GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Rhizobium leguminosarum 3841

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT RL_RS14210 RL_RS29250
hisM L-lysine ABC transporter, permease component 1 (HisM) RL_RS14220 RL_RS30845
hisQ L-lysine ABC transporter, permease component 2 (HisQ) RL_RS14215 RL_RS30840
hisP L-lysine ABC transporter, ATPase component HisP RL_RS29450 RL_RS11410
lysDH L-lysine 6-dehydrogenase RL_RS01960
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) RL_RS23620 RL_RS30640
lysN 2-aminoadipate transaminase RL_RS17735 RL_RS29560
hglS D-2-hydroxyglutarate synthase RL_RS23630
ydiJ (R)-2-hydroxyglutarate dehydrogenase RL_RS04995 RL_RS33825
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase RL_RS23625
amaD D-lysine oxidase RL_RS04110
atoB acetyl-CoA C-acetyltransferase RL_RS23800 RL_RS28905
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit RL_RS28910 RL_RS28880
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase RL_RS07970 RL_RS21430
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit RL_RS31205
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit RL_RS31210
davA 5-aminovaleramidase RL_RS35110 RL_RS22115
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase RL_RS28660 RL_RS28045
davT 5-aminovalerate aminotransferase RL_RS00545 RL_RS02885
dpkA 1-piperideine-2-carboxylate reductase RL_RS35465 RL_RS22985
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RL_RS01945 RL_RS33285
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit RL_RS28375 RL_RS35510
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit RL_RS28380 RL_RS22275
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RL_RS03115 RL_RS22285
gcdG succinyl-CoA:glutarate CoA-transferase RL_RS17180 RL_RS29880
gcdH glutaryl-CoA dehydrogenase RL_RS31715 RL_RS28910
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase RL_RS23685
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 RL_RS29275
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase RL_RS00545 RL_RS35975
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RL_RS26675
LHT L-lysine transporter
lysL L-lysine transporter LysL
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase RL_RS22620 RL_RS02885
patD 5-aminopentanal dehydrogenase RL_RS21625 RL_RS06630
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.

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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