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 (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