GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudomonas simiae WCS417

Best path

livF, livG, livJ, livH, livM, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) PS417_06595 PS417_02675
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) PS417_06600 PS417_02670
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PS417_06615 PS417_02655
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) PS417_06610 PS417_02660
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) PS417_06605 PS417_02665
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PS417_17545 PS417_11765
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PS417_17550 PS417_11770
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PS417_17555 PS417_02215
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PS417_17560 PS417_08905
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase PS417_13850 PS417_13840
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase PS417_07575 PS417_13845
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase PS417_13860 PS417_21440
fadA 2-methylacetoacetyl-CoA thiolase PS417_07580 PS417_10515
prpC 2-methylcitrate synthase PS417_21075 PS417_08870
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PS417_21070 PS417_07515
prpF methylaconitate isomerase PS417_21065 PS417_07225
acn (2R,3S)-2-methylcitrate dehydratase PS417_21070 PS417_14990
prpB 2-methylisocitrate lyase PS417_21080 PS417_16570
Alternative steps:
Bap2 L-isoleucine permease Bap2 PS417_01505 PS417_05405
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB PS417_08920
dddA 3-hydroxypropionate dehydrogenase PS417_10560 PS417_26345
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase PS417_13845 PS417_10680
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PS417_10925 PS417_03250
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) PS417_06600 PS417_16795
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) PS417_02665
natD L-isoleucine ABC transporter, permease component 2 (NatD)
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) PS417_06595 PS417_02675
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 PS417_19595 PS417_17030
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PS417_28215 PS417_02965
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PS417_17020 PS417_19580
pco propanyl-CoA oxidase PS417_00580 PS417_13850
prpD 2-methylcitrate dehydratase PS417_21060
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