GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Phaeobacter inhibens BS107

Best path

argT, hisM, hisQ, hisP, davB, davA, 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
argT L-lysine ABC transporter, substrate-binding component ArgT PGA1_262p02360 PGA1_c11570
hisM L-lysine ABC transporter, permease component 1 (HisM) PGA1_c11550 PGA1_262p02380
hisQ L-lysine ABC transporter, permease component 2 (HisQ) PGA1_262p02370 PGA1_c26600
hisP L-lysine ABC transporter, ATPase component HisP PGA1_c02010 PGA1_262p02350
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase PGA1_c26450 PGA1_c34700
davT 5-aminovalerate aminotransferase PGA1_c24230 PGA1_c28750
davD glutarate semialdehyde dehydrogenase PGA1_c29650 PGA1_c23170
gcdG succinyl-CoA:glutarate CoA-transferase PGA1_c27870 PGA1_c12340
gcdH glutaryl-CoA dehydrogenase PGA1_c15710 PGA1_c10280
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PGA1_c36500 PGA1_262p01980
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
Alternative steps:
alr lysine racemase PGA1_c17610 PGA1_c17050
amaA L-pipecolate oxidase PGA1_262p02210 PGA1_c11510
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) PGA1_c21670 PGA1_c05130
amaD D-lysine oxidase
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit PGA1_c10280 PGA1_c17340
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
cadA lysine decarboxylase PGA1_c19080 PGA1_c03800
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit PGA1_c06210
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit PGA1_c06200
dpkA 1-piperideine-2-carboxylate reductase PGA1_c31650
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit PGA1_c01240
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit PGA1_c01250
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
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 PGA1_c02540 PGA1_c08400
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase PGA1_c28770 PGA1_c24230
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 PGA1_c21250 PGA1_c24230
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase PGA1_c24230 PGA1_c28750
patD 5-aminopentanal dehydrogenase PGA1_c21670 PGA1_c29650
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase PGA1_c06340

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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