GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudomonas putida KT2440

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) PP_1137 PP_4863
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) PP_1138 PP_4864
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PP_1141 PP_4867
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) PP_1140 PP_4866
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) PP_1139 PP_4865
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PP_4401 PP_0555
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PP_4402 PP_0554
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PP_4403 PP_0338
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PP_4187 PP_4404
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase PP_2216 PP_3492
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase PP_2136 PP_2217
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase PP_2214 PP_2783
fadA 2-methylacetoacetyl-CoA thiolase PP_2137 PP_1377
prpC 2-methylcitrate synthase PP_2335 PP_4194
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PP_2336 PP_2112
prpF methylaconitate isomerase PP_2337 PP_2055
acn (2R,3S)-2-methylcitrate dehydratase PP_2336 PP_2339
prpB 2-methylisocitrate lyase PP_4116 PP_2334
Alternative steps:
Bap2 L-isoleucine permease Bap2 PP_3727 PP_1059
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB PP_4184
dddA 3-hydroxypropionate dehydrogenase PP_0056 PP_1949
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase PP_2217 PP_3284
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PP_0597 PP_4667
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) PP_1138 PP_2748
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) PP_4865
natD L-isoleucine ABC transporter, permease component 2 (NatD) PP_1140 PP_2768
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) PP_1137 PP_0615
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 PP_4067 PP_0558
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PP_5347 PP_0558
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PP_4065
pco propanyl-CoA oxidase PP_0158 PP_2216
prpD 2-methylcitrate dehydratase PP_2338
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