GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Rhizorhabdus wittichii RW1

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP SWIT_RS03485
cadA lysine decarboxylase SWIT_RS16155
patA cadaverine aminotransferase SWIT_RS21305 SWIT_RS07135
patD 5-aminopentanal dehydrogenase SWIT_RS08545 SWIT_RS08815
davT 5-aminovalerate aminotransferase SWIT_RS21085 SWIT_RS21305
davD glutarate semialdehyde dehydrogenase SWIT_RS07950 SWIT_RS21040
gcdG succinyl-CoA:glutarate CoA-transferase SWIT_RS21410 SWIT_RS01445
gcdH glutaryl-CoA dehydrogenase SWIT_RS04185 SWIT_RS21415
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SWIT_RS09105 SWIT_RS03300
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SWIT_RS14665 SWIT_RS10110
atoB acetyl-CoA C-acetyltransferase SWIT_RS03220 SWIT_RS10105
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase SWIT_RS08710
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) SWIT_RS08705 SWIT_RS21310
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit SWIT_RS03310 SWIT_RS10910
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit SWIT_RS04890 SWIT_RS21070
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit SWIT_RS26190 SWIT_RS04885
davA 5-aminovaleramidase SWIT_RS12510 SWIT_RS02840
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase SWIT_RS12225 SWIT_RS07940
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit SWIT_RS16135
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit SWIT_RS16140
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) SWIT_RS13325 SWIT_RS13330
hisP L-lysine ABC transporter, ATPase component HisP SWIT_RS13320 SWIT_RS04010
hisQ L-lysine ABC transporter, permease component 2 (HisQ) SWIT_RS13325
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 SWIT_RS08990 SWIT_RS11660
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase SWIT_RS21305 SWIT_RS21085
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 SWIT_RS17960 SWIT_RS21305
Slc7a1 L-lysine transporter Slc7a1 SWIT_RS22305
ydiJ (R)-2-hydroxyglutarate dehydrogenase SWIT_RS00695 SWIT_RS26905

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