GapMind for catabolism of small carbon sources


L-lysine catabolism in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_2958 Pf6N2E2_3856
hisM L-lysine ABC transporter, permease component 1 (HisM) Pf6N2E2_2960 Pf6N2E2_3858
hisQ L-lysine ABC transporter, permease component 2 (HisQ) Pf6N2E2_2959 Pf6N2E2_3857
hisP L-lysine ABC transporter, ATPase component HisP Pf6N2E2_2962 Pf6N2E2_3855
davB L-lysine 2-monooxygenase Pf6N2E2_4778
davA 5-aminovaleramidase Pf6N2E2_4777 Pf6N2E2_3172
davT 5-aminovalerate aminotransferase Pf6N2E2_4013 Pf6N2E2_373
davD glutarate semialdehyde dehydrogenase Pf6N2E2_4014 Pf6N2E2_368
gcdG succinyl-CoA:glutarate CoA-transferase Pf6N2E2_4035 Pf6N2E2_3139
gcdH glutaryl-CoA dehydrogenase Pf6N2E2_4036 Pf6N2E2_2191
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf6N2E2_1147 Pf6N2E2_1834
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
Alternative steps:
alr lysine racemase Pf6N2E2_4836 Pf6N2E2_4393
amaA L-pipecolate oxidase Pf6N2E2_3581
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Pf6N2E2_3582 Pf6N2E2_4014
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Pf6N2E2_1146 Pf6N2E2_1148
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) Pf6N2E2_1799
cadA lysine decarboxylase Pf6N2E2_3589 Pf6N2E2_3334
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Pf6N2E2_2111
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Pf6N2E2_2112
dpkA 1-piperideine-2-carboxylate reductase Pf6N2E2_1089
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Pf6N2E2_5984
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Pf6N2E2_5983
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase Pf6N2E2_134
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase Pf6N2E2_2163
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 Pf6N2E2_4692
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase Pf6N2E2_373 Pf6N2E2_4013
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Pf6N2E2_261
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL Pf6N2E2_2907 Pf6N2E2_2906
lysN 2-aminoadipate transaminase Pf6N2E2_5269 Pf6N2E2_1496
lysP L-lysine:H+ symporter LysP Pf6N2E2_4959 Pf6N2E2_5459
patA cadaverine aminotransferase Pf6N2E2_5326 Pf6N2E2_2395
patD 5-aminopentanal dehydrogenase Pf6N2E2_3131 Pf6N2E2_3126
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Pf6N2E2_3933 Pf6N2E2_1497

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