GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Novosphingobium barchaimii LL02

Best path

lysP, cadA, patA, patD, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
cadA lysine decarboxylase V474_RS10960 V474_RS15765
patA cadaverine aminotransferase V474_RS13815 V474_RS13220
patD 5-aminopentanal dehydrogenase V474_RS10060 V474_RS12520
davT 5-aminovalerate aminotransferase V474_RS13815 V474_RS23835
davD glutarate semialdehyde dehydrogenase V474_RS17175 V474_RS22325
gcdG succinyl-CoA:glutarate CoA-transferase V474_RS01235 V474_RS17140
gcdH glutaryl-CoA dehydrogenase V474_RS05240 V474_RS22780
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase V474_RS01310 V474_RS16345
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase V474_RS17855 V474_RS22775
atoB acetyl-CoA C-acetyltransferase V474_RS02980 V474_RS05390
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) V474_RS17175 V474_RS10060
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit V474_RS01300 V474_RS05240
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit V474_RS17305 V474_RS21635
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit V474_RS17310 V474_RS21640
davA 5-aminovaleramidase V474_RS06790 V474_RS03230
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase V474_RS24890
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit V474_RS18190 V474_RS20245
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit V474_RS20240
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 V474_RS15950 V474_RS07795
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 V474_RS13815
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 V474_RS13605 V474_RS23835
Slc7a1 L-lysine transporter Slc7a1 V474_RS08715
ydiJ (R)-2-hydroxyglutarate dehydrogenase V474_RS05805

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