GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Salinicoccus carnicancri Crm

Best path

lysP, davB, davA, 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 (24 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 C792_RS0110875
davT 5-aminovalerate aminotransferase C792_RS0103155 C792_RS0108435
davD glutarate semialdehyde dehydrogenase C792_RS0109240 C792_RS0112615
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) C792_RS0112015
Alternative steps:
alr lysine racemase C792_RS0111410 C792_RS14500
amaA L-pipecolate oxidase C792_RS0112355
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) C792_RS0112845 C792_RS0109240
amaD D-lysine oxidase C792_RS0106265 C792_RS0112580
argT L-lysine ABC transporter, substrate-binding component ArgT
atoB acetyl-CoA C-acetyltransferase C792_RS0112545 C792_RS0109325
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase C792_RS0102305
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit C792_RS0112540
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit C792_RS0112535
dpkA 1-piperideine-2-carboxylate reductase C792_RS0112705 C792_RS0104515
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C792_RS0109005 C792_RS0108985
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C792_RS0109330 C792_RS0108990
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase C792_RS0109335
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) C792_RS0101010 C792_RS0112495
hisP L-lysine ABC transporter, ATPase component HisP C792_RS0100130 C792_RS0103280
hisQ L-lysine ABC transporter, permease component 2 (HisQ) C792_RS0112495 C792_RS0103290
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 C792_RS0110600
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase C792_RS0108435
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase C792_RS0108030 C792_RS0111735
patA cadaverine aminotransferase C792_RS0103155 C792_RS0109810
patD 5-aminopentanal dehydrogenase C792_RS0112615 C792_RS0108995
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase

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