GapMind for catabolism of small carbon sources

 

L-valine catabolism in Bacteroides thetaiotaomicron VPI-5482

Best path

Bap2, vorA*, vorB, vorC, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-valine permease Bap2
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA BT0330 with BT0329
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB BT0331 BT2836
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC BT0333
acdH isobutyryl-CoA dehydrogenase BT1806
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BT4702
bch 3-hydroxyisobutyryl-CoA hydrolase
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase
pccA propionyl-CoA carboxylase, alpha subunit BT1915 BT1449
pccB propionyl-CoA carboxylase, beta subunit BT1450 BT1686
epi methylmalonyl-CoA epimerase BT1685
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BT2090
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BT2090 BT0340
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BT2072
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BT2072
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BT0312
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BT0312
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BT0311
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase BT4702
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) BT3837 BT1291
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) BT3837 BT1291
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)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BT3186 BT0309
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BT2090 BT2091
natA L-valine ABC transporter, ATPase component 1 (NatA) BT3837
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) BT3837 BT0562
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 BT2837
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BT1915 BT1449
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BT1886
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase BT_2070
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase

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