GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Halioglobus japonicus S1-36

Best path

lysP, davB, davA, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase
davT 5-aminovalerate aminotransferase C0029_RS18740 C0029_RS09770
davD glutarate semialdehyde dehydrogenase C0029_RS01440 C0029_RS01835
gcdG succinyl-CoA:glutarate CoA-transferase C0029_RS13315 C0029_RS04725
gcdH glutaryl-CoA dehydrogenase C0029_RS13310 C0029_RS16975
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C0029_RS04910 C0029_RS05670
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C0029_RS18685 C0029_RS02360
atoB acetyl-CoA C-acetyltransferase C0029_RS06075 C0029_RS04970
Alternative steps:
alr lysine racemase C0029_RS15255 C0029_RS02215
amaA L-pipecolate oxidase C0029_RS16470 C0029_RS09780
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) C0029_RS01440 C0029_RS01835
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit C0029_RS01670 C0029_RS09065
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase C0029_RS02990
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit C0029_RS06085
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit C0029_RS06080
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit C0029_RS05815
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM)
hisP L-lysine ABC transporter, ATPase component HisP C0029_RS11915 C0029_RS05165
hisQ L-lysine ABC transporter, permease component 2 (HisQ)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase C0029_RS16475
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 C0029_RS04750
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase C0029_RS13280 C0029_RS18740
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 C0029_RS15270
patA cadaverine aminotransferase C0029_RS18740 C0029_RS05155
patD 5-aminopentanal dehydrogenase C0029_RS01440 C0029_RS01835
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase C0029_RS05565 C0029_RS16560

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