GapMind for catabolism of small carbon sources


L-lysine catabolism in Marinomonas arctica 328

Best path

argT, hisM, hisQ, hisP, alr, amaD, dpkA, amaA, amaB, lysN, hglS, ydiJ


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 DK187_RS13620 DK187_RS16325
hisM L-lysine ABC transporter, permease component 1 (HisM) DK187_RS13630 DK187_RS16320
hisQ L-lysine ABC transporter, permease component 2 (HisQ) DK187_RS13625 DK187_RS07190
hisP L-lysine ABC transporter, ATPase component HisP DK187_RS13615 DK187_RS03055
alr lysine racemase DK187_RS19015
amaD D-lysine oxidase DK187_RS09135
dpkA 1-piperideine-2-carboxylate reductase DK187_RS07570
amaA L-pipecolate oxidase DK187_RS07475
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) DK187_RS07470 DK187_RS15780
lysN 2-aminoadipate transaminase DK187_RS02410 DK187_RS06905
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase DK187_RS12920
Alternative steps:
atoB acetyl-CoA C-acetyltransferase DK187_RS06190 DK187_RS08790
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit DK187_RS15195
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase DK187_RS19615 DK187_RS12845
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit DK187_RS06180
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit DK187_RS06185
davA 5-aminovaleramidase DK187_RS07055 DK187_RS03955
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase DK187_RS02405 DK187_RS15780
davT 5-aminovalerate aminotransferase DK187_RS02410 DK187_RS13600
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase DK187_RS04965 DK187_RS08785
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit DK187_RS06305 DK187_RS08780
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit DK187_RS08775 DK187_RS06300
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase DK187_RS08785 DK187_RS04955
gcdG succinyl-CoA:glutarate CoA-transferase DK187_RS07920
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase DK187_RS17315
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 DK187_RS02410 DK187_RS13985
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) DK187_RS04730
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase DK187_RS13600 DK187_RS02410
patD 5-aminopentanal dehydrogenase DK187_RS15780 DK187_RS02405
Slc7a1 L-lysine transporter Slc7a1

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 24 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 (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