GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudomonas baetica a390

Best path

livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) C0J26_RS09020 C0J26_RS03600
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) C0J26_RS09025 C0J26_RS03610
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) C0J26_RS09040
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) C0J26_RS09035 C0J26_RS03620
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) C0J26_RS09030
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit C0J26_RS11495
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit C0J26_RS11490
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component C0J26_RS11485 C0J26_RS02735
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component C0J26_RS19760 C0J26_RS25195
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase C0J26_RS15235 C0J26_RS15245
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase C0J26_RS25285 C0J26_RS15240
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase C0J26_RS15225 C0J26_RS21460
fadA 2-methylacetoacetyl-CoA thiolase C0J26_RS25280 C0J26_RS15230
prpC 2-methylcitrate synthase C0J26_RS24620 C0J26_RS19795
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) C0J26_RS24615 C0J26_RS25345
prpF methylaconitate isomerase C0J26_RS24610
acn (2R,3S)-2-methylcitrate dehydratase C0J26_RS24615 C0J26_RS11685
prpB 2-methylisocitrate lyase C0J26_RS24625 C0J26_RS16655
Alternative steps:
Bap2 L-isoleucine permease Bap2 C0J26_RS21710 C0J26_RS01700
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB C0J26_RS19745
dddA 3-hydroxypropionate dehydrogenase C0J26_RS15680 C0J26_RS28395
epi methylmalonyl-CoA epimerase C0J26_RS26785
hpcD 3-hydroxypropionyl-CoA dehydratase C0J26_RS15240 C0J26_RS15160
iolA malonate semialdehyde dehydrogenase (CoA-acylating) C0J26_RS04135 C0J26_RS04225
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) C0J26_RS09025 C0J26_RS03610
natB L-isoleucine ABC transporter, substrate-binding component NatB C0J26_RS09040
natC L-isoleucine ABC transporter, permease component 1 (NatC) C0J26_RS09030
natD L-isoleucine ABC transporter, permease component 2 (NatD)
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) C0J26_RS09020 C0J26_RS29750
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 C0J26_RS17000 C0J26_RS25630
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit C0J26_RS30885 C0J26_RS03790
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit C0J26_RS25615
pco propanyl-CoA oxidase C0J26_RS00745 C0J26_RS15235
prpD 2-methylcitrate dehydratase C0J26_RS24605
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.

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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