GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Shewanella oneidensis MR-1

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 (25 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 SO4092
davT 5-aminovalerate aminotransferase SO1276 SO0617
davD glutarate semialdehyde dehydrogenase SO1275 SO3496
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase SO1897 SO1679
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SO3088 SO1680
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SO0021 SO3088
atoB acetyl-CoA C-acetyltransferase SO1677 SO0020
Alternative steps:
alr lysine racemase SO0275 SO3916
amaA L-pipecolate oxidase SO1274
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) SO1275 SO0619
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT SO1044
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit SO1897 SO1679
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase SO4136 SO0314
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit SO1892
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit SO1891
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit SO3144
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit SO3145
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) SO1043
hisP L-lysine ABC transporter, ATPase component HisP SO1042 SO3692
hisQ L-lysine ABC transporter, permease component 2 (HisQ) SO1043
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 SO1276 SO0617
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 SO1276 SO0617
patA cadaverine aminotransferase SO0617 SO1276
patD 5-aminopentanal dehydrogenase SO4480 SO1275
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase SO2643

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