GapMind for catabolism of small carbon sources

 

L-valine catabolism in Escherichia coli BW25113

Best path

livF, livG, livJ, livH, livM, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) b3454 b3201
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) b3455 b3201
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) b3460 b3458
livH L-valine ABC transporter, permease component 1 (LivH/BraD) b3457
livM L-valine ABC transporter, permease component 2 (LivM/BraE) b3456
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH isobutyryl-CoA dehydrogenase b0039 b1695
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase b1393 b3846
bch 3-hydroxyisobutyryl-CoA hydrolase
mmsB 3-hydroxyisobutyrate dehydrogenase b3125 b3882
mmsA methylmalonate-semialdehyde dehydrogenase b1385 b2661
prpC 2-methylcitrate synthase b0333 b0720
prpD 2-methylcitrate dehydratase b0334
acn (2R,3S)-2-methylcitrate dehydratase b0118 b1276
prpB 2-methylisocitrate lyase b0331 b4015
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) b1276
Bap2 L-valine permease Bap2 b2156 b0576
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 b0115 b0727
brnQ L-valine:cation symporter BrnQ/BraZ/BraB b0401
dddA 3-hydroxypropionate dehydrogenase b0311
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase b1393 b2341
iolA malonate semialdehyde dehydrogenase (CoA-acylating) b2661 b0312
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component b0116 b3962
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit b2917
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit b2917 b4019
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components b2917
natA L-valine ABC transporter, ATPase component 1 (NatA) b3455 b3201
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) b3457
natE L-valine ABC transporter, ATPase component 2 (NatE) b3454 b1513
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 b3256
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit b3256
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 b0769
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