GapMind for catabolism of small carbon sources


L-lysine catabolism in Pseudomonas fluorescens FW300-N2C3

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT AO356_05495 AO356_09900
hisM L-lysine ABC transporter, permease component 1 (HisM) AO356_05505 AO356_09910
hisQ L-lysine ABC transporter, permease component 2 (HisQ) AO356_05500 AO356_09905
hisP L-lysine ABC transporter, ATPase component HisP AO356_05515 AO356_09895
davB L-lysine 2-monooxygenase AO356_14230
davA 5-aminovaleramidase AO356_14225 AO356_06560
davT 5-aminovalerate aminotransferase AO356_10715 AO356_26715
davD glutarate semialdehyde dehydrogenase AO356_10720 AO356_29070
gcdG succinyl-CoA:glutarate CoA-transferase AO356_10845 AO356_06355
gcdH glutaryl-CoA dehydrogenase AO356_10850 AO356_01580
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO356_26360 AO356_02330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO356_02330 AO356_29995
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
Alternative steps:
alr lysine racemase AO356_14490 AO356_12630
amaA L-pipecolate oxidase AO356_08505 AO356_29640
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) AO356_08510 AO356_28220
amaD D-lysine oxidase AO356_15895
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit AO356_26355 AO356_26365
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) AO356_29675
cadA lysine decarboxylase AO356_08535 AO356_07310
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit AO356_21650
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit AO356_21645
dpkA 1-piperideine-2-carboxylate reductase AO356_26080 AO356_29450
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit AO356_21850 AO356_20325
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit AO356_20320 AO356_21845
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase AO356_01105
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 AO356_13850
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase AO356_26715 AO356_10715
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AO356_26445
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL AO356_05265 AO356_05260
lysN 2-aminoadipate transaminase AO356_16720 AO356_24005
lysP L-lysine:H+ symporter LysP AO356_15120 AO356_17670
patA cadaverine aminotransferase AO356_27230 AO356_17010
patD 5-aminopentanal dehydrogenase AO356_06315 AO356_06290
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase AO356_29050 AO356_10305

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