GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Bacillus altitudinis 41KF2b

Best path

lysP, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP BA79_RS05520 BA79_RS12355
cadA lysine decarboxylase BA79_RS05730 BA79_RS00300
patA cadaverine aminotransferase BA79_RS05525 BA79_RS00430
patD 5-aminopentanal dehydrogenase BA79_RS13175 BA79_RS04010
davT 5-aminovalerate aminotransferase BA79_RS15810 BA79_RS00295
davD glutarate semialdehyde dehydrogenase BA79_RS15800 BA79_RS04010
gcdG succinyl-CoA:glutarate CoA-transferase BA79_RS12730
gcdH glutaryl-CoA dehydrogenase BA79_RS09030 BA79_RS18235
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BA79_RS18210 BA79_RS07305
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BA79_RS04985 BA79_RS09040
atoB acetyl-CoA C-acetyltransferase BA79_RS09045 BA79_RS04980
Alternative steps:
alr lysine racemase BA79_RS17535 BA79_RS00960
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BA79_RS15800 BA79_RS04010
amaD D-lysine oxidase BA79_RS00675
argT L-lysine ABC transporter, substrate-binding component ArgT BA79_RS09610 BA79_RS15890
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BA79_RS18235 BA79_RS09030
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit BA79_RS14645
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit BA79_RS14650
davA 5-aminovaleramidase BA79_RS12780
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BA79_RS07295
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit BA79_RS07300
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) BA79_RS08715 BA79_RS10125
hisP L-lysine ABC transporter, ATPase component HisP BA79_RS06410 BA79_RS09600
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BA79_RS09605 BA79_RS12820
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase BA79_RS13335
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
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase BA79_RS15810 BA79_RS00295
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase BA79_RS15810 BA79_RS04350
Slc7a1 L-lysine transporter Slc7a1 BA79_RS14915 BA79_RS14005
ydiJ (R)-2-hydroxyglutarate dehydrogenase BA79_RS18270

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.

Links

Downloads

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