GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Nocardiopsis baichengensis YIM 90130

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP C892_RS0102390
davB L-lysine 2-monooxygenase C892_RS0120575
davA 5-aminovaleramidase C892_RS0120580 C892_RS0107510
davT 5-aminovalerate aminotransferase C892_RS0108560 C892_RS0121435
davD glutarate semialdehyde dehydrogenase C892_RS0121440 C892_RS0126085
gcdG succinyl-CoA:glutarate CoA-transferase C892_RS0114505 C892_RS0124750
gcdH glutaryl-CoA dehydrogenase C892_RS0114500 C892_RS0127300
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C892_RS0126825 C892_RS0118260
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C892_RS0118260 C892_RS0113150
atoB acetyl-CoA C-acetyltransferase C892_RS0103915 C892_RS0127360
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) C892_RS0100725 C892_RS0113930
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit C892_RS0127300 C892_RS0122585
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
dpkA 1-piperideine-2-carboxylate reductase C892_RS0101275 C892_RS0119415
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit C892_RS0126840
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit C892_RS0126835
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) C892_RS0107845 C892_RS0116860
hisP L-lysine ABC transporter, ATPase component HisP C892_RS0107840 C892_RS0116870
hisQ L-lysine ABC transporter, permease component 2 (HisQ) C892_RS0107845 C892_RS0116860
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 C892_RS0109425
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase C892_RS0108560 C892_RS0121435
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) C892_RS0108640
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase C892_RS0116290 C892_RS0101165
patA cadaverine aminotransferase C892_RS0108700 C892_RS0112085
patD 5-aminopentanal dehydrogenase C892_RS0103645 C892_RS0100475
Slc7a1 L-lysine transporter Slc7a1 C892_RS0120615
ydiJ (R)-2-hydroxyglutarate dehydrogenase

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