GapMind for catabolism of small carbon sources

 

Definition of L-isoleucine catabolism

As rules and steps, or see full text

Rules

Overview: Isoleucine degradation in GapMind is based on MetaCyc pathway L-isoleucine degradation I (link). The other pathways are fermentative and do not lead to carbon incorporation (link, link).

Steps

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

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

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

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

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

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

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

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

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

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

Bap2: L-isoleucine permease Bap2

brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB

bcaP: L-isoleucine uptake transporter BcaP/CitA

pccA: propionyl-CoA carboxylase, alpha subunit

pccB: propionyl-CoA carboxylase, beta subunit

pccA1: propionyl-CoA carboxylase, biotin carboxyl carrier subunit

pccA2: propionyl-CoA carboxylase, biotin carboxylase subunit

mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components

mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit

mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit

prpC: 2-methylcitrate synthase

prpD: 2-methylcitrate dehydratase

acn: (2R,3S)-2-methylcitrate dehydratase

prpB: 2-methylisocitrate lyase

acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)

prpF: methylaconitate isomerase

epi: methylmalonyl-CoA epimerase

pco: propanyl-CoA oxidase

hpcD: 3-hydroxypropionyl-CoA dehydratase

dddA: 3-hydroxypropionate dehydrogenase

iolA: malonate semialdehyde dehydrogenase (CoA-acylating)

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

acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase

ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase

ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

fadA: 2-methylacetoacetyl-CoA thiolase

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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