GapMind for catabolism of small carbon sources

 

L-valine catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

livF, livG, livJ, livH, livM, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) Pf6N2E2_2926 Pf6N2E2_3576
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) Pf6N2E2_2925 Pf6N2E2_3577
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Pf6N2E2_2921 Pf6N2E2_3580
livH L-valine ABC transporter, permease component 1 (LivH/BraD) Pf6N2E2_2923 Pf6N2E2_3579
livM L-valine ABC transporter, permease component 2 (LivM/BraE) Pf6N2E2_2924 Pf6N2E2_3578
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Pf6N2E2_481 Pf6N2E2_665
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Pf6N2E2_480 Pf6N2E2_666
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Pf6N2E2_479 Pf6N2E2_3675
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Pf6N2E2_478 Pf6N2E2_5857
acdH isobutyryl-CoA dehydrogenase Pf6N2E2_1148 Pf6N2E2_1146
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf6N2E2_1147 Pf6N2E2_1834
bch 3-hydroxyisobutyryl-CoA hydrolase Pf6N2E2_1149 Pf6N2E2_2773
mmsB 3-hydroxyisobutyrate dehydrogenase Pf6N2E2_3451 Pf6N2E2_1929
mmsA methylmalonate-semialdehyde dehydrogenase Pf6N2E2_3452 Pf6N2E2_3462
prpC 2-methylcitrate synthase Pf6N2E2_6062 Pf6N2E2_5850
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Pf6N2E2_6063 Pf6N2E2_2301
prpF methylaconitate isomerase Pf6N2E2_6064
acn (2R,3S)-2-methylcitrate dehydratase Pf6N2E2_6063 Pf6N2E2_564
prpB 2-methylisocitrate lyase Pf6N2E2_6061 Pf6N2E2_279
Alternative steps:
Bap2 L-valine permease Bap2 Pf6N2E2_5459 Pf6N2E2_1423
bcaP L-valine uptake transporter BcaP/CitA
brnQ L-valine:cation symporter BrnQ/BraZ/BraB Pf6N2E2_5860
dddA 3-hydroxypropionate dehydrogenase Pf6N2E2_2094 Pf6N2E2_4677
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Pf6N2E2_1147 Pf6N2E2_1934
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Pf6N2E2_515 Pf6N2E2_3462
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) Pf6N2E2_2925 Pf6N2E2_1705
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) Pf6N2E2_2924
natD L-valine ABC transporter, permease component 2 (NatD)
natE L-valine ABC transporter, ATPase component 2 (NatE) Pf6N2E2_2926 Pf6N2E2_3576
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 Pf6N2E2_2194 Pf6N2E2_2411
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Pf6N2E2_4278 Pf6N2E2_3512
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Pf6N2E2_2192 Pf6N2E2_2409
pco propanyl-CoA oxidase Pf6N2E2_4036 Pf6N2E2_1146
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.

Links

Downloads

Related tools

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