GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Algoriphagus aquaeductus T4

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 CLV31_RS14580
patA cadaverine aminotransferase CLV31_RS13960 CLV31_RS11440
patD 5-aminopentanal dehydrogenase
davT 5-aminovalerate aminotransferase CLV31_RS11440 CLV31_RS13960
davD glutarate semialdehyde dehydrogenase CLV31_RS07110
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase CLV31_RS15640 CLV31_RS21080
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CLV31_RS05805 CLV31_RS13180
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CLV31_RS03385 CLV31_RS11275
atoB acetyl-CoA C-acetyltransferase CLV31_RS09120 CLV31_RS03395
Alternative steps:
alr lysine racemase CLV31_RS07595
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) CLV31_RS12285
amaD D-lysine oxidase CLV31_RS05710
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit CLV31_RS14820 CLV31_RS09630
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit CLV31_RS11365 CLV31_RS16400
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit CLV31_RS11360 CLV31_RS16400
davA 5-aminovaleramidase CLV31_RS12815 CLV31_RS08480
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase CLV31_RS11755
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit CLV31_RS08315
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit CLV31_RS08320
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 CLV31_RS07770 CLV31_RS09345
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 CLV31_RS13960 CLV31_RS11440
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CLV31_RS15940
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase CLV31_RS12305 CLV31_RS13960
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase CLV31_RS17725

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