GapMind for catabolism of small carbon sources

 

L-lysine catabolism in Cereibacter sphaeroides ATCC 17029

Best path

bgtB, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
hisP L-lysine ABC transporter, ATPase component HisP RSPH17029_RS10165 RSPH17029_RS02015
davB L-lysine 2-monooxygenase
davA 5-aminovaleramidase RSPH17029_RS11495 RSPH17029_RS17110
davT 5-aminovalerate aminotransferase RSPH17029_RS04315 RSPH17029_RS17535
davD glutarate semialdehyde dehydrogenase RSPH17029_RS13480 RSPH17029_RS04350
gcdG succinyl-CoA:glutarate CoA-transferase RSPH17029_RS00595
gcdH glutaryl-CoA dehydrogenase RSPH17029_RS14905 RSPH17029_RS05935
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RSPH17029_RS00050 RSPH17029_RS17990
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RSPH17029_RS16015 RSPH17029_RS04435
atoB acetyl-CoA C-acetyltransferase RSPH17029_RS12120 RSPH17029_RS19805
Alternative steps:
alr lysine racemase RSPH17029_RS08060
amaA L-pipecolate oxidase RSPH17029_RS11565 RSPH17029_RS10235
amaB L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) RSPH17029_RS14890 RSPH17029_RS04350
amaD D-lysine oxidase RSPH17029_RS05050
argT L-lysine ABC transporter, substrate-binding component ArgT RSPH17029_RS10170 RSPH17029_RS17495
bcd butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit RSPH17029_RS19795 RSPH17029_RS05935
cadA lysine decarboxylase RSPH17029_RS06845
ctfA butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit RSPH17029_RS02855
ctfB butanoyl-CoA:acetoacetate CoA-transferase, beta subunit RSPH17029_RS02850
dpkA 1-piperideine-2-carboxylate reductase RSPH17029_RS12675
etfA butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit RSPH17029_RS01640
etfB butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit RSPH17029_RS01645
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hglS D-2-hydroxyglutarate synthase
hisM L-lysine ABC transporter, permease component 1 (HisM) RSPH17029_RS10180 RSPH17029_RS17505
hisQ L-lysine ABC transporter, permease component 2 (HisQ) RSPH17029_RS17505 RSPH17029_RS15650
kal 3-aminobutyryl-CoA deaminase
kamA L-lysine 2,3-aminomutase RSPH17029_RS20025
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 RSPH17029_RS18915
kdd 3,5-diaminohexanoate dehydrogenase
lat L-lysine 6-aminotransferase RSPH17029_RS04315 RSPH17029_RS20165
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RSPH17029_RS10685
LHT L-lysine transporter
lysDH L-lysine 6-dehydrogenase
lysL L-lysine transporter LysL
lysN 2-aminoadipate transaminase RSPH17029_RS15545 RSPH17029_RS12225
lysP L-lysine:H+ symporter LysP
patA cadaverine aminotransferase RSPH17029_RS03665 RSPH17029_RS04315
patD 5-aminopentanal dehydrogenase RSPH17029_RS04350 RSPH17029_RS16005
Slc7a1 L-lysine transporter Slc7a1
ydiJ (R)-2-hydroxyglutarate dehydrogenase RSPH17029_RS02455 RSPH17029_RS18355

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 Apr 10 2024. 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