GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
lat L-lysine 6-aminotransferase Echvi_2919 Echvi_0150
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Echvi_0535 Echvi_0481
lysN 2-aminoadipate transaminase Echvi_0675 Echvi_3848
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase Echvi_3865
Alternative steps:
alr lysine racemase Echvi_1545
amaA L-pipecolate oxidase
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
atoB acetyl-CoA C-acetyltransferase Echvi_3705 Echvi_1071
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Echvi_1212 Echvi_1473
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase Echvi_0909
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Echvi_3272
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Echvi_3271
davA 5-aminovaleramidase
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase Echvi_0481 Echvi_3822
davT 5-aminovalerate aminotransferase Echvi_2919 Echvi_3848
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Echvi_4069 Echvi_0069
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Echvi_2952
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Echvi_2951
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Echvi_1069 Echvi_3304
gcdG succinyl-CoA:glutarate CoA-transferase Echvi_1686 Echvi_1687
gcdH glutaryl-CoA dehydrogenase Echvi_2990 Echvi_0738
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hisM L-lysine ABC transporter, permease component 1 (HisM)
hisP L-lysine ABC transporter, ATPase component HisP Echvi_4044 Echvi_1582
hisQ L-lysine ABC transporter, permease component 2 (HisQ)
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
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Echvi_3348
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
patA cadaverine aminotransferase Echvi_2919 Echvi_0577
patD 5-aminopentanal dehydrogenase Echvi_0481
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