GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Sinorhizobium meliloti 1021

Best path

argT, hisM, hisQ, hisP, lysDH, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT SMc00140 SM_b20706
hisM L-lysine ABC transporter, permease component 1 (HisM) SMc00138 SMa0492
hisQ L-lysine ABC transporter, permease component 2 (HisQ) SMc00139 SMc02258
hisP L-lysine ABC transporter, ATPase component HisP SMc02260 SMa0083
lysDH L-lysine 6-dehydrogenase SMc02503
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) SMc04385 SM_b20891
lysN 2-aminoadipate transaminase SMc04386 SMc01578
hglS D-2-hydroxyglutarate synthase SMc04383
ydiJ (R)-2-hydroxyglutarate dehydrogenase SMc04384 SMa0244
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase SMc01576
amaD D-lysine oxidase SMc00797
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit SMa1400 SM_b21121
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase SMa0682 SMa2402
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
davA 5-aminovaleramidase SMc01962 SMc02442
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase SMc02780 SMa0805
davT 5-aminovalerate aminotransferase SM_b21186 SMc02413
dpkA 1-piperideine-2-carboxylate reductase SM_b20261 SMa1459
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SMc01153 SMc01669
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit SMa0819 SMc00728
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit SMa0822 SMc00729
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SMc02227 SMc00727
gcdG succinyl-CoA:glutarate CoA-transferase SM_b21182 SM_b21089
gcdH glutaryl-CoA dehydrogenase SM_b21181 SM_b21121
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase SMc00355
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 SM_b20275 SMc01637
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase SM_b21186 SMc02413
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) SM_b20101
LHT L-lysine transporter
lysL L-lysine transporter LysL SMa1668 SMa1667
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase SMc02138 SM_b21186
patD 5-aminopentanal dehydrogenase SMc01656 SMc00094
Slc7a1 L-lysine transporter Slc7a1

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, 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