GapMind for catabolism of small carbon sources

 

L-valine catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, bch, mmsB, mmsA, pco, hpcD, dddA, iolA

Also see fitness data for the top candidates

Rules

Overview: Valine degradation in GapMind is based on MetaCyc pathway L-valine degradation I (link). The other pathways do not produce any fixed carbon and are not included.

47 steps (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) DvMF_2611 DvMF_2754
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) DvMF_2610 DvMF_2753
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DvMF_2607 DvMF_2750
livH L-valine ABC transporter, permease component 1 (LivH/BraD) DvMF_1165 DvMF_2608
livM L-valine ABC transporter, permease component 2 (LivM/BraE) DvMF_2609 DvMF_2752
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA DvMF_2056 with DvMF_2057
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB DvMF_2055 DvMF_0603
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
acdH isobutyryl-CoA dehydrogenase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
bch 3-hydroxyisobutyryl-CoA hydrolase
mmsB 3-hydroxyisobutyrate dehydrogenase DvMF_2927 DvMF_2320
mmsA methylmalonate-semialdehyde dehydrogenase DvMF_2146
pco propanyl-CoA oxidase DvMF_0766
hpcD 3-hydroxypropionyl-CoA dehydratase
dddA 3-hydroxypropionate dehydrogenase
iolA malonate semialdehyde dehydrogenase (CoA-acylating) DvMF_2146
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase DvMF_3021
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-valine permease Bap2
bcaP L-valine 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-valine:cation symporter BrnQ/BraZ/BraB
epi methylmalonyl-CoA epimerase
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component DvMF_0222 DvMF_0898
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-valine ABC transporter, ATPase component 1 (NatA) DvMF_2753 DvMF_1163
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC)
natD L-valine ABC transporter, permease component 2 (NatD) DvMF_2751 DvMF_2608
natE L-valine ABC transporter, ATPase component 2 (NatE) DvMF_2754 DvMF_2611
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA DvMF_0184 DvMF_0603
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB DvMF_0185 DvMF_0604
pccA propionyl-CoA carboxylase, alpha subunit DvMF_0417 DvMF_0817
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit DvMF_0417 DvMF_0817
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
phtJ L-valine uptake permease PhtJ
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