GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Rhodanobacter denitrificans FW104-10B01

Best path

lysP, lat, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP LRK54_RS02890 LRK54_RS15610
lat L-lysine 6-aminotransferase LRK54_RS04500 LRK54_RS03035
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) LRK54_RS15965 LRK54_RS04485
lysN 2-aminoadipate transaminase LRK54_RS00725 LRK54_RS04500
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase LRK54_RS03180 LRK54_RS12175
Alternative steps:
alr lysine racemase LRK54_RS00585
amaA L-pipecolate oxidase
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
atoB acetyl-CoA C-acetyltransferase LRK54_RS15265 LRK54_RS00050
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit LRK54_RS02105 LRK54_RS15275
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase LRK54_RS00965
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit LRK54_RS18155
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit LRK54_RS18155
davA 5-aminovaleramidase LRK54_RS00825 LRK54_RS00340
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
davT 5-aminovalerate aminotransferase LRK54_RS04500 LRK54_RS06590
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase LRK54_RS15165 LRK54_RS16925
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit LRK54_RS05550
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit LRK54_RS05545
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase LRK54_RS00055 LRK54_RS16925
gcdG succinyl-CoA:glutarate CoA-transferase LRK54_RS07425
gcdH glutaryl-CoA dehydrogenase LRK54_RS02070 LRK54_RS02105
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hisM L-lysine ABC transporter, permease component 1 (HisM)
hisP L-lysine ABC transporter, ATPase component HisP LRK54_RS14735 LRK54_RS02365
hisQ L-lysine ABC transporter, permease component 2 (HisQ)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase LRK54_RS02485
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
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
patA cadaverine aminotransferase LRK54_RS04500 LRK54_RS06590
patD 5-aminopentanal dehydrogenase LRK54_RS02575 LRK54_RS08020
Slc7a1 L-lysine transporter Slc7a1 LRK54_RS01525 LRK54_RS10455

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