GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Shewanella loihica PV-4

Best path

lysP, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase Shew_0409
davT 5-aminovalerate aminotransferase Shew_3172 Shew_0578
davD glutarate semialdehyde dehydrogenase Shew_3173 Shew_0967
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Shew_0900 Shew_2570
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shew_1670 Shew_0019
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shew_0019 Shew_2425
atoB acetyl-CoA C-acetyltransferase Shew_1667 Shew_0018
Alternative steps:
alr lysine racemase Shew_0202 Shew_3277
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Shew_3173 Shew_0580
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT Shew_3166
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Shew_2570 Shew_1669
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase Shew_3392
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Shew_2575
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Shew_2576
dpkA 1-piperideine-2-carboxylate reductase Shew_2955
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Shew_2583 Shew_2678
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Shew_2584
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) Shew_3165
hisP L-lysine ABC transporter, ATPase component HisP Shew_3164 Shew_0723
hisQ L-lysine ABC transporter, permease component 2 (HisQ) Shew_3165
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 Shew_3172 Shew_1012
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Shew_0530
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase Shew_3172 Shew_0578
patA cadaverine aminotransferase Shew_3172 Shew_0578
patD 5-aminopentanal dehydrogenase Shew_3574 Shew_3173
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Shew_1550

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