GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Geobacter daltonii FRC-32

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase GEOB_RS05490 GEOB_RS11655
davT 5-aminovalerate aminotransferase GEOB_RS05585 GEOB_RS14935
davD glutarate semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
gcdG succinyl-CoA:glutarate CoA-transferase GEOB_RS12030
gcdH glutaryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS01170
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase GEOB_RS00800 GEOB_RS01210
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase GEOB_RS00795 GEOB_RS00835
atoB acetyl-CoA C-acetyltransferase GEOB_RS01200 GEOB_RS00490
Alternative steps:
alr lysine racemase GEOB_RS07065 GEOB_RS18150
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) GEOB_RS17645
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit GEOB_RS10880 GEOB_RS10905
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
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit GEOB_RS01240 GEOB_RS08990
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit GEOB_RS08985 GEOB_RS01235
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM)
hisP L-lysine ABC transporter, ATPase component HisP GEOB_RS11710 GEOB_RS02825
hisQ L-lysine ABC transporter, permease component 2 (HisQ)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase GEOB_RS13790
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 GEOB_RS14935 GEOB_RS05585
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase GEOB_RS05585 GEOB_RS02285
patA cadaverine aminotransferase GEOB_RS05585
patD 5-aminopentanal dehydrogenase GEOB_RS17645
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase GEOB_RS04305 GEOB_RS04150

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