GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Verminephrobacter eiseniae EF01-2

Best path

argT, hisM, hisQ, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT VEIS_RS09425 VEIS_RS01670
hisM L-lysine ABC transporter, permease component 1 (HisM) VEIS_RS09420 VEIS_RS01680
hisQ L-lysine ABC transporter, permease component 2 (HisQ) VEIS_RS09415 VEIS_RS01675
hisP L-lysine ABC transporter, ATPase component HisP VEIS_RS01685 VEIS_RS16195
cadA lysine decarboxylase VEIS_RS16955 VEIS_RS08470
patA cadaverine aminotransferase VEIS_RS09290 VEIS_RS08300
patD 5-aminopentanal dehydrogenase VEIS_RS16060 VEIS_RS10210
davT 5-aminovalerate aminotransferase VEIS_RS09290 VEIS_RS15235
davD glutarate semialdehyde dehydrogenase VEIS_RS19570 VEIS_RS10490
gcdG succinyl-CoA:glutarate CoA-transferase VEIS_RS08450 VEIS_RS10765
gcdH glutaryl-CoA dehydrogenase VEIS_RS08445 VEIS_RS06515
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase VEIS_RS02240 VEIS_RS18720
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase VEIS_RS24060 VEIS_RS08750
atoB acetyl-CoA C-acetyltransferase VEIS_RS18480 VEIS_RS06505
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase VEIS_RS21610 VEIS_RS00915
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) VEIS_RS03845 VEIS_RS17310
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit VEIS_RS04310 VEIS_RS17155
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit VEIS_RS12710 VEIS_RS19500
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit VEIS_RS12705 VEIS_RS19495
davA 5-aminovaleramidase VEIS_RS13835 VEIS_RS23785
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase VEIS_RS04355 VEIS_RS20325
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit VEIS_RS10230 VEIS_RS22715
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
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 VEIS_RS09255 VEIS_RS19215
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase VEIS_RS15550 VEIS_RS04035
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase VEIS_RS01340
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase VEIS_RS14130 VEIS_RS01810
lysP L-lysine:H+ symporter LysP VEIS_RS13795
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase VEIS_RS18330 VEIS_RS22710

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