GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Galbibacter marinus ck-I2-15

Best path

lysP, lat, amaB, lysN, hglS, ydiJ

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
lat L-lysine 6-aminotransferase I215_RS02430 I215_RS12775
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) I215_RS08785
lysN 2-aminoadipate transaminase I215_RS06940 I215_RS12775
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase I215_RS10655
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaD D-lysine oxidase I215_RS04945
argT L-lysine ABC transporter, substrate-binding component ArgT
atoB acetyl-CoA C-acetyltransferase I215_RS13275 I215_RS07615
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit I215_RS12960 I215_RS09715
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase I215_RS07650
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit I215_RS00830
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit I215_RS00825
davA 5-aminovaleramidase I215_RS13730
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase I215_RS02025
davT 5-aminovalerate aminotransferase I215_RS02430 I215_RS12775
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I215_RS00560 I215_RS04020
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit I215_RS05185
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit I215_RS05190
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase I215_RS07610 I215_RS10610
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase I215_RS10995 I215_RS12960
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 I215_RS00120 I215_RS04690
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)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
patA cadaverine aminotransferase I215_RS12775 I215_RS02430
patD 5-aminopentanal dehydrogenase I215_RS02025
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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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