livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
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).
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| livF | L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) | WP_011885758.1 | WP_011881646.1 |
| livG | L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) | WP_011885759.1 | WP_011881645.1 |
| livJ | L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | WP_043292326.1 | WP_011882928.1 |
| livH | L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | WP_012467843.1 | WP_011880725.1 |
| livM | L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | WP_011880724.1 | WP_011885760.1 |
| ofo | branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | WP_011882983.1 | WP_011886186.1 |
| acdH | (2S)-2-methylbutanoyl-CoA dehydrogenase | WP_011880691.1 | WP_011880846.1 |
| ech | 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | WP_011885989.1 | WP_011883164.1 |
| ivdG | 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | WP_043292554.1 | WP_011883958.1 |
| fadA | 2-methylacetoacetyl-CoA thiolase | WP_011884947.1 | WP_011879792.1 |
| prpC | 2-methylcitrate synthase | WP_011881025.1 | WP_011881720.1 |
| acnD | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) | WP_011881024.1 | WP_011881710.1 |
| prpF | methylaconitate isomerase | WP_011881023.1 | WP_011879868.1 |
| acn | (2R,3S)-2-methylcitrate dehydratase | WP_011881024.1 | WP_011879819.1 |
| prpB | 2-methylisocitrate lyase | WP_011885172.1 | WP_011881026.1 |
| Alternative steps: | |||
| Bap2 | L-isoleucine permease Bap2 | WP_011881451.1 | WP_011881650.1 |
| bcaP | L-isoleucine uptake transporter BcaP/CitA | WP_011886294.1 | |
| bkdA | branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | WP_011884991.1 | |
| bkdB | branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | WP_011884990.1 | |
| bkdC | branched-chain alpha-ketoacid dehydrogenase, E2 component | WP_011885425.1 | WP_011884604.1 |
| brnQ | L-isoleucine:cation symporter BrnQ/BraZ/BraB | ||
| dddA | 3-hydroxypropionate dehydrogenase | WP_011882794.1 | WP_011880327.1 |
| epi | methylmalonyl-CoA epimerase | ||
| hpcD | 3-hydroxypropionyl-CoA dehydratase | WP_011881868.1 | WP_011883164.1 |
| iolA | malonate semialdehyde dehydrogenase (CoA-acylating) | WP_011884470.1 | WP_011882148.1 |
| lpd | branched-chain alpha-ketoacid dehydrogenase, E3 component | WP_011882684.1 | WP_011885424.1 |
| mcm-large | methylmalonyl-CoA mutase, large (catalytic) subunit | WP_011880186.1 | |
| mcm-small | methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | WP_011880186.1 | WP_011886165.1 |
| mcmA | methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | WP_011880186.1 | |
| natA | L-isoleucine ABC transporter, ATPase component 1 (NatA) | WP_011882802.1 | WP_011881645.1 |
| natB | L-isoleucine ABC transporter, substrate-binding component NatB | ||
| natC | L-isoleucine ABC transporter, permease component 1 (NatC) | WP_011885760.1 | WP_011881644.1 |
| natD | L-isoleucine ABC transporter, permease component 2 (NatD) | WP_011880725.1 | WP_011880637.1 |
| natE | L-isoleucine ABC transporter, ATPase component 2 (NatE) | WP_011885758.1 | WP_011882803.1 |
| ofoA | branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA | ||
| ofoB | branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB | ||
| pccA | propionyl-CoA carboxylase, alpha subunit | WP_011880843.1 | WP_011883218.1 |
| pccA1 | propionyl-CoA carboxylase, biotin carboxyl carrier subunit | WP_011881198.1 | WP_011883218.1 |
| pccA2 | propionyl-CoA carboxylase, biotin carboxylase subunit | ||
| pccB | propionyl-CoA carboxylase, beta subunit | WP_011880845.1 | |
| pco | propanyl-CoA oxidase | WP_011884927.1 | WP_011883419.1 |
| prpD | 2-methylcitrate dehydratase | WP_011881711.1 | |
| 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 24 2021. The underlying query database was built on Sep 17 2021.
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:
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