GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Methylocapsa aurea KYG

Best path

lysP, lat, amaB, lysN, hglS, ydiJ

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
lat L-lysine 6-aminotransferase DL86_RS06705 DL86_RS01865
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) DL86_RS09925 DL86_RS17780
lysN 2-aminoadipate transaminase DL86_RS11215 DL86_RS06705
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase DL86_RS02935 DL86_RS09045
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT DL86_RS12660 DL86_RS15435
atoB acetyl-CoA C-acetyltransferase DL86_RS05200 DL86_RS10295
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit DL86_RS00105 DL86_RS07065
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase DL86_RS13630 DL86_RS09855
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit DL86_RS11555 DL86_RS08810
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit DL86_RS11550 DL86_RS08805
davA 5-aminovaleramidase
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase DL86_RS14335 DL86_RS09925
davT 5-aminovalerate aminotransferase DL86_RS01865 DL86_RS06705
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase DL86_RS15400 DL86_RS06940
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit DL86_RS15280 DL86_RS12485
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit DL86_RS15285 DL86_RS12490
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase DL86_RS06940 DL86_RS07960
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase DL86_RS07065 DL86_RS00105
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hisM L-lysine ABC transporter, permease component 1 (HisM) DL86_RS08975 DL86_RS08970
hisP L-lysine ABC transporter, ATPase component HisP DL86_RS08980 DL86_RS02760
hisQ L-lysine ABC transporter, permease component 2 (HisQ) DL86_RS08970
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase DL86_RS00895
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
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
patA cadaverine aminotransferase DL86_RS06885 DL86_RS01865
patD 5-aminopentanal dehydrogenase DL86_RS14335 DL86_RS09925
Slc7a1 L-lysine transporter Slc7a1 DL86_RS06255

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