GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Desulfovibrio vulgaris Hildenborough

Best path

livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) DVU0551 DVU0716
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) DVU2741 DVU0550
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DVU0547 DVU0712
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) DVU2743 DVU0548
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) DVU0549 DVU0714
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA DVU3348 with DVU3347 DVU1946
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB DVU3349 DVU1945
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase 206645 DVU3137
fadA 2-methylacetoacetyl-CoA thiolase
pco propanyl-CoA oxidase DVU2064
hpcD 3-hydroxypropionyl-CoA dehydratase
dddA 3-hydroxypropionate dehydrogenase
iolA malonate semialdehyde dehydrogenase (CoA-acylating) DVU3319
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
epi methylmalonyl-CoA epimerase
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component DVU1423 DVU1037
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) DVU2741 DVU0715
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) DVU0713
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) DVU0551 DVU0716
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA DVU1569 DVU1945
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB DVU1570 DVU1946
pccA propionyl-CoA carboxylase, alpha subunit DVU1834 DVU2226
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit DVU1834 DVU2226
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase

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