GapMind for catabolism of small carbon sources

 

L-valine catabolism in Magnetospirillum magneticum AMB-1

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) AMB_RS09120 AMB_RS10230
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) AMB_RS09125 AMB_RS08465
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AMB_RS15010
livH L-valine ABC transporter, permease component 1 (LivH/BraD) AMB_RS09135 AMB_RS08455
livM L-valine ABC transporter, permease component 2 (LivM/BraE) AMB_RS09130 AMB_RS08460
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH isobutyryl-CoA dehydrogenase AMB_RS18215 AMB_RS18150
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AMB_RS03265 AMB_RS13070
bch 3-hydroxyisobutyryl-CoA hydrolase AMB_RS18135 AMB_RS12890
mmsB 3-hydroxyisobutyrate dehydrogenase AMB_RS18155
mmsA methylmalonate-semialdehyde dehydrogenase AMB_RS04115 AMB_RS06710
pccA propionyl-CoA carboxylase, alpha subunit AMB_RS21445 AMB_RS03465
pccB propionyl-CoA carboxylase, beta subunit AMB_RS21450 AMB_RS03475
epi methylmalonyl-CoA epimerase AMB_RS12960
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AMB_RS01570
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AMB_RS01570
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AMB_RS22255 AMB_RS18485
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AMB_RS18485
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AMB_RS11705
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AMB_RS11710 AMB_RS00370
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AMB_RS20045 AMB_RS11715
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase AMB_RS03265 AMB_RS13040
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AMB_RS04115 AMB_RS06710
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AMB_RS11730 AMB_RS20050
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AMB_RS01570
natA L-valine ABC transporter, ATPase component 1 (NatA) AMB_RS10235 AMB_RS08465
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) AMB_RS09130
natD L-valine ABC transporter, permease component 2 (NatD) AMB_RS08455
natE L-valine ABC transporter, ATPase component 2 (NatE) AMB_RS09120 AMB_RS10230
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA AMB_RS10840
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB AMB_RS10845
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AMB_RS21445 AMB_RS13620
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase AMB_RS16315 AMB_RS03480
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase AMB_RS14105
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase AMB_RS01270
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