GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Rhizobium etli CFN 42

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 RHE_RS12350 RHE_RS23445
hisM L-lysine ABC transporter, permease component 1 (HisM) RHE_RS12360 RHE_RS30300
hisQ L-lysine ABC transporter, permease component 2 (HisQ) RHE_RS12355 RHE_RS24425
hisP L-lysine ABC transporter, ATPase component HisP RHE_RS11715 RHE_RS23640
lysDH L-lysine 6-dehydrogenase RHE_RS01815
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) RHE_RS20725 RHE_RS16180
lysN 2-aminoadipate transaminase RHE_RS15340 RHE_RS23780
hglS D-2-hydroxyglutarate synthase RHE_RS20715
ydiJ (R)-2-hydroxyglutarate dehydrogenase RHE_RS04520 RHE_RS04070
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase RHE_RS20720
amaD D-lysine oxidase RHE_RS03755
atoB acetyl-CoA C-acetyltransferase RHE_RS20545 RHE_RS23190
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit RHE_RS23195 RHE_RS23165
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase RHE_RS07235 RHE_RS18555
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit RHE_RS25065
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit RHE_RS25070
davA 5-aminovaleramidase RHE_RS19225
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase RHE_RS23010 RHE_RS00470
davT 5-aminovalerate aminotransferase RHE_RS00475 RHE_RS02610
dpkA 1-piperideine-2-carboxylate reductase RHE_RS00300 RHE_RS28335
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RHE_RS01800 RHE_RS02825
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit RHE_RS30505 RHE_RS28535
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit RHE_RS30500 RHE_RS28540
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RHE_RS02825 RHE_RS19395
gcdG succinyl-CoA:glutarate CoA-transferase RHE_RS14710
gcdH glutaryl-CoA dehydrogenase RHE_RS25445 RHE_RS23195
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase RHE_RS20660
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 RHE_RS23475
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase RHE_RS00475 RHE_RS10975
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 RHE_RS25845
patA cadaverine aminotransferase RHE_RS19705 RHE_RS02610
patD 5-aminopentanal dehydrogenase RHE_RS18735 RHE_RS05810
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