GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Belnapia rosea CPCC 100156

Best path

lysP, davB, davA, 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
lysP L-lysine:H+ symporter LysP
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase BLR02_RS09725
davT 5-aminovalerate aminotransferase BLR02_RS01300 BLR02_RS12085
davD glutarate semialdehyde dehydrogenase BLR02_RS07320 BLR02_RS18460
gcdG succinyl-CoA:glutarate CoA-transferase BLR02_RS18395 BLR02_RS04245
gcdH glutaryl-CoA dehydrogenase BLR02_RS06730 BLR02_RS03525
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLR02_RS23955 BLR02_RS03400
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLR02_RS03400 BLR02_RS23340
atoB acetyl-CoA C-acetyltransferase BLR02_RS13910 BLR02_RS06650
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase BLR02_RS23630
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BLR02_RS07320 BLR02_RS04250
amaD D-lysine oxidase BLR02_RS22685 BLR02_RS18895
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BLR02_RS03525 BLR02_RS16555
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase BLR02_RS11410 BLR02_RS01030
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit BLR02_RS16700 BLR02_RS16990
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit BLR02_RS16705 BLR02_RS27295
dpkA 1-piperideine-2-carboxylate reductase BLR02_RS22355 BLR02_RS15670
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BLR02_RS23345 BLR02_RS25820
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit BLR02_RS23350
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) BLR02_RS10410 BLR02_RS19470
hisP L-lysine ABC transporter, ATPase component HisP BLR02_RS24955 BLR02_RS10420
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BLR02_RS19470 BLR02_RS19475
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase BLR02_RS17805
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 BLR02_RS01565
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase BLR02_RS13175 BLR02_RS05825
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BLR02_RS05550
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase BLR02_RS01735 BLR02_RS01730
patA cadaverine aminotransferase BLR02_RS01300 BLR02_RS18365
patD 5-aminopentanal dehydrogenase BLR02_RS04250 BLR02_RS07320
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase BLR02_RS19165 BLR02_RS18505

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