GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Sphingobium czechense LL01

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
cadA lysine decarboxylase V473_RS17630 V473_RS02020
patA cadaverine aminotransferase V473_RS02290 V473_RS20290
patD 5-aminopentanal dehydrogenase V473_RS05540 V473_RS05490
davT 5-aminovalerate aminotransferase V473_RS02290 V473_RS18720
davD glutarate semialdehyde dehydrogenase V473_RS08475 V473_RS20300
gcdG succinyl-CoA:glutarate CoA-transferase V473_RS05465 V473_RS08220
gcdH glutaryl-CoA dehydrogenase V473_RS17395 V473_RS17555
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase V473_RS04380 V473_RS05770
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase V473_RS00615 V473_RS18225
atoB acetyl-CoA C-acetyltransferase V473_RS07145 V473_RS00635
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) V473_RS05540 V473_RS08475
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit V473_RS04405 V473_RS17395
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit V473_RS02865 V473_RS08605
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit V473_RS00560 V473_RS08315
davA 5-aminovaleramidase V473_RS09535 V473_RS11880
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase V473_RS03950
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit V473_RS11155
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit V473_RS11160
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 V473_RS03740 V473_RS04645
hisQ L-lysine ABC transporter, permease component 2 (HisQ)
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 V473_RS20665 V473_RS17055
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase V473_RS02290 V473_RS00850
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 V473_RS02585 V473_RS18720
Slc7a1 L-lysine transporter Slc7a1 V473_RS03185
ydiJ (R)-2-hydroxyglutarate dehydrogenase V473_RS06300 V473_RS08145

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