GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Photobacterium jeanii R-40508

Best path

argT, hisM, hisQ, hisP, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT A3K86_RS13005 A3K86_RS01795
hisM L-lysine ABC transporter, permease component 1 (HisM) A3K86_RS13015 A3K86_RS01785
hisQ L-lysine ABC transporter, permease component 2 (HisQ) A3K86_RS13010 A3K86_RS01790
hisP L-lysine ABC transporter, ATPase component HisP A3K86_RS13000 A3K86_RS01690
lat L-lysine 6-aminotransferase A3K86_RS14790 A3K86_RS09055
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) A3K86_RS14375 A3K86_RS09065
lysN 2-aminoadipate transaminase A3K86_RS09055 A3K86_RS14790
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase A3K86_RS14390
Alternative steps:
alr lysine racemase A3K86_RS09910 A3K86_RS17975
amaA L-pipecolate oxidase
amaD D-lysine oxidase
atoB acetyl-CoA C-acetyltransferase A3K86_RS19875 A3K86_RS15935
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit A3K86_RS15925 A3K86_RS15945
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase A3K86_RS14790
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
davA 5-aminovaleramidase
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase A3K86_RS14375 A3K86_RS19720
davT 5-aminovalerate aminotransferase A3K86_RS09055 A3K86_RS14790
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A3K86_RS15920 A3K86_RS17390
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit A3K86_RS15855
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit A3K86_RS15860
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A3K86_RS17390 A3K86_RS06710
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase A3K86_RS15945 A3K86_RS15925
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase A3K86_RS09920
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 A3K86_RS22285 A3K86_RS03615
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase A3K86_RS09055 A3K86_RS14790
patD 5-aminopentanal dehydrogenase A3K86_RS19720 A3K86_RS14375
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