GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Mesorhizobium ciceri WSM1271

Best path

argT, hisM, hisQ, hisP, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argT L-lysine ABC transporter, substrate-binding component ArgT Mesci_3923 Mesci_0696
hisM L-lysine ABC transporter, permease component 1 (HisM) Mesci_3925 Mesci_2592
hisQ L-lysine ABC transporter, permease component 2 (HisQ) Mesci_3924 Mesci_2593
hisP L-lysine ABC transporter, ATPase component HisP Mesci_2595 Mesci_0317
cadA lysine decarboxylase Mesci_1913 Mesci_4422
patA cadaverine aminotransferase Mesci_5987 Mesci_3346
patD 5-aminopentanal dehydrogenase Mesci_0148 Mesci_2633
davT 5-aminovalerate aminotransferase Mesci_0044 Mesci_5987
davD glutarate semialdehyde dehydrogenase Mesci_3425 Mesci_5665
gcdG succinyl-CoA:glutarate CoA-transferase Mesci_3113 Mesci_0263
gcdH glutaryl-CoA dehydrogenase Mesci_1983 Mesci_4845
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Mesci_6037 Mesci_4665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Mesci_1071 Mesci_6001
atoB acetyl-CoA C-acetyltransferase Mesci_1329 Mesci_1095
Alternative steps:
alr lysine racemase Mesci_5949
amaA L-pipecolate oxidase Mesci_5236 Mesci_5113
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Mesci_1990 Mesci_0274
amaD D-lysine oxidase Mesci_4581
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Mesci_4845 Mesci_3403
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
davA 5-aminovaleramidase Mesci_1603
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase Mesci_6229 Mesci_1736
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Mesci_5837 Mesci_1575
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Mesci_5836 Mesci_1576
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 Mesci_2845
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 Mesci_0422 Mesci_4327
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase Mesci_0044 Mesci_5288
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Mesci_2427
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase Mesci_0885
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase Mesci_6223 Mesci_2249
lysP L-lysine:H+ symporter LysP
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Mesci_5065 Mesci_2577

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