GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Pantoea rwandensis LMG 26275

Best path

lysP, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP HA51_RS22655 HA51_RS20955
cadA lysine decarboxylase HA51_RS00930 HA51_RS21250
patA cadaverine aminotransferase HA51_RS00935 HA51_RS17860
patD 5-aminopentanal dehydrogenase HA51_RS23800 HA51_RS23475
davT 5-aminovalerate aminotransferase HA51_RS23810 HA51_RS00875
davD glutarate semialdehyde dehydrogenase HA51_RS14080 HA51_RS24745
gcdG succinyl-CoA:glutarate CoA-transferase HA51_RS04960
gcdH glutaryl-CoA dehydrogenase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HA51_RS26560 HA51_RS11045
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HA51_RS26560 HA51_RS11045
atoB acetyl-CoA C-acetyltransferase HA51_RS19810 HA51_RS26555
Alternative steps:
alr lysine racemase HA51_RS16035
amaA L-pipecolate oxidase HA51_RS13830
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) HA51_RS24745 HA51_RS14080
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT HA51_RS11180 HA51_RS13765
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit HA51_RS19820
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit HA51_RS19815
davA 5-aminovaleramidase HA51_RS14945
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase HA51_RS14985 HA51_RS15440
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase HA51_RS09070
hisM L-lysine ABC transporter, permease component 1 (HisM) HA51_RS11190 HA51_RS25185
hisP L-lysine ABC transporter, ATPase component HisP HA51_RS11195 HA51_RS24875
hisQ L-lysine ABC transporter, permease component 2 (HisQ) HA51_RS11185 HA51_RS12100
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase HA51_RS09745
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 HA51_RS14135 HA51_RS00875
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL HA51_RS09025
lysN 2-aminoadipate transaminase HA51_RS09850 HA51_RS00170
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase HA51_RS19595

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