GapMind for catabolism of small carbon sources


L-lysine catabolism in Burkholderia phytofirmans PsJN

Best path

argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB

Also see fitness data for the top candidates


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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT BPHYT_RS35100 BPHYT_RS29525
hisM L-lysine ABC transporter, permease component 1 (HisM) BPHYT_RS05500 BPHYT_RS07680
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BPHYT_RS05505 BPHYT_RS07675
hisP L-lysine ABC transporter, ATPase component HisP BPHYT_RS24015 BPHYT_RS07685
cadA lysine decarboxylase BPHYT_RS04980 BPHYT_RS06500
patA cadaverine aminotransferase BPHYT_RS27170 BPHYT_RS07695
patD 5-aminopentanal dehydrogenase BPHYT_RS09900 BPHYT_RS25160
davT 5-aminovalerate aminotransferase BPHYT_RS22435 BPHYT_RS07695
davD glutarate semialdehyde dehydrogenase BPHYT_RS22430 BPHYT_RS34305
gcdG succinyl-CoA:glutarate CoA-transferase BPHYT_RS13985 BPHYT_RS31850
gcdH glutaryl-CoA dehydrogenase BPHYT_RS03780 BPHYT_RS23260
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHYT_RS17335 BPHYT_RS28020
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHYT_RS13545 BPHYT_RS03225
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
Alternative steps:
alr lysine racemase BPHYT_RS12240
amaA L-pipecolate oxidase BPHYT_RS13575 BPHYT_RS30200
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BPHYT_RS32650 BPHYT_RS28770
amaD D-lysine oxidase BPHYT_RS10270 BPHYT_RS22250
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BPHYT_RS28040 BPHYT_RS02220
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit BPHYT_RS13675 BPHYT_RS21415
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit BPHYT_RS13670 BPHYT_RS21420
davA 5-aminovaleramidase BPHYT_RS22155 BPHYT_RS00250
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase BPHYT_RS24365 BPHYT_RS21000
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BPHYT_RS14800 BPHYT_RS20830
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit BPHYT_RS20825 BPHYT_RS14805
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 BPHYT_RS31475 BPHYT_RS22385
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase BPHYT_RS22435 BPHYT_RS10155
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BPHYT_RS28480 BPHYT_RS01855
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase BPHYT_RS11250
lysL L-lysine transporter LysL BPHYT_RS27675
lysN 2-aminoadipate transaminase BPHYT_RS05965 BPHYT_RS22435
lysP L-lysine:H+ symporter LysP BPHYT_RS15500 BPHYT_RS21680
Slc7a1 L-lysine transporter Slc7a1 BPHYT_RS33230 BPHYT_RS01785
ydiJ (R)-2-hydroxyglutarate dehydrogenase BPHYT_RS32905 BPHYT_RS13750

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.



Related tools

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