GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Photobacterium gaetbulicola Gung47

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 H744_RS14470 H744_RS20565
hisM L-lysine ABC transporter, permease component 1 (HisM) H744_RS14480 H744_RS20575
hisQ L-lysine ABC transporter, permease component 2 (HisQ) H744_RS14475 H744_RS20570
hisP L-lysine ABC transporter, ATPase component HisP H744_RS14465 H744_RS06570
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase
davT 5-aminovalerate aminotransferase H744_RS11460 H744_RS16550
davD glutarate semialdehyde dehydrogenase H744_RS01660 H744_RS03200
gcdG succinyl-CoA:glutarate CoA-transferase H744_RS02205
gcdH glutaryl-CoA dehydrogenase H744_RS04345 H744_RS04325
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H744_RS10395 H744_RS04320
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H744_RS10395 H744_RS14605
atoB acetyl-CoA C-acetyltransferase H744_RS02875 H744_RS04335
Alternative steps:
alr lysine racemase H744_RS11345 H744_RS17550
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) H744_RS01660 H744_RS03200
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit H744_RS04345 H744_RS04325
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase H744_RS16550 H744_RS20235
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit H744_RS02900
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit H744_RS02895
dpkA 1-piperideine-2-carboxylate reductase H744_RS07445
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit H744_RS04135
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit H744_RS04140
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase H744_RS09120
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 H744_RS16550 H744_RS07770
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H744_RS05515
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL H744_RS18230
lysN 2-aminoadipate transaminase H744_RS11460 H744_RS16550
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase H744_RS07795 H744_RS16550
patD 5-aminopentanal dehydrogenase H744_RS01660 H744_RS06160
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase H744_RS16715

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