GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Caulobacter crescentus NA1000

Best path

lysP, lat, amaB, lysN, hglS, ydiJ

Also see fitness data for the top candidates

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
lat L-lysine 6-aminotransferase CCNA_03233 CCNA_02326
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) CCNA_01274 CCNA_00865
lysN 2-aminoadipate transaminase CCNA_01603 CCNA_02244
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase CCNA_03500
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT CCNA_01508
atoB acetyl-CoA C-acetyltransferase CCNA_00820 CCNA_00544
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit CCNA_01412 CCNA_02254
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase CCNA_00365 CCNA_01372
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit CCNA_00206 CCNA_02488
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit CCNA_02489 CCNA_00207
davA 5-aminovaleramidase CCNA_00871
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase CCNA_03242 CCNA_03243
davT 5-aminovalerate aminotransferase CCNA_00620 CCNA_02326
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CCNA_00006 CCNA_01794
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit CCNA_00763
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit CCNA_00764
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CCNA_00123 CCNA_03293
gcdG succinyl-CoA:glutarate CoA-transferase CCNA_03677 CCNA_02410
gcdH glutaryl-CoA dehydrogenase CCNA_02254 CCNA_01412
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hisM L-lysine ABC transporter, permease component 1 (HisM) CCNA_01507
hisP L-lysine ABC transporter, ATPase component HisP CCNA_01506 CCNA_02751
hisQ L-lysine ABC transporter, permease component 2 (HisQ) CCNA_01507
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase CCNA_00753
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) CCNA_03278
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
patA cadaverine aminotransferase CCNA_02326 CCNA_00620
patD 5-aminopentanal dehydrogenase CCNA_03243 CCNA_03695
Slc7a1 L-lysine transporter Slc7a1 CCNA_01242 CCNA_00435

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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