GapMind for catabolism of small carbon sources

 

L-valine catabolism in Dechlorosoma suillum PS

Best path

livF, livG, livJ, livH, livM, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) Dsui_2057 Dsui_0626
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) Dsui_2058 Dsui_0627
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Dsui_0630 Dsui_2061
livH L-valine ABC transporter, permease component 1 (LivH/BraD) Dsui_0629 Dsui_2060
livM L-valine ABC transporter, permease component 2 (LivM/BraE) Dsui_0628 Dsui_2059
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Dsui_0379
acdH isobutyryl-CoA dehydrogenase Dsui_0977 Dsui_0975
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dsui_1378 Dsui_0323
bch 3-hydroxyisobutyryl-CoA hydrolase Dsui_1378 Dsui_0981
mmsB 3-hydroxyisobutyrate dehydrogenase Dsui_3436 Dsui_3438
mmsA methylmalonate-semialdehyde dehydrogenase Dsui_0437 Dsui_0105
pccA propionyl-CoA carboxylase, alpha subunit Dsui_0516 Dsui_0982
pccB propionyl-CoA carboxylase, beta subunit Dsui_0517 Dsui_0980
epi methylmalonyl-CoA epimerase Dsui_0512
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Dsui_0519 Dsui_1105
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Dsui_0519
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Dsui_2205 Dsui_2347
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Dsui_2347
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 Dsui_1577 Dsui_2218
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase Dsui_1378 Dsui_0521
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Dsui_0437 Dsui_0105
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Dsui_1576 Dsui_2219
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Dsui_0519 Dsui_1105
natA L-valine ABC transporter, ATPase component 1 (NatA) Dsui_2058 Dsui_0627
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) Dsui_0628
natD L-valine ABC transporter, permease component 2 (NatD) Dsui_0629 Dsui_2060
natE L-valine ABC transporter, ATPase component 2 (NatE) Dsui_0841 Dsui_2057
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 Dsui_0516 Dsui_0389
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase Dsui_1637 Dsui_3369
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase Dsui_0011
prpC 2-methylcitrate synthase Dsui_2216
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, 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