GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Oceanisphaera arctica V1-41

Best path

argT, hisM, hisQ, hisP, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT UN63_RS02420 UN63_RS03185
hisM L-lysine ABC transporter, permease component 1 (HisM) UN63_RS03175 UN63_RS13370
hisQ L-lysine ABC transporter, permease component 2 (HisQ) UN63_RS03180 UN63_RS13375
hisP L-lysine ABC transporter, ATPase component HisP UN63_RS03190 UN63_RS01060
cadA lysine decarboxylase UN63_RS14765
patA cadaverine aminotransferase UN63_RS12600 UN63_RS03535
patD 5-aminopentanal dehydrogenase UN63_RS03450 UN63_RS08090
davT 5-aminovalerate aminotransferase UN63_RS03445 UN63_RS03535
davD glutarate semialdehyde dehydrogenase UN63_RS08090 UN63_RS03450
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) UN63_RS15945
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) UN63_RS15950
Alternative steps:
alr lysine racemase UN63_RS13050
amaA L-pipecolate oxidase UN63_RS14970
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) UN63_RS03450 UN63_RS08875
amaD D-lysine oxidase UN63_RS12645 UN63_RS09045
atoB acetyl-CoA C-acetyltransferase UN63_RS04220 UN63_RS09000
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit UN63_RS13340 UN63_RS08990
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit UN63_RS00285
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit UN63_RS00280
davA 5-aminovaleramidase UN63_RS06465 UN63_RS03755
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase UN63_RS12655
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase UN63_RS10750 UN63_RS14495
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit UN63_RS08955
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase UN63_RS14495 UN63_RS01710
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase UN63_RS13340 UN63_RS08990
hglS D-2-hydroxyglutarate synthase UN63_RS02525
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase UN63_RS16265
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 UN63_RS11135
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase UN63_RS03445 UN63_RS03985
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase UN63_RS03445 UN63_RS05985
lysP L-lysine:H+ symporter LysP
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase UN63_RS16475

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