GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Paraburkholderia phymatum STM815

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT BPHY_RS11010 BPHY_RS19095
hisM L-lysine ABC transporter, permease component 1 (HisM) BPHY_RS11020 BPHY_RS09105
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BPHY_RS11015 BPHY_RS09110
hisP L-lysine ABC transporter, ATPase component HisP BPHY_RS25585 BPHY_RS09100
cadA lysine decarboxylase BPHY_RS11130 BPHY_RS32100
patA cadaverine aminotransferase BPHY_RS31375 BPHY_RS09090
patD 5-aminopentanal dehydrogenase BPHY_RS28155 BPHY_RS23615
davT 5-aminovalerate aminotransferase BPHY_RS24335 BPHY_RS23215
davD glutarate semialdehyde dehydrogenase BPHY_RS24330 BPHY_RS16380
gcdG succinyl-CoA:glutarate CoA-transferase BPHY_RS08225 BPHY_RS31935
gcdH glutaryl-CoA dehydrogenase BPHY_RS12365 BPHY_RS18015
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHY_RS13655 BPHY_RS24290
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHY_RS01920 BPHY_RS35840
atoB acetyl-CoA C-acetyltransferase BPHY_RS04915 BPHY_RS04940
Alternative steps:
alr lysine racemase BPHY_RS06895
amaA L-pipecolate oxidase BPHY_RS12025 BPHY_RS32820
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BPHY_RS19605 BPHY_RS16780
amaD D-lysine oxidase BPHY_RS17405 BPHY_RS27330
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BPHY_RS00875 BPHY_RS25695
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit BPHY_RS07975 BPHY_RS22420
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit BPHY_RS07970 BPHY_RS22425
davA 5-aminovaleramidase
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase BPHY_RS16945
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BPHY_RS38175 BPHY_RS24240
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit BPHY_RS38180 BPHY_RS24235
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 BPHY_RS05475 BPHY_RS16660
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase BPHY_RS24335 BPHY_RS23215
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BPHY_RS00525
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase BPHY_RS06310
lysL L-lysine transporter LysL BPHY_RS05525
lysN 2-aminoadipate transaminase BPHY_RS24335 BPHY_RS10775
lysP L-lysine:H+ symporter LysP BPHY_RS03010 BPHY_RS32965
Slc7a1 L-lysine transporter Slc7a1 BPHY_RS00475
ydiJ (R)-2-hydroxyglutarate dehydrogenase BPHY_RS08050 BPHY_RS25630

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 Apr 09 2024. 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