GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Streptacidiphilus oryzae TH49

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP BS73_RS16535 BS73_RS10785
cadA lysine decarboxylase BS73_RS13335 BS73_RS03380
patA cadaverine aminotransferase BS73_RS23310 BS73_RS08925
patD 5-aminopentanal dehydrogenase BS73_RS14255 BS73_RS14245
davT 5-aminovalerate aminotransferase BS73_RS14180 BS73_RS19430
davD glutarate semialdehyde dehydrogenase BS73_RS19435 BS73_RS01225
gcdG succinyl-CoA:glutarate CoA-transferase BS73_RS32920 BS73_RS15390
gcdH glutaryl-CoA dehydrogenase BS73_RS32915 BS73_RS25270
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BS73_RS14910 BS73_RS05650
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BS73_RS08975 BS73_RS07230
atoB acetyl-CoA C-acetyltransferase BS73_RS10365 BS73_RS08675
Alternative steps:
alr lysine racemase BS73_RS22945
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BS73_RS14245 BS73_RS09095
amaD D-lysine oxidase BS73_RS28575
argT L-lysine ABC transporter, substrate-binding component ArgT BS73_RS15730 BS73_RS01475
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BS73_RS23895 BS73_RS25270
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit BS73_RS10025
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit BS73_RS10020
davA 5-aminovaleramidase BS73_RS19230 BS73_RS27285
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase BS73_RS02125 BS73_RS01855
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BS73_RS09575
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit BS73_RS09580
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) BS73_RS15735 BS73_RS01490
hisP L-lysine ABC transporter, ATPase component HisP BS73_RS15740 BS73_RS01465
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BS73_RS15735 BS73_RS01470
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 BS73_RS10685
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase BS73_RS14180 BS73_RS19430
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BS73_RS18665
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL BS73_RS07700
lysN 2-aminoadipate transaminase BS73_RS22570 BS73_RS19430
Slc7a1 L-lysine transporter Slc7a1 BS73_RS12665 BS73_RS16585
ydiJ (R)-2-hydroxyglutarate dehydrogenase BS73_RS19425 BS73_RS04750

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