GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Sphingomonas koreensis DSMZ 15582

Best path

Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Ga0059261_2273 Ga0059261_0016
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Ga0059261_2272 Ga0059261_0017
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Ga0059261_2271 Ga0059261_3712
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Ga0059261_3715 Ga0059261_1343
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase Ga0059261_3681 Ga0059261_3793
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Ga0059261_3685 Ga0059261_0837
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Ga0059261_2816 Ga0059261_2801
fadA 2-methylacetoacetyl-CoA thiolase Ga0059261_0982 Ga0059261_2888
pccA propionyl-CoA carboxylase, alpha subunit Ga0059261_3993 Ga0059261_4056
pccB propionyl-CoA carboxylase, beta subunit Ga0059261_3982 Ga0059261_4055
epi methylmalonyl-CoA epimerase Ga0059261_3985
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Ga0059261_3988
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Ga0059261_3988
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Ga0059261_3296
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Ga0059261_3296
bcaP L-isoleucine uptake transporter BcaP/CitA Ga0059261_1577 Ga0059261_1053
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase Ga0059261_2257 Ga0059261_2901
hpcD 3-hydroxypropionyl-CoA dehydratase Ga0059261_3685 Ga0059261_2668
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Ga0059261_3677 Ga0059261_3374
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) Ga0059261_2542 Ga0059261_4235
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) Ga0059261_2542 Ga0059261_2250
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)
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Ga0059261_3988
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) Ga0059261_2542
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) Ga0059261_2542 Ga0059261_2703
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA Ga0059261_0325
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB Ga0059261_0324
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Ga0059261_3993 Ga0059261_0292
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase Ga0059261_2164
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase Ga0059261_0941
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase Ga0059261_0523
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB Ga0059261_0325
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 (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