GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Rhizobium leguminosarum bv. trifolii WSM1325

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT RLEG_RS11315 RLEG_RS34805
hisM L-lysine ABC transporter, permease component 1 (HisM) RLEG_RS11325 RLEG_RS28485
hisQ L-lysine ABC transporter, permease component 2 (HisQ) RLEG_RS11320 RLEG_RS28490
hisP L-lysine ABC transporter, ATPase component HisP RLEG_RS34600 RLEG_RS08715
lysDH L-lysine 6-dehydrogenase RLEG_RS00010
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) RLEG_RS20360 RLEG_RS02225
lysN 2-aminoadipate transaminase RLEG_RS14800 RLEG_RS34460
hglS D-2-hydroxyglutarate synthase RLEG_RS20370
ydiJ (R)-2-hydroxyglutarate dehydrogenase RLEG_RS02945
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase RLEG_RS20365
amaD D-lysine oxidase RLEG_RS02155
atoB acetyl-CoA C-acetyltransferase RLEG_RS20540 RLEG_RS35140
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit RLEG_RS35135 RLEG_RS35160
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase RLEG_RS05780 RLEG_RS13095
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit RLEG_RS27925
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit RLEG_RS27920
davA 5-aminovaleramidase RLEG_RS27155
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase RLEG_RS35305 RLEG_RS21595
davT 5-aminovalerate aminotransferase RLEG_RS21600 RLEG_RS00940
dpkA 1-piperideine-2-carboxylate reductase RLEG_RS23920 RLEG_RS19760
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RLEG_RS23030 RLEG_RS26045
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit RLEG_RS24450 RLEG_RS19085
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit RLEG_RS24455 RLEG_RS23965
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RLEG_RS01235 RLEG_RS19090
gcdG succinyl-CoA:glutarate CoA-transferase RLEG_RS14235
gcdH glutaryl-CoA dehydrogenase RLEG_RS27635 RLEG_RS35135
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase RLEG_RS20425
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 RLEG_RS34775
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase RLEG_RS21600 RLEG_RS19395
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysL L-lysine transporter LysL
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase RLEG_RS19395 RLEG_RS00940
patD 5-aminopentanal dehydrogenase RLEG_RS18405 RLEG_RS04395
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 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