GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Alicycliphilus denitrificans K601

Best path

argT, hisM, hisQ, hisP, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT ALIDE2_RS18840 ALIDE2_RS08490
hisM L-lysine ABC transporter, permease component 1 (HisM) ALIDE2_RS18830 ALIDE2_RS08495
hisQ L-lysine ABC transporter, permease component 2 (HisQ) ALIDE2_RS18835 ALIDE2_RS17655
hisP L-lysine ABC transporter, ATPase component HisP ALIDE2_RS18825 ALIDE2_RS03245
cadA lysine decarboxylase ALIDE2_RS15130 ALIDE2_RS15560
patA cadaverine aminotransferase ALIDE2_RS17550
patD 5-aminopentanal dehydrogenase ALIDE2_RS01490 ALIDE2_RS07695
davT 5-aminovalerate aminotransferase ALIDE2_RS17550 ALIDE2_RS06730
davD glutarate semialdehyde dehydrogenase ALIDE2_RS08540 ALIDE2_RS18720
gcdG succinyl-CoA:glutarate CoA-transferase ALIDE2_RS09305 ALIDE2_RS17345
gcdH glutaryl-CoA dehydrogenase ALIDE2_RS17340 ALIDE2_RS20710
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ALIDE2_RS08370 ALIDE2_RS05800
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ALIDE2_RS03170 ALIDE2_RS20405
atoB acetyl-CoA C-acetyltransferase ALIDE2_RS11830 ALIDE2_RS00660
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase ALIDE2_RS17665
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) ALIDE2_RS06625 ALIDE2_RS08540
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit ALIDE2_RS20685 ALIDE2_RS14275
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit ALIDE2_RS12990 ALIDE2_RS19470
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit ALIDE2_RS12985 ALIDE2_RS18190
davA 5-aminovaleramidase ALIDE2_RS22725
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase ALIDE2_RS14425 ALIDE2_RS03250
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit ALIDE2_RS07615 ALIDE2_RS12730
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit ALIDE2_RS09255 ALIDE2_RS05825
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
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
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase ALIDE2_RS17550 ALIDE2_RS06730
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) ALIDE2_RS11990
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase ALIDE2_RS12330
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase ALIDE2_RS15675 ALIDE2_RS21035
lysP L-lysine:H+ symporter LysP ALIDE2_RS12155
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase ALIDE2_RS07255 ALIDE2_RS00340

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