GapMind for catabolism of small carbon sources

 

L-valine catabolism in Shewanella amazonensis SB2B

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-valine:cation symporter BrnQ/BraZ/BraB Sama_2740
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Sama_1709
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Sama_1710 Sama_2795
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Sama_1711 Sama_1428
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Sama_0377 Sama_3543
acdH isobutyryl-CoA dehydrogenase Sama_1377 Sama_1362
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Sama_1378 Sama_0032
bch 3-hydroxyisobutyryl-CoA hydrolase Sama_1379
mmsB 3-hydroxyisobutyrate dehydrogenase Sama_1380 Sama_1975
mmsA methylmalonate-semialdehyde dehydrogenase Sama_1376 Sama_2650
prpC 2-methylcitrate synthase Sama_3295 Sama_1422
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Sama_3296
prpF methylaconitate isomerase Sama_3297
acn (2R,3S)-2-methylcitrate dehydratase Sama_3296 Sama_0382
prpB 2-methylisocitrate lyase Sama_2380 Sama_3294
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 Sama_1378 Sama_2167
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Sama_2650 Sama_1376
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) Sama_3087 Sama_2641
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) Sama_3087 Sama_3081
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) Sama_3087 Sama_0772
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) Sama_3588 Sama_0760
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 Sama_1359 Sama_3196
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Sama_1359 Sama_3196
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Sama_1361
pco propanyl-CoA oxidase Sama_2796
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