GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pseudomonas benzenivorans DSM 8628

Best path

argT, hisM, hisQ, hisP, lysDH, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT BLS63_RS24440 BLS63_RS01130
hisM L-lysine ABC transporter, permease component 1 (HisM) BLS63_RS24450 BLS63_RS01120
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BLS63_RS24445 BLS63_RS01125
hisP L-lysine ABC transporter, ATPase component HisP BLS63_RS24435 BLS63_RS01135
lysDH L-lysine 6-dehydrogenase BLS63_RS01140
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BLS63_RS01085 BLS63_RS26230
lysN 2-aminoadipate transaminase BLS63_RS01095 BLS63_RS09835
hglS D-2-hydroxyglutarate synthase BLS63_RS01105
ydiJ (R)-2-hydroxyglutarate dehydrogenase BLS63_RS10140 BLS63_RS16595
Alternative steps:
alr lysine racemase BLS63_RS25835 BLS63_RS19105
amaA L-pipecolate oxidase BLS63_RS23770 BLS63_RS19080
amaD D-lysine oxidase BLS63_RS03560
atoB acetyl-CoA C-acetyltransferase BLS63_RS22810 BLS63_RS21120
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BLS63_RS24295 BLS63_RS24330
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase BLS63_RS01145 BLS63_RS11680
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit BLS63_RS21205 BLS63_RS25510
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit BLS63_RS25505 BLS63_RS21195
davA 5-aminovaleramidase BLS63_RS08900 BLS63_RS16685
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase BLS63_RS26230 BLS63_RS15725
davT 5-aminovalerate aminotransferase BLS63_RS01095 BLS63_RS26240
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLS63_RS21705 BLS63_RS07890
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BLS63_RS18395
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit BLS63_RS18400
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLS63_RS07890 BLS63_RS21115
gcdG succinyl-CoA:glutarate CoA-transferase BLS63_RS14580 BLS63_RS17670
gcdH glutaryl-CoA dehydrogenase BLS63_RS14585 BLS63_RS24330
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
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 BLS63_RS25275
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase BLS63_RS07545 BLS63_RS01095
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BLS63_RS24405
LHT L-lysine transporter
lysL L-lysine transporter LysL BLS63_RS10640
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase BLS63_RS07545 BLS63_RS19255
patD 5-aminopentanal dehydrogenase BLS63_RS09095 BLS63_RS09120
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