GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Marinobacter adhaerens HP15

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT HP15_3031 HP15_2918
hisM L-lysine ABC transporter, permease component 1 (HisM) HP15_3033 HP15_3032
hisQ L-lysine ABC transporter, permease component 2 (HisQ) HP15_3032 HP15_2919
hisP L-lysine ABC transporter, ATPase component HisP HP15_2193 HP15_3030
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase HP15_2074 HP15_3653
davT 5-aminovalerate aminotransferase HP15_3708 HP15_3042
davD glutarate semialdehyde dehydrogenase HP15_2020 HP15_3404
gcdG succinyl-CoA:glutarate CoA-transferase HP15_1416 HP15_2609
gcdH glutaryl-CoA dehydrogenase HP15_3936 HP15_2
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HP15_908 HP15_12
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HP15_1512 HP15_3941
atoB acetyl-CoA C-acetyltransferase HP15_2996 HP15_5
Alternative steps:
alr lysine racemase HP15_352
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) HP15_2020 HP15_2655
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit HP15_2 HP15_1005
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase HP15_3835 HP15_3785
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit HP15_1755
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
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 HP15_2514
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 HP15_3708
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) HP15_2488
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase HP15_1371 HP15_3708
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase HP15_3042 HP15_3708
patD 5-aminopentanal dehydrogenase HP15_3626 HP15_4032
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase HP15_2553

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