GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Desulfoscipio geothermicus DSM 3669

Best path

lysP, cadA, patA, patD, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
cadA lysine decarboxylase
patA cadaverine aminotransferase BM299_RS02515 BM299_RS04985
patD 5-aminopentanal dehydrogenase
davT 5-aminovalerate aminotransferase BM299_RS02525 BM299_RS08235
davD glutarate semialdehyde dehydrogenase
gcdG succinyl-CoA:glutarate CoA-transferase BM299_RS01175
gcdH glutaryl-CoA dehydrogenase BM299_RS11335 BM299_RS06045
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BM299_RS00820 BM299_RS18360
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BM299_RS08140 BM299_RS17110
atoB acetyl-CoA C-acetyltransferase BM299_RS18350 BM299_RS11340
Alternative steps:
alr lysine racemase BM299_RS11030 BM299_RS08220
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT BM299_RS08595 BM299_RS05460
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BM299_RS06045 BM299_RS06015
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 BM299_RS03315
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase BM299_RS11870 BM299_RS12810
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BM299_RS10480 BM299_RS04220
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit BM299_RS04215 BM299_RS10485
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) BM299_RS18040 BM299_RS05465
hisP L-lysine ABC transporter, ATPase component HisP BM299_RS00225 BM299_RS18035
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BM299_RS05465 BM299_RS18040
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase BM299_RS06535 BM299_RS08870
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 BM299_RS02525 BM299_RS08235
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 BM299_RS08755 BM299_RS02525
Slc7a1 L-lysine transporter Slc7a1 BM299_RS10185
ydiJ (R)-2-hydroxyglutarate dehydrogenase BM299_RS10985 BM299_RS04225

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