GapMind for catabolism of small carbon sources


L-lysine catabolism in Ruegeria conchae TW15

Best path

bgtB, hisP, lysDH, amaB, lysN, hglS, ydiJ


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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) G7G_RS0111055 G7G_RS0111530
hisP L-lysine ABC transporter, ATPase component HisP G7G_RS0105150 G7G_RS0100240
lysDH L-lysine 6-dehydrogenase G7G_RS0104205
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) G7G_RS0104210 G7G_RS0103600
lysN 2-aminoadipate transaminase G7G_RS0104975 G7G_RS0101615
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase G7G_RS0112035 G7G_RS0120340
Alternative steps:
alr lysine racemase G7G_RS0115185 G7G_RS0108365
amaA L-pipecolate oxidase G7G_RS0110025 G7G_RS0105110
amaD D-lysine oxidase G7G_RS0111605
argT L-lysine ABC transporter, substrate-binding component ArgT G7G_RS0105145 G7G_RS0111525
atoB acetyl-CoA C-acetyltransferase G7G_RS0122070 G7G_RS0116445
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit G7G_RS0117695 G7G_RS0106645
cadA lysine decarboxylase G7G_RS0113840
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit G7G_RS0111965
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit G7G_RS0111960
davA 5-aminovaleramidase G7G_RS0116370
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase G7G_RS0118970 G7G_RS0122450
davT 5-aminovalerate aminotransferase G7G_RS0121165 G7G_RS0112215
dpkA 1-piperideine-2-carboxylate reductase G7G_RS0111560 G7G_RS0110095
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase G7G_RS0116465 G7G_RS0104515
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit G7G_RS0101920
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit G7G_RS0101925
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase G7G_RS0102205 G7G_RS0108810
gcdG succinyl-CoA:glutarate CoA-transferase G7G_RS0104670 G7G_RS0122435
gcdH glutaryl-CoA dehydrogenase G7G_RS0107335 G7G_RS0117695
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hisM L-lysine ABC transporter, permease component 1 (HisM) G7G_RS0105135 G7G_RS0111055
hisQ L-lysine ABC transporter, permease component 2 (HisQ) G7G_RS0111055 G7G_RS0111530
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 G7G_RS0108590
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase G7G_RS0121165 G7G_RS0112215
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysL L-lysine transporter LysL
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase G7G_RS0112215 G7G_RS0106455
patD 5-aminopentanal dehydrogenase G7G_RS0103600 G7G_RS0121155
Slc7a1 L-lysine transporter Slc7a1 G7G_RS0104810

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