GapMind for catabolism of small carbon sources

 

L-valine catabolism in Shewanella sp. ANA-3

Best path

brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-valine:cation symporter BrnQ/BraZ/BraB Shewana3_3332
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Shewana3_2131
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Shewana3_2130
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Shewana3_2129 Shewana3_0427
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Shewana3_0428 Shewana3_4345
acdH isobutyryl-CoA dehydrogenase Shewana3_2769 Shewana3_1672
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shewana3_2768 Shewana3_0024
bch 3-hydroxyisobutyryl-CoA hydrolase Shewana3_2767
mmsB 3-hydroxyisobutyrate dehydrogenase Shewana3_2766 Shewana3_2554
mmsA methylmalonate-semialdehyde dehydrogenase Shewana3_2770 Shewana3_3107
prpC 2-methylcitrate synthase Shewana3_3826 Shewana3_1705
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Shewana3_3827
prpF methylaconitate isomerase Shewana3_3828
acn (2R,3S)-2-methylcitrate dehydratase Shewana3_3827 Shewana3_0433
prpB 2-methylisocitrate lyase Shewana3_3825 Shewana3_2942
Alternative steps:
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Shewana3_2768 Shewana3_1461
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Shewana3_3107 Shewana3_2770
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) Shewana3_0673 Shewana3_0880
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) Shewana3_0673 Shewana3_3192
livH L-valine ABC transporter, permease component 1 (LivH/BraD)
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE)
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) Shewana3_0673 Shewana3_1620
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)
natE L-valine ABC transporter, ATPase component 2 (NatE) Shewana3_0880 Shewana3_2749
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA propionyl-CoA carboxylase, alpha subunit Shewana3_1669 Shewana3_3438
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Shewana3_1669 Shewana3_3438
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Shewana3_1671
pco propanyl-CoA oxidase
phtJ L-valine uptake permease PhtJ
prpD 2-methylcitrate dehydratase
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