GapMind for catabolism of small carbon sources

 

L-valine catabolism in Synechococcus elongatus PCC 7942

Best path

natA, natB, natC, natD, natE, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-valine ABC transporter, ATPase component 1 (NatA) Synpcc7942_1893 Synpcc7942_2493
natB L-valine ABC transporter, substrate-binding component NatB Synpcc7942_1861
natC L-valine ABC transporter, permease component 1 (NatC) Synpcc7942_1894
natD L-valine ABC transporter, permease component 2 (NatD) Synpcc7942_2177 Synpcc7942_2495
natE L-valine ABC transporter, ATPase component 2 (NatE) Synpcc7942_0815 Synpcc7942_2492
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH isobutyryl-CoA dehydrogenase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Synpcc7942_0597
bch 3-hydroxyisobutyryl-CoA hydrolase
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase
prpC 2-methylcitrate synthase Synpcc7942_0612
prpD 2-methylcitrate dehydratase
acn (2R,3S)-2-methylcitrate dehydratase Synpcc7942_0903
prpB 2-methylisocitrate lyase
Alternative steps:
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 Synpcc7942_1944
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Synpcc7942_0143
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Synpcc7942_0597
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) Synpcc7942_2492 Synpcc7942_0815
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) Synpcc7942_2493 Synpcc7942_1893
livH L-valine ABC transporter, permease component 1 (LivH/BraD) Synpcc7942_2495 Synpcc7942_2177
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE) Synpcc7942_2494
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Synpcc7942_1198 Synpcc7942_0842
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
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 Synpcc7942_1379
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Synpcc7942_1379
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
phtJ L-valine uptake permease PhtJ
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