GapMind for catabolism of small carbon sources

 

L-valine catabolism in Phaeobacter inhibens BS107

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 (31 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 PGA1_c17080 PGA1_c04490
acdH isobutyryl-CoA dehydrogenase PGA1_c10280 PGA1_c17340
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PGA1_c36500 PGA1_262p01980
bch 3-hydroxyisobutyryl-CoA hydrolase PGA1_c17350 PGA1_262p01980
mmsB 3-hydroxyisobutyrate dehydrogenase PGA1_c17360 PGA1_c14880
mmsA methylmalonate-semialdehyde dehydrogenase PGA1_c17300 PGA1_c21670
pccA propionyl-CoA carboxylase, alpha subunit PGA1_c21540 PGA1_c10330
pccB propionyl-CoA carboxylase, beta subunit PGA1_c21600 PGA1_c10320
epi methylmalonyl-CoA epimerase PGA1_c24490
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit PGA1_c21510 PGA1_c03840
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit PGA1_c21510 PGA1_c03840
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase PGA1_c18830
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PGA1_c18830
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PGA1_c23140 PGA1_c17550
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PGA1_c23150 PGA1_c17560
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PGA1_c23180 PGA1_c03590
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase PGA1_c30400 PGA1_c21660
hpcD 3-hydroxypropionyl-CoA dehydratase PGA1_c36500 PGA1_262p01980
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PGA1_c17300 PGA1_c21670
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) PGA1_c02620 PGA1_c32560
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) PGA1_c02610 PGA1_c32620
livH L-valine ABC transporter, permease component 1 (LivH/BraD) PGA1_c02590 PGA1_c16550
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE) PGA1_c02600 PGA1_c32580
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PGA1_c17390 PGA1_c23190
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components PGA1_c21510 PGA1_c03840
natA L-valine ABC transporter, ATPase component 1 (NatA) PGA1_c15910 PGA1_c02610
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) PGA1_c15940
natE L-valine ABC transporter, ATPase component 2 (NatE) PGA1_c15920 PGA1_c02620
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 PGA1_c21540 PGA1_c12600
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase PGA1_c15710
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase PGA1_c28860 PGA1_c16970
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