GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

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

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT AO353_16970 AO353_11995
hisM L-lysine ABC transporter, permease component 1 (HisM) AO353_16960 AO353_01530
hisQ L-lysine ABC transporter, permease component 2 (HisQ) AO353_16965 AO353_11990
hisP L-lysine ABC transporter, ATPase component HisP AO353_12000 AO353_16950
davB L-lysine 2-monooxygenase AO353_07420
davA 5-aminovaleramidase AO353_07425 AO353_28330
davT 5-aminovalerate aminotransferase AO353_11510 AO353_28215
davD glutarate semialdehyde dehydrogenase AO353_11505 AO353_28230
gcdG succinyl-CoA:glutarate CoA-transferase AO353_11105 AO353_23060
gcdH glutaryl-CoA dehydrogenase AO353_11100 AO353_20350
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO353_25675 AO353_00510
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO353_00510 AO353_27535
atoB acetyl-CoA C-acetyltransferase AO353_25685 AO353_27945
Alternative steps:
alr lysine racemase AO353_07155 AO353_09145
amaA L-pipecolate oxidase AO353_13335 AO353_24430
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) AO353_13330 AO353_11505
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit AO353_25680 AO353_25670
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) AO353_25590
cadA lysine decarboxylase AO353_23560 AO353_13300
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit AO353_27935
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit AO353_27940
dpkA 1-piperideine-2-carboxylate reductase AO353_23830 AO353_25185
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit AO353_01230
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit AO353_01235
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase AO353_21295
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 AO353_07745
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase AO353_28215 AO353_11510
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL AO353_03465 AO353_20050
lysN 2-aminoadipate transaminase AO353_28215 AO353_11510
lysP L-lysine:H+ symporter LysP AO353_24825 AO353_16120
patA cadaverine aminotransferase AO353_10500 AO353_15640
patD 5-aminopentanal dehydrogenase AO353_04290 AO353_04265
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase AO353_08505 AO353_21310

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, 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