GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Xanthobacter autotrophicus Py2

Best path

bgtB, hisP, 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 (30 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)
hisP L-lysine ABC transporter, ATPase component HisP XAUT_RS08010 XAUT_RS23035
cadA lysine decarboxylase XAUT_RS21175 XAUT_RS10760
patA cadaverine aminotransferase XAUT_RS06110 XAUT_RS21405
patD 5-aminopentanal dehydrogenase XAUT_RS16460 XAUT_RS01855
davT 5-aminovalerate aminotransferase XAUT_RS21405 XAUT_RS06110
davD glutarate semialdehyde dehydrogenase XAUT_RS16460 XAUT_RS13655
gcdG succinyl-CoA:glutarate CoA-transferase XAUT_RS23885 XAUT_RS06250
gcdH glutaryl-CoA dehydrogenase XAUT_RS23880 XAUT_RS21625
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase XAUT_RS16635 XAUT_RS04570
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase XAUT_RS04535 XAUT_RS04610
atoB acetyl-CoA C-acetyltransferase XAUT_RS23630 XAUT_RS15615
Alternative steps:
alr lysine racemase XAUT_RS24100
amaA L-pipecolate oxidase XAUT_RS12125 XAUT_RS09765
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) XAUT_RS17675 XAUT_RS16460
amaD D-lysine oxidase XAUT_RS11170
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit XAUT_RS04580 XAUT_RS23635
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit XAUT_RS11815 XAUT_RS05620
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit XAUT_RS11820 XAUT_RS05615
davA 5-aminovaleramidase XAUT_RS15515
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase XAUT_RS17685
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit XAUT_RS00705 XAUT_RS10855
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit XAUT_RS00710 XAUT_RS10860
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) XAUT_RS00875 XAUT_RS10440
hisQ L-lysine ABC transporter, permease component 2 (HisQ) XAUT_RS08015 XAUT_RS10440
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase XAUT_RS19775
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 XAUT_RS24025 XAUT_RS02155
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase XAUT_RS05230 XAUT_RS21405
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) XAUT_RS14090
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase XAUT_RS13770 XAUT_RS21405
lysP L-lysine:H+ symporter LysP
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase XAUT_RS08085 XAUT_RS12675

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 Apr 09 2024. 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