GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Moritella dasanensis ArB 0140

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT A923_RS0116620 A923_RS0121525
hisM L-lysine ABC transporter, permease component 1 (HisM) A923_RS0121515 A923_RS0116630
hisQ L-lysine ABC transporter, permease component 2 (HisQ) A923_RS0121520 A923_RS0116625
hisP L-lysine ABC transporter, ATPase component HisP A923_RS0121530 A923_RS0106855
lysDH L-lysine 6-dehydrogenase A923_RS0109690
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) A923_RS0109685 A923_RS0105090
lysN 2-aminoadipate transaminase A923_RS0114085 A923_RS0118545
hglS D-2-hydroxyglutarate synthase
ydiJ (R)-2-hydroxyglutarate dehydrogenase A923_RS0104040
Alternative steps:
alr lysine racemase A923_RS0120550 A923_RS0116710
amaA L-pipecolate oxidase
amaD D-lysine oxidase
atoB acetyl-CoA C-acetyltransferase A923_RS0119275 A923_RS0119825
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit A923_RS0101015
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) A923_RS0109790
cadA lysine decarboxylase A923_RS0119105 A923_RS22190
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
davA 5-aminovaleramidase
davB L-lysine 2-monooxygenase
davD glutarate semialdehyde dehydrogenase A923_RS0105090 A923_RS0108515
davT 5-aminovalerate aminotransferase A923_RS0118545 A923_RS0109340
dpkA 1-piperideine-2-carboxylate reductase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A923_RS0104120 A923_RS0110330
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit A923_RS0100950
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A923_RS0119830 A923_RS0104120
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase A923_RS0101015
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase A923_RS0111475
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 A923_RS0109340
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) A923_RS0105505
LHT L-lysine transporter
lysL L-lysine transporter LysL A923_RS0112915
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase A923_RS0118545 A923_RS0109340
patD 5-aminopentanal dehydrogenase A923_RS0108515 A923_RS0109940
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