GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Dinoroseobacter shibae DFL-12

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT Dshi_2222
hisM L-lysine ABC transporter, permease component 1 (HisM) Dshi_2224 Dshi_0320
hisQ L-lysine ABC transporter, permease component 2 (HisQ) Dshi_2223 Dshi_2224
hisP L-lysine ABC transporter, ATPase component HisP Dshi_0321 Dshi_2221
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase Dshi_3506
davT 5-aminovalerate aminotransferase Dshi_1446 Dshi_0798
davD glutarate semialdehyde dehydrogenase Dshi_2887 Dshi_0577
gcdG succinyl-CoA:glutarate CoA-transferase Dshi_3269 Dshi_1057
gcdH glutaryl-CoA dehydrogenase Dshi_2357 Dshi_1297
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dshi_3370 Dshi_0835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Dshi_3826 Dshi_0835
atoB acetyl-CoA C-acetyltransferase Dshi_3066 Dshi_3331
Alternative steps:
alr lysine racemase Dshi_2298 Dshi_1759
amaA L-pipecolate oxidase Dshi_2227
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Dshi_2887 Dshi_0577
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Dshi_1297 Dshi_1750
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase Dshi_1767 Dshi_1375
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Dshi_1136
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Dshi_1134
dpkA 1-piperideine-2-carboxylate reductase Dshi_2039 Dshi_2546
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Dshi_0216
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
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 Dshi_3475
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase Dshi_2042 Dshi_1366
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 Dshi_0762 Dshi_0798
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase Dshi_0798 Dshi_1446
patD 5-aminopentanal dehydrogenase Dshi_2887 Dshi_1095
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Dshi_2076 Dshi_3324

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