GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudomonas fluorescens FW300-N1B4

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) Pf1N1B4_3214 Pf1N1B4_1378
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) Pf1N1B4_3215 Pf1N1B4_1379
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Pf1N1B4_3218 Pf1N1B4_1382
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) Pf1N1B4_3217 Pf1N1B4_1381
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) Pf1N1B4_3216 Pf1N1B4_1380
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Pf1N1B4_4480 Pf1N1B4_1020
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Pf1N1B4_4479 Pf1N1B4_1019
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Pf1N1B4_4478 Pf1N1B4_1018
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Pf1N1B4_4477 Pf1N1B4_3683
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase Pf1N1B4_4787 Pf1N1B4_4789
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Pf1N1B4_3903 Pf1N1B4_4788
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Pf1N1B4_4785 Pf1N1B4_730
fadA 2-methylacetoacetyl-CoA thiolase Pf1N1B4_3904 Pf1N1B4_4786
prpC 2-methylcitrate synthase Pf1N1B4_3820 Pf1N1B4_3676
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Pf1N1B4_3821 Pf1N1B4_3888
prpF methylaconitate isomerase Pf1N1B4_3822 Pf1N1B4_4463
acn (2R,3S)-2-methylcitrate dehydratase Pf1N1B4_3821 Pf1N1B4_4564
prpB 2-methylisocitrate lyase Pf1N1B4_3819 Pf1N1B4_4042
Alternative steps:
Bap2 L-isoleucine permease Bap2 Pf1N1B4_801 Pf1N1B4_1639
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB Pf1N1B4_3686
dddA 3-hydroxypropionate dehydrogenase Pf1N1B4_4450 Pf1N1B4_2416
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Pf1N1B4_4788 Pf1N1B4_5593
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Pf1N1B4_4277 Pf1N1B4_1238
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) Pf1N1B4_3215 Pf1N1B4_1346
natB L-isoleucine ABC transporter, substrate-binding component NatB Pf1N1B4_1382
natC L-isoleucine ABC transporter, permease component 1 (NatC) Pf1N1B4_3216
natD L-isoleucine ABC transporter, permease component 2 (NatD)
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) Pf1N1B4_3214 Pf1N1B4_1378
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 Pf1N1B4_225 Pf1N1B4_3984
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Pf1N1B4_2010 Pf1N1B4_1309
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Pf1N1B4_3986 Pf1N1B4_222
pco propanyl-CoA oxidase Pf1N1B4_1816
prpD 2-methylcitrate dehydratase Pf1N1B4_3823
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