GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Shewanella oneidensis MR-1

Best path

brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates

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).

45 steps (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB SO0949
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SO2339
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SO2340
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component SO2341 SO1931
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component SO0426 SO4702
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase SO1679 SO1897
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase SO0021 SO3088
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase SO1683 SO2776
fadA 2-methylacetoacetyl-CoA thiolase SO3089 SO1677
prpC 2-methylcitrate synthase SO0344 SO1926
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SO0343
prpF methylaconitate isomerase SO0342
acn (2R,3S)-2-methylcitrate dehydratase SO0343 SO0432
prpB 2-methylisocitrate lyase SO0345 SO1484
Alternative steps:
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase SO1680 SO3088
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SO1678 SO3496
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) SO3960 SO4655
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) SO3960 SO3602
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE)
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) SO3960 SO1865
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) SO1042 SO2258
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
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 SO1894 SO0840
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SO1894 SO0840
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit SO1896
pco propanyl-CoA oxidase
prpD 2-methylcitrate dehydratase
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 17 2021. The underlying query database was built on Sep 17 2021.

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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, the preprint on GapMind for carbon sources, 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