GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Acidovorax sp. GW101-3H11

Best path

lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB

Also see fitness data for the top candidates

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysP L-lysine:H+ symporter LysP
cadA lysine decarboxylase Ac3H11_2914 Ac3H11_519
patA cadaverine aminotransferase Ac3H11_1332 Ac3H11_4179
patD 5-aminopentanal dehydrogenase Ac3H11_1496 Ac3H11_1480
davT 5-aminovalerate aminotransferase Ac3H11_4179 Ac3H11_1332
davD glutarate semialdehyde dehydrogenase Ac3H11_1480 Ac3H11_4184
gcdG succinyl-CoA:glutarate CoA-transferase Ac3H11_3532 Ac3H11_198
gcdH glutaryl-CoA dehydrogenase Ac3H11_3533 Ac3H11_2991
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ac3H11_4006 Ac3H11_2775
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ac3H11_1914 Ac3H11_4658
atoB acetyl-CoA C-acetyltransferase Ac3H11_178 Ac3H11_2303
Alternative steps:
alr lysine racemase
amaA L-pipecolate oxidase
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) Ac3H11_1605 Ac3H11_612
amaD D-lysine oxidase
argT L-lysine ABC transporter, substrate-binding component ArgT Ac3H11_2555 Ac3H11_3325
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit Ac3H11_2996 Ac3H11_2359
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit Ac3H11_132 Ac3H11_3922
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit Ac3H11_131 Ac3H11_3921
davA 5-aminovaleramidase Ac3H11_517 Ac3H11_1207
davB L-lysine 2-monooxygenase
dpkA 1-piperideine-2-carboxylate reductase Ac3H11_1121 Ac3H11_4531
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit Ac3H11_3189 Ac3H11_2705
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit Ac3H11_2706 Ac3H11_3190
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) Ac3H11_2554 Ac3H11_4900
hisP L-lysine ABC transporter, ATPase component HisP Ac3H11_1958 Ac3H11_3200
hisQ L-lysine ABC transporter, permease component 2 (HisQ) Ac3H11_3326 Ac3H11_2554
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 Ac3H11_1929
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase Ac3H11_4179
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Ac3H11_4104
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase Ac3H11_2284
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase Ac3H11_1602 Ac3H11_4179
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase Ac3H11_2934

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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