GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Sphingomonas koreensis DSMZ 15582

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 (22 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 Ga0059261_3603
davT 5-aminovalerate aminotransferase Ga0059261_4131 Ga0059261_3205
davD glutarate semialdehyde dehydrogenase Ga0059261_0516 Ga0059261_1680
gcdG succinyl-CoA:glutarate CoA-transferase Ga0059261_2166 Ga0059261_2807
gcdH glutaryl-CoA dehydrogenase Ga0059261_2164 Ga0059261_4052
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ga0059261_3685 Ga0059261_2668
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ga0059261_2816 Ga0059261_0837
atoB acetyl-CoA C-acetyltransferase Ga0059261_0982 Ga0059261_2888
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Ga0059261_1680 Ga0059261_1006
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Ga0059261_3681 Ga0059261_4052
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase Ga0059261_3753 Ga0059261_2416
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Ga0059261_0265
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Ga0059261_0263
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Ga0059261_2885 Ga0059261_2280
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Ga0059261_2279 Ga0059261_2886
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM)
hisP L-lysine ABC transporter, ATPase component HisP Ga0059261_0341 Ga0059261_3653
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
lat L-lysine 6-aminotransferase Ga0059261_4131 Ga0059261_3205
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase Ga0059261_2226 Ga0059261_4131
patA cadaverine aminotransferase Ga0059261_4131 Ga0059261_3205
patD 5-aminopentanal dehydrogenase Ga0059261_1680 Ga0059261_3374
Slc7a1 L-lysine transporter Slc7a1 Ga0059261_1577
ydiJ (R)-2-hydroxyglutarate dehydrogenase Ga0059261_1572 Ga0059261_1691

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