GapMind for catabolism of small carbon sources

 

Definition of L-leucine catabolism

As rules and steps, or see full text

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.

Steps

livF: L-leucine ABC transporter, ATPase component 1 (LivF/BraG)

livG: L-leucine ABC transporter, ATPase component 2 (LivG/BraF)

livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)

livH: L-leucine ABC transporter, permease component 1 (LivH/BraD)

livM: L-leucine ABC transporter, permease component 2 (LivM/BraE)

natA: L-leucine ABC transporter, ATPase component 1 (NatA)

natB: L-leucine ABC transporter, substrate-binding component NatB

natC: L-leucine ABC transporter, permease component 1 (NatC)

natD: L-leucine ABC transporter, permease component 2 (NatD)

natE: L-leucine ABC transporter, ATPase component 2 (NatE)

aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ

aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)

aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)

aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP

leuT: L-leucine:Na+ symporter LeuT

brnQ: L-leucine:Na+ symporter BrnQ/BraB

bcaP: L-leucine uptake transporter BcaP

Bap2: L-leucine permease Bap2

AAP1: L-leucine permease AAP1

ilvE: L-leucine transaminase

bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit

bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit

bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component

lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component

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

ofoA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA

ofoB: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB

ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused

liuA: isovaleryl-CoA dehydrogenase

liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit

liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit

liuC: 3-methylglutaconyl-CoA hydratase

liuE: hydroxymethylglutaryl-CoA lyase

atoA: acetoacetyl-CoA transferase, A subunit

atoD: acetoacetyl-CoA transferase, B subunit

aacS: acetoacetyl-CoA synthetase

atoB: acetyl-CoA C-acetyltransferase

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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