GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudomonas fluorescens FW300-N2E3

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) AO353_17105 AO353_13360
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) AO353_17110 AO353_13355
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AO353_17125 AO353_13340
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) AO353_17120 AO353_13345
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) AO353_17115 AO353_13350
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AO353_26635 AO353_15575
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AO353_26640 AO353_15580
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AO353_26645 AO353_15585
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AO353_26650 AO353_01825
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase AO353_25680 AO353_25670
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase AO353_00510 AO353_25675
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase AO353_25690 AO353_04045
fadA 2-methylacetoacetyl-CoA thiolase AO353_00505 AO353_25685
prpC 2-methylcitrate synthase AO353_00895 AO353_01860
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AO353_00890 AO353_00565
prpF methylaconitate isomerase AO353_00885 AO353_26715
acn (2R,3S)-2-methylcitrate dehydratase AO353_00890 AO353_21605
prpB 2-methylisocitrate lyase AO353_00900 AO353_27735
Alternative steps:
Bap2 L-isoleucine permease Bap2 AO353_24825 AO353_16120
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB AO353_01810
dddA 3-hydroxypropionate dehydrogenase AO353_26740 AO353_07810
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase AO353_25675 AO353_24830
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AO353_21350 AO353_06080
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) AO353_17110 AO353_13530
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) AO353_17120
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) AO353_17105 AO353_13360
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 AO353_20335 AO353_19305
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AO353_10030 AO353_13675
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit AO353_20345 AO353_19320
pco propanyl-CoA oxidase AO353_11100
prpD 2-methylcitrate dehydratase AO353_00880
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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