GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Amantichitinum ursilacus IGB-41

Best path

lysP, cadA, patA, patD, davT, davD, glaH, lhgD

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 WG78_RS03005
cadA lysine decarboxylase WG78_RS18835 WG78_RS18780
patA cadaverine aminotransferase WG78_RS16665 WG78_RS06780
patD 5-aminopentanal dehydrogenase WG78_RS16670 WG78_RS14820
davT 5-aminovalerate aminotransferase WG78_RS16665 WG78_RS06780
davD glutarate semialdehyde dehydrogenase WG78_RS16670 WG78_RS14820
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) WG78_RS12675
Alternative steps:
alr lysine racemase WG78_RS07315
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) WG78_RS16670 WG78_RS17855
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT WG78_RS08855 WG78_RS15280
atoB acetyl-CoA C-acetyltransferase WG78_RS19070 WG78_RS04410
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit
bgtB* L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) WG78_RS15275 with WG78_RS15280
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
davA 5-aminovaleramidase WG78_RS21195
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit WG78_RS10680
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit WG78_RS10685
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase WG78_RS04405 WG78_RS04575
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) WG78_RS08860 WG78_RS15275
hisP L-lysine ABC transporter, ATPase component HisP WG78_RS16125 WG78_RS16145
hisQ L-lysine ABC transporter, permease component 2 (HisQ) WG78_RS08860 WG78_RS15275
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 WG78_RS16665 WG78_RS06780
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase WG78_RS09250 WG78_RS16665
Slc7a1 L-lysine transporter Slc7a1 WG78_RS04860
ydiJ (R)-2-hydroxyglutarate dehydrogenase WG78_RS13215

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