GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Novosphingobium aromaticivorans DSM 12444

Best path

lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase SARO_RS15710
davT 5-aminovalerate aminotransferase SARO_RS13120 SARO_RS15955
davD glutarate semialdehyde dehydrogenase SARO_RS17165 SARO_RS14885
gcdG succinyl-CoA:glutarate CoA-transferase SARO_RS18980 SARO_RS17240
gcdH glutaryl-CoA dehydrogenase SARO_RS17970 SARO_RS08250
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SARO_RS04305 SARO_RS07105
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SARO_RS02760 SARO_RS18115
atoB acetyl-CoA C-acetyltransferase SARO_RS04040 SARO_RS05335
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase SARO_RS07710
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) SARO_RS17185 SARO_RS04690
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit SARO_RS08250 SARO_RS04295
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase SARO_RS09085
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit SARO_RS02835 SARO_RS19990
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit SARO_RS19995 SARO_RS02825
dpkA 1-piperideine-2-carboxylate reductase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit SARO_RS16090
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit SARO_RS16095
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM)
hisP L-lysine ABC transporter, ATPase component HisP SARO_RS05745 SARO_RS11475
hisQ L-lysine ABC transporter, permease component 2 (HisQ)
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 SARO_RS13120 SARO_RS14875
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase SARO_RS02235 SARO_RS13120
patA cadaverine aminotransferase SARO_RS15955 SARO_RS14875
patD 5-aminopentanal dehydrogenase SARO_RS19930 SARO_RS14550
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase SARO_RS06455 SARO_RS04075

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