GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

argT, hisM, hisQ, hisP, lysDH, amaB, lysN, hglS, ydiJ

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT CEV31_RS11200 CEV31_RS14700
hisM L-lysine ABC transporter, permease component 1 (HisM) CEV31_RS11190 CEV31_RS20080
hisQ L-lysine ABC transporter, permease component 2 (HisQ) CEV31_RS11195 CEV31_RS20085
hisP L-lysine ABC transporter, ATPase component HisP CEV31_RS18525 CEV31_RS20075
lysDH L-lysine 6-dehydrogenase CEV31_RS14690
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) CEV31_RS02495 CEV31_RS04895
lysN 2-aminoadipate transaminase CEV31_RS01885 CEV31_RS08835
hglS D-2-hydroxyglutarate synthase CEV31_RS02490
ydiJ (R)-2-hydroxyglutarate dehydrogenase CEV31_RS07780 CEV31_RS20510
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase CEV31_RS02480 CEV31_RS14305
amaD D-lysine oxidase CEV31_RS14705
atoB acetyl-CoA C-acetyltransferase CEV31_RS03605 CEV31_RS02650
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit CEV31_RS05790 CEV31_RS01035
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase CEV31_RS07945 CEV31_RS13805
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
davA 5-aminovaleramidase CEV31_RS04230
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase CEV31_RS02995 CEV31_RS17495
davT 5-aminovalerate aminotransferase CEV31_RS07275 CEV31_RS17075
dpkA 1-piperideine-2-carboxylate reductase CEV31_RS09235 CEV31_RS18030
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CEV31_RS05620 CEV31_RS09090
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit CEV31_RS04320
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CEV31_RS15760 CEV31_RS04315
gcdG succinyl-CoA:glutarate CoA-transferase CEV31_RS11730 CEV31_RS09080
gcdH glutaryl-CoA dehydrogenase CEV31_RS11735 CEV31_RS05790
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
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
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase CEV31_RS17075 CEV31_RS17470
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CEV31_RS17795 CEV31_RS18945
LHT L-lysine transporter
lysL L-lysine transporter LysL
lysP L-lysine:H+ symporter LysP CEV31_RS18290 CEV31_RS20665
patA cadaverine aminotransferase CEV31_RS17075 CEV31_RS07275
patD 5-aminopentanal dehydrogenase CEV31_RS19025 CEV31_RS08350
Slc7a1 L-lysine transporter Slc7a1

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