GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Sphingomonas histidinilytica UM2

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP B5X82_RS24315
cadA lysine decarboxylase B5X82_RS12155
patA cadaverine aminotransferase B5X82_RS16580 B5X82_RS09405
patD 5-aminopentanal dehydrogenase B5X82_RS22090 B5X82_RS22235
davT 5-aminovalerate aminotransferase B5X82_RS11660 B5X82_RS09405
davD glutarate semialdehyde dehydrogenase B5X82_RS11705 B5X82_RS22235
gcdG succinyl-CoA:glutarate CoA-transferase B5X82_RS20105 B5X82_RS09500
gcdH glutaryl-CoA dehydrogenase B5X82_RS04280 B5X82_RS20685
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B5X82_RS19780 B5X82_RS16280
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B5X82_RS15560 B5X82_RS24290
atoB acetyl-CoA C-acetyltransferase B5X82_RS18105 B5X82_RS24295
Alternative steps:
alr lysine racemase B5X82_RS01530
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) B5X82_RS15880 B5X82_RS11705
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit B5X82_RS24130 B5X82_RS20685
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit B5X82_RS06855 B5X82_RS11675
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit B5X82_RS06850 B5X82_RS24530
davA 5-aminovaleramidase B5X82_RS17730
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase B5X82_RS18785 B5X82_RS06555
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit B5X82_RS12175
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit B5X82_RS12170
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) B5X82_RS14910 B5X82_RS14915
hisP L-lysine ABC transporter, ATPase component HisP B5X82_RS14905 B5X82_RS22845
hisQ L-lysine ABC transporter, permease component 2 (HisQ) B5X82_RS14910
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 B5X82_RS07075 B5X82_RS18255
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase B5X82_RS11660 B5X82_RS16580
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) B5X82_RS10020
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase B5X82_RS04015 B5X82_RS11660
Slc7a1 L-lysine transporter Slc7a1 B5X82_RS10835
ydiJ (R)-2-hydroxyglutarate dehydrogenase B5X82_RS16575 B5X82_RS02190

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.

Links

Downloads

Related tools

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