GapMind for catabolism of small carbon sources

 

L-valine catabolism in Dinoroseobacter shibae DFL-12

Best path

Bap2, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-valine permease Bap2
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Dshi_1762
acdH isobutyryl-CoA dehydrogenase Dshi_1750 Dshi_1297
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dshi_3370 Dshi_0835
bch 3-hydroxyisobutyryl-CoA hydrolase Dshi_1751 Dshi_1753
mmsB 3-hydroxyisobutyrate dehydrogenase Dshi_1752 Dshi_3047
mmsA methylmalonate-semialdehyde dehydrogenase Dshi_1747 Dshi_0577
pccA propionyl-CoA carboxylase, alpha subunit Dshi_0723 Dshi_1301
pccB propionyl-CoA carboxylase, beta subunit Dshi_0718 Dshi_1300
epi methylmalonyl-CoA epimerase Dshi_2630
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Dshi_0726 Dshi_2855
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Dshi_0726 Dshi_2855
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Dshi_1851 Dshi_2060
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Dshi_1851
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Dshi_2158 Dshi_0534
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Dshi_2159 Dshi_0535
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Dshi_1967 Dshi_2884
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase Dshi_0804 Dshi_1428
hpcD 3-hydroxypropionyl-CoA dehydratase Dshi_3370 Dshi_1048
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Dshi_1747 Dshi_0577
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) Dshi_3728 Dshi_0381
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) Dshi_0375 Dshi_3727
livH L-valine ABC transporter, permease component 1 (LivH/BraD) Dshi_3725 Dshi_0861
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE) Dshi_0379 Dshi_1978
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Dshi_1966 Dshi_2886
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Dshi_0726 Dshi_2855
natA L-valine ABC transporter, ATPase component 1 (NatA) Dshi_1521 Dshi_1981
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) Dshi_1979 Dshi_1518
natE L-valine ABC transporter, ATPase component 2 (NatE) Dshi_1520 Dshi_1980
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Dshi_0723 Dshi_1395
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase Dshi_2357 Dshi_1297
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase Dshi_0689 Dshi_1092
prpC 2-methylcitrate synthase Dshi_1806
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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