GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudomonas litoralis 2SM5

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) BLU11_RS03750 BLU11_RS01420
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) BLU11_RS03755 BLU11_RS01420
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BLU11_RS03770
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) BLU11_RS03765
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) BLU11_RS03760
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BLU11_RS15475
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase BLU11_RS02525 BLU11_RS12305
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BLU11_RS06160 BLU11_RS12290
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BLU11_RS02515 BLU11_RS11675
fadA 2-methylacetoacetyl-CoA thiolase BLU11_RS06165 BLU11_RS15740
prpC 2-methylcitrate synthase BLU11_RS05820 BLU11_RS04740
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BLU11_RS05825 BLU11_RS05430
prpF methylaconitate isomerase BLU11_RS05830
acn (2R,3S)-2-methylcitrate dehydratase BLU11_RS05825 BLU11_RS08620
prpB 2-methylisocitrate lyase BLU11_RS05815
Alternative steps:
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BLU11_RS15975
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLU11_RS15970
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BLU11_RS15965 BLU11_RS11795
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB BLU11_RS04790
dddA 3-hydroxypropionate dehydrogenase BLU11_RS15245
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase BLU11_RS15435 BLU11_RS12290
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLU11_RS18585 BLU11_RS12285
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BLU11_RS04775 BLU11_RS17200
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) BLU11_RS03755 BLU11_RS01420
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)
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) BLU11_RS03750 BLU11_RS16110
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 BLU11_RS15495 BLU11_RS15720
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLU11_RS16535 BLU11_RS02630
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BLU11_RS10715
pccB propionyl-CoA carboxylase, beta subunit BLU11_RS15485 BLU11_RS15710
pco propanyl-CoA oxidase BLU11_RS13665
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 24 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