GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pseudomonas litoralis 2SM5

Best path

argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT BLU11_RS14495
hisM L-lysine ABC transporter, permease component 1 (HisM) BLU11_RS14485 BLU11_RS14490
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BLU11_RS14490 BLU11_RS14485
hisP L-lysine ABC transporter, ATPase component HisP BLU11_RS14500 BLU11_RS18455
cadA lysine decarboxylase BLU11_RS04715 BLU11_RS12970
patA cadaverine aminotransferase BLU11_RS10765 BLU11_RS18745
patD 5-aminopentanal dehydrogenase BLU11_RS01865 BLU11_RS07285
davT 5-aminovalerate aminotransferase BLU11_RS00885 BLU11_RS10765
davD glutarate semialdehyde dehydrogenase BLU11_RS14925 BLU11_RS07285
gcdG succinyl-CoA:glutarate CoA-transferase BLU11_RS06185 BLU11_RS15305
gcdH glutaryl-CoA dehydrogenase BLU11_RS13665 BLU11_RS12305
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLU11_RS12290 BLU11_RS02050
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLU11_RS06160 BLU11_RS15910
atoB acetyl-CoA C-acetyltransferase BLU11_RS15740 BLU11_RS15515
Alternative steps:
alr lysine racemase BLU11_RS18780 BLU11_RS18590
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BLU11_RS07285 BLU11_RS07260
amaD D-lysine oxidase BLU11_RS05195
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BLU11_RS12305 BLU11_RS02525
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit BLU11_RS15505 BLU11_RS15730
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit BLU11_RS15735 BLU11_RS15510
davA 5-aminovaleramidase BLU11_RS14770 BLU11_RS00810
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase BLU11_RS07195
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BLU11_RS08390 BLU11_RS15930
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit BLU11_RS08395 BLU11_RS15925
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 BLU11_RS11645
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 BLU11_RS00885 BLU11_RS14805
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BLU11_RS14525
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase BLU11_RS00885 BLU11_RS10765
lysP L-lysine:H+ symporter LysP
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase BLU11_RS07215 BLU11_RS13390

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