GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Brucella inopinata BO1

Best path

argT, hisM, hisQ, hisP, lysDH, amaB, lysN, hglS, ydiJ

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
argT L-lysine ABC transporter, substrate-binding component ArgT BIBO1_RS07950 BIBO1_RS09035
hisM L-lysine ABC transporter, permease component 1 (HisM) BIBO1_RS07940 BIBO1_RS17105
hisQ L-lysine ABC transporter, permease component 2 (HisQ) BIBO1_RS07945 BIBO1_RS19985
hisP L-lysine ABC transporter, ATPase component HisP BIBO1_RS20000 BIBO1_RS07180
lysDH L-lysine 6-dehydrogenase BIBO1_RS16845
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BIBO1_RS18765 BIBO1_RS10860
lysN 2-aminoadipate transaminase BIBO1_RS11000 BIBO1_RS09965
hglS D-2-hydroxyglutarate synthase BIBO1_RS18760
ydiJ (R)-2-hydroxyglutarate dehydrogenase BIBO1_RS13480 BIBO1_RS15670
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase BIBO1_RS18745
amaD D-lysine oxidase BIBO1_RS16860 BIBO1_RS12260
atoB acetyl-CoA C-acetyltransferase BIBO1_RS17190 BIBO1_RS16830
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit BIBO1_RS17185 BIBO1_RS06840
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase BIBO1_RS13655 BIBO1_RS15590
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit BIBO1_RS16820
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit BIBO1_RS16825
davA 5-aminovaleramidase BIBO1_RS12585
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase BIBO1_RS11605 BIBO1_RS17145
davT 5-aminovalerate aminotransferase BIBO1_RS13055 BIBO1_RS18510
dpkA 1-piperideine-2-carboxylate reductase BIBO1_RS15945 BIBO1_RS18330
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BIBO1_RS06755 BIBO1_RS15870
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit BIBO1_RS05850
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BIBO1_RS18180 BIBO1_RS05845
gcdG succinyl-CoA:glutarate CoA-transferase BIBO1_RS15880 BIBO1_RS08425
gcdH glutaryl-CoA dehydrogenase BIBO1_RS08430 BIBO1_RS17185
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
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
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase BIBO1_RS13055 BIBO1_RS10785
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BIBO1_RS19215
LHT L-lysine transporter
lysL L-lysine transporter LysL
lysP L-lysine:H+ symporter LysP BIBO1_RS14845
patA cadaverine aminotransferase BIBO1_RS18510 BIBO1_RS13055
patD 5-aminopentanal dehydrogenase BIBO1_RS20005 BIBO1_RS14100
Slc7a1 L-lysine transporter Slc7a1

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