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 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