GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Synechococcus elongatus PCC 7942

Best path

natA, natB, natC, natD, natE, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB

Also see fitness data for the top candidates

Rules

Overview: Leucine degradation in GapMind is based on MetaCyc pathway L-leucine degradation I, via branched alpha-keto acid dehydrogenase (link). Other pathways for are not included here because they are not linked to sequence (link) or do not result in carbon incorporation.

39 steps (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-leucine ABC transporter, ATPase component 1 (NatA) Synpcc7942_1893 Synpcc7942_2493
natB L-leucine ABC transporter, substrate-binding component NatB Synpcc7942_1861
natC L-leucine ABC transporter, permease component 1 (NatC) Synpcc7942_1894
natD L-leucine ABC transporter, permease component 2 (NatD) Synpcc7942_2177 Synpcc7942_2495
natE L-leucine ABC transporter, ATPase component 2 (NatE) Synpcc7942_0815 Synpcc7942_2492
ilvE L-leucine transaminase Synpcc7942_1029 Synpcc7942_1335
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Synpcc7942_1379
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase Synpcc7942_0597
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase
atoB acetyl-CoA C-acetyltransferase
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Synpcc7942_0246
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Synpcc7942_0248
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Synpcc7942_0249 Synpcc7942_1680
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Synpcc7942_0247
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Synpcc7942_1944
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Synpcc7942_0143
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) Synpcc7942_2492 Synpcc7942_0815
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Synpcc7942_2493 Synpcc7942_1893
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) Synpcc7942_2495 Synpcc7942_2177
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) Synpcc7942_2494
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Synpcc7942_1198 Synpcc7942_0842
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC

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, 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