GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Dyella japonica UNC79MFTsu3.2

Best path

Bap2, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2 N515DRAFT_2630 N515DRAFT_3653
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit N515DRAFT_0356
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit N515DRAFT_0355 N515DRAFT_0481
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component N515DRAFT_2156 N515DRAFT_0354
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component N515DRAFT_2155 N515DRAFT_2778
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase N515DRAFT_0492 N515DRAFT_0941
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase N515DRAFT_2687 N515DRAFT_0416
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase N515DRAFT_3783 N515DRAFT_2826
fadA 2-methylacetoacetyl-CoA thiolase N515DRAFT_0938 N515DRAFT_2688
prpC 2-methylcitrate synthase N515DRAFT_0021 N515DRAFT_2064
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) N515DRAFT_0029 N515DRAFT_1419
prpF methylaconitate isomerase N515DRAFT_0030
acn (2R,3S)-2-methylcitrate dehydratase N515DRAFT_0029 N515DRAFT_1420
prpB 2-methylisocitrate lyase N515DRAFT_4123 N515DRAFT_0020
Alternative steps:
bcaP L-isoleucine uptake transporter BcaP/CitA N515DRAFT_0722 N515DRAFT_2925
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase N515DRAFT_4337
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase N515DRAFT_1164 N515DRAFT_0416
iolA malonate semialdehyde dehydrogenase (CoA-acylating) N515DRAFT_3729 N515DRAFT_2488
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) N515DRAFT_3950 N515DRAFT_1248
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) N515DRAFT_3950 N515DRAFT_1562
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 N515DRAFT_0973
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit N515DRAFT_0973
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components N515DRAFT_0973
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) N515DRAFT_3950 N515DRAFT_1085
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) N515DRAFT_3950 N515DRAFT_1687
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 N515DRAFT_0927 N515DRAFT_3374
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit N515DRAFT_3374 N515DRAFT_0927
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit N515DRAFT_0936
pco propanyl-CoA oxidase N515DRAFT_0484 N515DRAFT_0492
prpD 2-methylcitrate dehydratase N515DRAFT_0031
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, 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