GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_00224 H281DRAFT_03659
hisM L-lysine ABC transporter, permease component 1 (HisM) H281DRAFT_00222 H281DRAFT_06475
hisQ L-lysine ABC transporter, permease component 2 (HisQ) H281DRAFT_00223 H281DRAFT_06474
hisP L-lysine ABC transporter, ATPase component HisP H281DRAFT_05293 H281DRAFT_06476
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase H281DRAFT_03146 H281DRAFT_05434
davT 5-aminovalerate aminotransferase H281DRAFT_03179 H281DRAFT_06478
davD glutarate semialdehyde dehydrogenase H281DRAFT_03178 H281DRAFT_03540
gcdG succinyl-CoA:glutarate CoA-transferase H281DRAFT_04444 H281DRAFT_01169
gcdH glutaryl-CoA dehydrogenase H281DRAFT_04737 H281DRAFT_01204
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H281DRAFT_05725 H281DRAFT_02514
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H281DRAFT_00361 H281DRAFT_04625
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
Alternative steps:
alr lysine racemase H281DRAFT_00589
amaA L-pipecolate oxidase H281DRAFT_02574 H281DRAFT_06337
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) H281DRAFT_01833 H281DRAFT_03540
amaD D-lysine oxidase H281DRAFT_05881 H281DRAFT_03160
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit H281DRAFT_06133 H281DRAFT_02091
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase H281DRAFT_00160 H281DRAFT_04542
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit H281DRAFT_04495 H281DRAFT_01597
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit H281DRAFT_04496 H281DRAFT_01596
dpkA 1-piperideine-2-carboxylate reductase H281DRAFT_05357 H281DRAFT_02928
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit H281DRAFT_04285 H281DRAFT_03367
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit H281DRAFT_01168 H281DRAFT_03903
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
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 H281DRAFT_03174 H281DRAFT_00641
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase H281DRAFT_03179 H281DRAFT_02621
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H281DRAFT_02167
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase H281DRAFT_05221
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase H281DRAFT_00271 H281DRAFT_03179
lysP L-lysine:H+ symporter LysP H281DRAFT_04042 H281DRAFT_01668
patA cadaverine aminotransferase H281DRAFT_02621 H281DRAFT_06478
patD 5-aminopentanal dehydrogenase H281DRAFT_03016 H281DRAFT_02464
Slc7a1 L-lysine transporter Slc7a1 H281DRAFT_02180
ydiJ (R)-2-hydroxyglutarate dehydrogenase H281DRAFT_02585 H281DRAFT_04480

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, 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