GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Halostagnicola larsenii XH-48

Best path

lysP, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase HALLA_RS05235
davT 5-aminovalerate aminotransferase HALLA_RS19230 HALLA_RS14145
davD glutarate semialdehyde dehydrogenase HALLA_RS14430 HALLA_RS18080
gcdG succinyl-CoA:glutarate CoA-transferase HALLA_RS19310 HALLA_RS14165
gcdH glutaryl-CoA dehydrogenase HALLA_RS17630 HALLA_RS18715
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HALLA_RS14450 HALLA_RS09800
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HALLA_RS04740 HALLA_RS09800
atoB acetyl-CoA C-acetyltransferase HALLA_RS05820 HALLA_RS14160
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase HALLA_RS11000
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) HALLA_RS11100 HALLA_RS16180
amaD D-lysine oxidase HALLA_RS17125
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit HALLA_RS03870 HALLA_RS05220
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase HALLA_RS15355 HALLA_RS19695
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
dpkA 1-piperideine-2-carboxylate reductase HALLA_RS16880 HALLA_RS13410
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit HALLA_RS11585 HALLA_RS09365
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit HALLA_RS09360
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 HALLA_RS13735 HALLA_RS16435
hisQ L-lysine ABC transporter, permease component 2 (HisQ) HALLA_RS15170
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 HALLA_RS14145 HALLA_RS19230
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase HALLA_RS04085 HALLA_RS07440
patA cadaverine aminotransferase HALLA_RS19230 HALLA_RS00755
patD 5-aminopentanal dehydrogenase HALLA_RS18050 HALLA_RS14430
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase HALLA_RS15890

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