GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Maridesulfovibrio zosterae DSM 11974

Best path

lysP, cadA, patA, patD, davT, davD, glaH, lhgD

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
cadA lysine decarboxylase H589_RS0102990 H589_RS0118055
patA cadaverine aminotransferase H589_RS0100395 H589_RS0118050
patD 5-aminopentanal dehydrogenase H589_RS0109990 H589_RS0102680
davT 5-aminovalerate aminotransferase H589_RS0118185 H589_RS0104130
davD glutarate semialdehyde dehydrogenase H589_RS0109990 H589_RS0118155
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H589_RS0100555
Alternative steps:
alr lysine racemase H589_RS0108510
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) H589_RS0109990
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT H589_RS0110285 H589_RS0100435
atoB acetyl-CoA C-acetyltransferase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
davA 5-aminovaleramidase
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H589_RS0116710
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) H589_RS0118130 H589_RS0115925
hisP L-lysine ABC transporter, ATPase component HisP H589_RS0105875 H589_RS0112205
hisQ L-lysine ABC transporter, permease component 2 (HisQ) H589_RS0118130 H589_RS0115925
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase H589_RS0118140
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 H589_RS0118185 H589_RS0100395
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase H589_RS0118185 H589_RS0105035
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase H589_RS0101760

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