GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

lysP, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP AU252_RS04790 AU252_RS13875
cadA lysine decarboxylase AU252_RS08395
patA cadaverine aminotransferase AU252_RS02890 AU252_RS16125
patD 5-aminopentanal dehydrogenase AU252_RS16120 AU252_RS22315
davT 5-aminovalerate aminotransferase AU252_RS16125 AU252_RS02890
davD glutarate semialdehyde dehydrogenase AU252_RS01005 AU252_RS04095
gcdG succinyl-CoA:glutarate CoA-transferase AU252_RS00300 AU252_RS01440
gcdH glutaryl-CoA dehydrogenase AU252_RS16430 AU252_RS00305
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AU252_RS07800 AU252_RS00745
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
atoB acetyl-CoA C-acetyltransferase AU252_RS00950 AU252_RS16800
Alternative steps:
alr lysine racemase AU252_RS17270 AU252_RS04555
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) AU252_RS01555 AU252_RS01045
amaD D-lysine oxidase AU252_RS13920 AU252_RS09265
argT L-lysine ABC transporter, substrate-binding component ArgT AU252_RS15960
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit AU252_RS00840 AU252_RS03420
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit AU252_RS10770 AU252_RS07725
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit AU252_RS03410 AU252_RS07730
davA 5-aminovaleramidase AU252_RS04565 AU252_RS09230
davB L-lysine 2-monooxygenase AU252_RS04545 AU252_RS09225
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit AU252_RS01240 AU252_RS01425
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit AU252_RS01430 AU252_RS01245
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) AU252_RS13395 AU252_RS05495
hisP L-lysine ABC transporter, ATPase component HisP AU252_RS17760 AU252_RS05490
hisQ L-lysine ABC transporter, permease component 2 (HisQ) AU252_RS09255 AU252_RS15205
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 AU252_RS00920
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase AU252_RS16125
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase AU252_RS16745 AU252_RS16125
Slc7a1 L-lysine transporter Slc7a1 AU252_RS16215 AU252_RS04550
ydiJ (R)-2-hydroxyglutarate dehydrogenase AU252_RS06485

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.

Links

Downloads

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:

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