GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Rhodobacter maris JA276

Best path

argT, hisM, hisQ, hisP, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT CRO22_RS13230 CRO22_RS16325
hisM L-lysine ABC transporter, permease component 1 (HisM) CRO22_RS13220 CRO22_RS16315
hisQ L-lysine ABC transporter, permease component 2 (HisQ) CRO22_RS13225 CRO22_RS06045
hisP L-lysine ABC transporter, ATPase component HisP CRO22_RS16330 CRO22_RS03080
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase CRO22_RS04160 CRO22_RS06295
davT 5-aminovalerate aminotransferase CRO22_RS14915 CRO22_RS01970
davD glutarate semialdehyde dehydrogenase CRO22_RS15345 CRO22_RS11970
gcdG succinyl-CoA:glutarate CoA-transferase CRO22_RS07065 CRO22_RS07020
gcdH glutaryl-CoA dehydrogenase CRO22_RS09210 CRO22_RS11805
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CRO22_RS09335 CRO22_RS06210
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CRO22_RS06210 CRO22_RS03430
atoB acetyl-CoA C-acetyltransferase CRO22_RS02395 CRO22_RS07180
Alternative steps:
alr lysine racemase CRO22_RS01510
amaA L-pipecolate oxidase CRO22_RS13255 CRO22_RS16290
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) CRO22_RS13265 CRO22_RS15345
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit CRO22_RS11805 CRO22_RS10865
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase CRO22_RS05210
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit CRO22_RS06345
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit CRO22_RS06340
dpkA 1-piperideine-2-carboxylate reductase CRO22_RS13175
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit CRO22_RS03420
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase CRO22_RS02945
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 CRO22_RS14915 CRO22_RS01710
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 CRO22_RS13270 CRO22_RS06675
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase CRO22_RS01970 CRO22_RS14915
patD 5-aminopentanal dehydrogenase CRO22_RS11970 CRO22_RS10475
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase CRO22_RS11570 CRO22_RS06380

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