GapMind for catabolism of small carbon sources


L-lysine catabolism in Herbaspirillum seropedicae SmR1

Best path

lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB

Also see fitness data for the top candidates


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
cadA lysine decarboxylase HSERO_RS17280 HSERO_RS16435
patA cadaverine aminotransferase HSERO_RS05420 HSERO_RS17580
patD 5-aminopentanal dehydrogenase HSERO_RS05645 HSERO_RS09465
davT 5-aminovalerate aminotransferase HSERO_RS05420 HSERO_RS19685
davD glutarate semialdehyde dehydrogenase HSERO_RS05395 HSERO_RS05645
gcdG succinyl-CoA:glutarate CoA-transferase HSERO_RS18350 HSERO_RS14050
gcdH glutaryl-CoA dehydrogenase HSERO_RS23440 HSERO_RS04640
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HSERO_RS19405 HSERO_RS20665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HSERO_RS01260 HSERO_RS04630
atoB acetyl-CoA C-acetyltransferase HSERO_RS01180 HSERO_RS04635
Alternative steps:
alr lysine racemase HSERO_RS19210
amaA L-pipecolate oxidase HSERO_RS05840
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) HSERO_RS05645 HSERO_RS22910
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT HSERO_RS10775 HSERO_RS21615
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit HSERO_RS04640 HSERO_RS12750
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit HSERO_RS23190 HSERO_RS20000
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit HSERO_RS23185 HSERO_RS19995
davA 5-aminovaleramidase
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase HSERO_RS00880 HSERO_RS22840
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit HSERO_RS14225 HSERO_RS07560
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit HSERO_RS14220 HSERO_RS07555
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) HSERO_RS11445 HSERO_RS23035
hisP L-lysine ABC transporter, ATPase component HisP HSERO_RS00320 HSERO_RS19240
hisQ L-lysine ABC transporter, permease component 2 (HisQ) HSERO_RS05830 HSERO_RS11445
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 HSERO_RS17240
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase HSERO_RS19685 HSERO_RS05420
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) HSERO_RS21645
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase HSERO_RS05420 HSERO_RS09050
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase HSERO_RS16560 HSERO_RS19115

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 17 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