N1B4_4705 with Pf1N1B4_4706
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Pf1N1B4_391 Pf1N1B4_5613
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Pf1N1B4_392 Pf1N1B4_5612
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase Pf1N1B4_5865
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 Pf1N1B4_2430 Pf1N1B4_5996
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase Pf1N1B4_4910 Pf1N1B4_1733
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Pf1N1B4_4264
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL Pf1N1B4_613 Pf1N1B4_614
lysN 2-aminoadipate transaminase Pf1N1B4_1045 Pf1N1B4_4425
lysP L-lysine:H+ symporter LysP Pf1N1B4_801 Pf1N1B4_1639
patA cadaverine aminotransferase Pf1N1B4_2980 Pf1N1B4_3440
patD 5-aminopentanal dehydrogenase Pf1N1B4_3024 Pf1N1B4_3029
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Pf1N1B4_4229 Pf1N1B4_2274

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.



Related tools

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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 paper from 2022 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