GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Azospirillum brasilense Sp245

Best path

argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB

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 AZOBR_RS27130 AZOBR_RS00685
hisM L-lysine ABC transporter, permease component 1 (HisM) AZOBR_RS00675 AZOBR_RS23520
hisQ L-lysine ABC transporter, permease component 2 (HisQ) AZOBR_RS00680 AZOBR_RS23520
hisP L-lysine ABC transporter, ATPase component HisP AZOBR_RS00690 AZOBR_RS08670
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase AZOBR_RS30770 AZOBR_RS08170
davT 5-aminovalerate aminotransferase AZOBR_RS19630 AZOBR_RS19025
davD glutarate semialdehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
gcdG succinyl-CoA:glutarate CoA-transferase AZOBR_RS19675 AZOBR_RS29180
gcdH glutaryl-CoA dehydrogenase AZOBR_RS19670 AZOBR_RS22310
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AZOBR_RS01260 AZOBR_RS26485
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
atoB acetyl-CoA C-acetyltransferase AZOBR_RS30610 AZOBR_RS28180
Alternative steps:
alr lysine racemase AZOBR_RS07795 AZOBR_RS08350
amaA L-pipecolate oxidase AZOBR_RS32385 AZOBR_RS25655
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) AZOBR_RS32620 AZOBR_RS29185
amaD D-lysine oxidase AZOBR_RS30970
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit AZOBR_RS22300 AZOBR_RS22365
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase AZOBR_RS14105 AZOBR_RS10990
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
dpkA 1-piperideine-2-carboxylate reductase AZOBR_RS31690 AZOBR_RS03120
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit AZOBR_RS05475 AZOBR_RS16915
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit AZOBR_RS05480 AZOBR_RS29740
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 AZOBR_RS01360
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 AZOBR_RS27000 AZOBR_RS23055
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase AZOBR_RS19630 AZOBR_RS03635
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AZOBR_RS33525
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase AZOBR_RS29980
lysL L-lysine transporter LysL AZOBR_RS13260
lysN 2-aminoadipate transaminase AZOBR_RS12970 AZOBR_RS19630
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase AZOBR_RS19590 AZOBR_RS19630
patD 5-aminopentanal dehydrogenase AZOBR_RS09720 AZOBR_RS19635
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase AZOBR_RS05770 AZOBR_RS29745

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