GapMind for catabolism of small carbon sources


L-lysine catabolism in Chromobacterium vaccinii MWU205

Best path

lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB


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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP VL52_RS10410 VL52_RS13800
cadA lysine decarboxylase VL52_RS08800 VL52_RS21315
patA cadaverine aminotransferase VL52_RS18210 VL52_RS15525
patD 5-aminopentanal dehydrogenase VL52_RS20940 VL52_RS21455
davT 5-aminovalerate aminotransferase VL52_RS20935 VL52_RS15525
davD glutarate semialdehyde dehydrogenase VL52_RS20940 VL52_RS07105
gcdG succinyl-CoA:glutarate CoA-transferase VL52_RS20890
gcdH glutaryl-CoA dehydrogenase VL52_RS20895 VL52_RS19965
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase VL52_RS18865 VL52_RS21030
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase VL52_RS10360 VL52_RS21015
atoB acetyl-CoA C-acetyltransferase VL52_RS14225 VL52_RS21005
Alternative steps:
alr lysine racemase VL52_RS02040 VL52_RS04340
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) VL52_RS20940 VL52_RS11940
amaD D-lysine oxidase VL52_RS09530
argT L-lysine ABC transporter, substrate-binding component ArgT VL52_RS06115 VL52_RS17825
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit VL52_RS21025 VL52_RS19965
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
davA 5-aminovaleramidase VL52_RS11175 VL52_RS13590
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase VL52_RS10855
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit VL52_RS02625
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit VL52_RS02630
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) VL52_RS06125 VL52_RS17815
hisP L-lysine ABC transporter, ATPase component HisP VL52_RS06130 VL52_RS19750
hisQ L-lysine ABC transporter, permease component 2 (HisQ) VL52_RS06120 VL52_RS17820
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 VL52_RS20935 VL52_RS22675
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) VL52_RS05540
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL VL52_RS02445
lysN 2-aminoadipate transaminase VL52_RS20935 VL52_RS15525
Slc7a1 L-lysine transporter Slc7a1 VL52_RS03530
ydiJ (R)-2-hydroxyglutarate dehydrogenase VL52_RS22685 VL52_RS20375

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