GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudomonas stutzeri RCH2

Best path

livF, livG, livJ, livH, livM, ofo, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) Psest_1308 Psest_3854
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) Psest_1309 Psest_1089
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Psest_1312
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) Psest_1311 Psest_3855
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) Psest_1310 Psest_1093
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Psest_3517
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase Psest_2445 Psest_2440
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Psest_2654 Psest_2437
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Psest_2447 Psest_1147
fadA 2-methylacetoacetyl-CoA thiolase Psest_2653 Psest_1076
prpC 2-methylcitrate synthase Psest_2320 Psest_2499
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Psest_2319 Psest_2521
prpF methylaconitate isomerase Psest_2318
acn (2R,3S)-2-methylcitrate dehydratase Psest_2319 Psest_2309
prpB 2-methylisocitrate lyase Psest_2321 Psest_2567
Alternative steps:
Bap2 L-isoleucine permease Bap2 Psest_1697
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Psest_2219 Psest_1429
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Psest_1427 Psest_2218
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Psest_0447 Psest_2217
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB Psest_2489
dddA 3-hydroxypropionate dehydrogenase Psest_2633
epi methylmalonyl-CoA epimerase Psest_4071
hpcD 3-hydroxypropionyl-CoA dehydratase Psest_2437 Psest_3109
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Psest_2436 Psest_3781
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Psest_2492 Psest_1663
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) Psest_1309 Psest_1089
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) Psest_1310
natD L-isoleucine ABC transporter, permease component 2 (NatD) Psest_1092 Psest_3855
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) Psest_1308 Psest_1090
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 Psest_1080 Psest_1019
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Psest_4085 Psest_1019
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Psest_1083
pco propanyl-CoA oxidase Psest_3830
prpD 2-methylcitrate dehydratase
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