GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Sporolactobacillus vineae SL153

Best path

lysP, davB, davA, davT, davD, glaH, lhgD

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
lysP L-lysine:H+ symporter LysP RH97_RS02150 RH97_RS11340
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase RH97_RS09110 RH97_RS09270
davT 5-aminovalerate aminotransferase RH97_RS08100 RH97_RS02445
davD glutarate semialdehyde dehydrogenase RH97_RS06550 RH97_RS02580
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RH97_RS07265
Alternative steps:
alr lysine racemase RH97_RS10855 RH97_RS10675
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) RH97_RS06550 RH97_RS06770
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT RH97_RS08085 RH97_RS07900
atoB acetyl-CoA C-acetyltransferase RH97_RS08940 RH97_RS04710
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit RH97_RS08905
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase RH97_RS02145 RH97_RS10665
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit RH97_RS08945 RH97_RS04720
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit RH97_RS08950 RH97_RS04725
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RH97_RS08930 RH97_RS07390
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit RH97_RS08915
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit RH97_RS08920
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RH97_RS08935 RH97_RS05205
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase RH97_RS08905
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) RH97_RS08090 RH97_RS02560
hisP L-lysine ABC transporter, ATPase component HisP RH97_RS07910 RH97_RS08095
hisQ L-lysine ABC transporter, permease component 2 (HisQ) RH97_RS02560 RH97_RS07905
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 RH97_RS08100 RH97_RS02445
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL RH97_RS03115
lysN 2-aminoadipate transaminase RH97_RS04630 RH97_RS08100
patA cadaverine aminotransferase RH97_RS10690 RH97_RS08100
patD 5-aminopentanal dehydrogenase RH97_RS02580 RH97_RS06550
Slc7a1 L-lysine transporter Slc7a1 RH97_RS05565 RH97_RS05570
ydiJ (R)-2-hydroxyglutarate dehydrogenase

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