GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pseudomonas simiae WCS417

Best path

argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB

Also see fitness data for the top candidates

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT PS417_06415 PS417_01495
hisM L-lysine ABC transporter, permease component 1 (HisM) PS417_06405 PS417_01485
hisQ L-lysine ABC transporter, permease component 2 (HisQ) PS417_06410 PS417_01490
hisP L-lysine ABC transporter, ATPase component HisP PS417_01500 PS417_06395
davB L-lysine 2-monooxygenase PS417_25910
davA 5-aminovaleramidase PS417_25915 PS417_04280
davT 5-aminovalerate aminotransferase PS417_00900 PS417_23355
davD glutarate semialdehyde dehydrogenase PS417_00895 PS417_17840
gcdG succinyl-CoA:glutarate CoA-transferase PS417_00585 PS417_14920
gcdH glutaryl-CoA dehydrogenase PS417_00580 PS417_17015
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PS417_13845 PS417_07575
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PS417_07575 PS417_21215
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
Alternative steps:
alr lysine racemase PS417_25660 PS417_27695
amaA L-pipecolate oxidase PS417_02650 PS417_15495
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) PS417_02645 PS417_00895
amaD D-lysine oxidase PS417_03805
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit PS417_13850 PS417_13840
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase PS417_12240 PS417_04005
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit PS417_10525
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit PS417_10520
dpkA 1-piperideine-2-carboxylate reductase PS417_12515
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit PS417_21295
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit PS417_21300
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase PS417_15555
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 PS417_26280 PS417_07250
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase PS417_00900 PS417_19505
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL PS417_22325 PS417_22320
lysN 2-aminoadipate transaminase PS417_23355 PS417_19025
lysP L-lysine:H+ symporter LysP PS417_05405 PS417_01505
patA cadaverine aminotransferase PS417_08025 PS417_21710
patD 5-aminopentanal dehydrogenase PS417_05920 PS417_05945
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase PS417_27035

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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