GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Amphritea japonica JAMM 1866

Best path

argT, hisM, hisQ, hisP, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT G329_RS0106210
hisM L-lysine ABC transporter, permease component 1 (HisM) G329_RS0106200 G329_RS0114590
hisQ L-lysine ABC transporter, permease component 2 (HisQ) G329_RS0106205 G329_RS0106200
hisP L-lysine ABC transporter, ATPase component HisP G329_RS0106215 G329_RS0114595
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase
davT 5-aminovalerate aminotransferase G329_RS0106030 G329_RS0100460
davD glutarate semialdehyde dehydrogenase G329_RS0106155 G329_RS0102155
gcdG succinyl-CoA:glutarate CoA-transferase G329_RS0102150 G329_RS0108890
gcdH glutaryl-CoA dehydrogenase G329_RS0102145 G329_RS0108885
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase G329_RS0102710 G329_RS0103740
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase G329_RS0113855 G329_RS0100985
atoB acetyl-CoA C-acetyltransferase G329_RS0116640 G329_RS0102470
Alternative steps:
alr lysine racemase G329_RS0116810 G329_RS0102210
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) G329_RS0103905 G329_RS0112925
amaD D-lysine oxidase G329_RS0107865 G329_RS0108075
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit G329_RS0105925 G329_RS0108885
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase G329_RS0102320 G329_RS0103955
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit G329_RS0112465
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit G329_RS0112460
dpkA 1-piperideine-2-carboxylate reductase G329_RS0107860
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit G329_RS0101155
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) G329_RS0108040
hglS D-2-hydroxyglutarate synthase
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase G329_RS0104545
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 G329_RS0100460 G329_RS0116795
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) G329_RS0108045
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase G329_RS0107530 G329_RS0109750
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase G329_RS0100460 G329_RS0106030
patD 5-aminopentanal dehydrogenase G329_RS0103095 G329_RS0101520
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase G329_RS0109785

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