argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
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.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| argT | L-lysine ABC transporter, substrate-binding component ArgT | CV091_RS09955 | CV091_RS05365 |
| hisM | L-lysine ABC transporter, permease component 1 (HisM) | CV091_RS09965 | CV091_RS05375 |
| hisQ | L-lysine ABC transporter, permease component 2 (HisQ) | CV091_RS09960 | CV091_RS00365 |
| hisP | L-lysine ABC transporter, ATPase component HisP | CV091_RS05360 | CV091_RS19380 |
| cadA | lysine decarboxylase | CV091_RS15520 | |
| patA | cadaverine aminotransferase | CV091_RS06535 | CV091_RS07085 |
| patD | 5-aminopentanal dehydrogenase | CV091_RS14855 | CV091_RS05715 |
| davT | 5-aminovalerate aminotransferase | CV091_RS09670 | CV091_RS06535 |
| davD | glutarate semialdehyde dehydrogenase | CV091_RS15630 | CV091_RS09535 |
| gcdG | succinyl-CoA:glutarate CoA-transferase | CV091_RS05080 | CV091_RS11120 |
| gcdH | glutaryl-CoA dehydrogenase | CV091_RS03175 | CV091_RS01060 |
| ech | (S)-3-hydroxybutanoyl-CoA hydro-lyase | CV091_RS16630 | CV091_RS05225 |
| fadB | (S)-3-hydroxybutanoyl-CoA dehydrogenase | CV091_RS05225 | CV091_RS16190 |
| atoB | acetyl-CoA C-acetyltransferase | CV091_RS08390 | CV091_RS12260 |
| Alternative steps: | |||
| alr | lysine racemase | ||
| amaA | L-pipecolate oxidase | CV091_RS00330 | CV091_RS13510 |
| amaB | L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | CV091_RS10640 | CV091_RS05715 |
| amaD | D-lysine oxidase | CV091_RS12940 | |
| bcd | butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit | CV091_RS01060 | CV091_RS03710 |
| bgtB | L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | ||
| ctfA | butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit | CV091_RS14305 | |
| ctfB | butanoyl-CoA:acetoacetate CoA-transferase, beta subunit | CV091_RS14310 | |
| davA | 5-aminovaleramidase | CV091_RS18025 | |
| davB | L-lysine 2-monooxygenase | ||
| dpkA | 1-piperideine-2-carboxylate reductase | CV091_RS10615 | CV091_RS07015 |
| etfA | butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit | CV091_RS16180 | |
| etfB | butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit | ||
| glaH | glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | ||
| hglS | D-2-hydroxyglutarate synthase | CV091_RS11225 | |
| 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 | CV091_RS13820 | CV091_RS11130 |
| kdd | 3,5-diaminohexanoate dehydrogenase | ||
| lat | L-lysine 6-aminotransferase | CV091_RS15910 | CV091_RS09670 |
| 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 | CV091_RS05515 | CV091_RS16395 |
| lysP | L-lysine:H+ symporter LysP | ||
| Slc7a1 | L-lysine transporter Slc7a1 | ||
| ydiJ | (R)-2-hydroxyglutarate dehydrogenase | CV091_RS14235 | |
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.
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:
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