GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Stutzerimonas stutzeri A1501

Best path

argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT PST_RS20435 PST_RS11840
hisM L-lysine ABC transporter, permease component 1 (HisM) PST_RS20445 PST_RS11845
hisQ L-lysine ABC transporter, permease component 2 (HisQ) PST_RS20440 PST_RS11845
hisP L-lysine ABC transporter, ATPase component HisP PST_RS20430 PST_RS00075
cadA lysine decarboxylase PST_RS11335 PST_RS18410
patA cadaverine aminotransferase PST_RS08350 PST_RS00235
patD 5-aminopentanal dehydrogenase PST_RS08835 PST_RS18325
davT 5-aminovalerate aminotransferase PST_RS03780 PST_RS08350
davD glutarate semialdehyde dehydrogenase PST_RS00500 PST_RS03775
gcdG succinyl-CoA:glutarate CoA-transferase PST_RS02290 PST_RS08605
gcdH glutaryl-CoA dehydrogenase PST_RS02285 PST_RS09725
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PST_RS09740 PST_RS06175
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PST_RS08735 PST_RS00510
atoB acetyl-CoA C-acetyltransferase PST_RS03530 PST_RS16155
Alternative steps:
alr lysine racemase PST_RS03850 PST_RS18190
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) PST_RS00500 PST_RS03775
amaD D-lysine oxidase PST_RS04985
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit PST_RS09700 PST_RS09725
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit PST_RS16145
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit PST_RS16150
davA 5-aminovaleramidase PST_RS15165
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit PST_RS13060
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit PST_RS13065
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
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
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase PST_RS03780 PST_RS00340
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) PST_RS19980
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL PST_RS03495 PST_RS19795
lysN 2-aminoadipate transaminase PST_RS03780 PST_RS11765
lysP L-lysine:H+ symporter LysP PST_RS13100
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase PST_RS02070

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 Apr 09 2024. 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 (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:

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