GapMind for catabolism of small carbon sources

 

L-valine catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

livF, livG, livJ, livH, livM, ofo, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) H281DRAFT_04059 H281DRAFT_01585
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) H281DRAFT_04060 H281DRAFT_02375
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H281DRAFT_02161 H281DRAFT_02405
livH L-valine ABC transporter, permease component 1 (LivH/BraD) H281DRAFT_04062 H281DRAFT_06397
livM L-valine ABC transporter, permease component 2 (LivM/BraE) H281DRAFT_04061 H281DRAFT_05513
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused H281DRAFT_05847 H281DRAFT_01671
acdH isobutyryl-CoA dehydrogenase H281DRAFT_01204 H281DRAFT_02091
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H281DRAFT_05725 H281DRAFT_02514
bch 3-hydroxyisobutyryl-CoA hydrolase H281DRAFT_01199 H281DRAFT_00756
mmsB 3-hydroxyisobutyrate dehydrogenase H281DRAFT_01201 H281DRAFT_05314
mmsA methylmalonate-semialdehyde dehydrogenase H281DRAFT_01202 H281DRAFT_02373
prpC 2-methylcitrate synthase H281DRAFT_06634 H281DRAFT_06327
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) H281DRAFT_02981 H281DRAFT_06210
prpF methylaconitate isomerase H281DRAFT_02982 H281DRAFT_01376
acn (2R,3S)-2-methylcitrate dehydratase H281DRAFT_02981 H281DRAFT_06606
prpB 2-methylisocitrate lyase H281DRAFT_00580 H281DRAFT_02542
Alternative steps:
Bap2 L-valine permease Bap2 H281DRAFT_04042 H281DRAFT_01668
bcaP L-valine uptake transporter BcaP/CitA H281DRAFT_02180
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 H281DRAFT_00467 H281DRAFT_05114
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase H281DRAFT_02374 H281DRAFT_00975
epi methylmalonyl-CoA epimerase H281DRAFT_04643
hpcD 3-hydroxypropionyl-CoA dehydratase H281DRAFT_05725 H281DRAFT_02514
iolA malonate semialdehyde dehydrogenase (CoA-acylating) H281DRAFT_02373 H281DRAFT_03264
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component H281DRAFT_00468 H281DRAFT_05115
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit H281DRAFT_01038 H281DRAFT_02110
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit H281DRAFT_01038 H281DRAFT_02076
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components H281DRAFT_02110 H281DRAFT_01038
natA L-valine ABC transporter, ATPase component 1 (NatA) H281DRAFT_04060 H281DRAFT_02383
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) H281DRAFT_04452
natD L-valine ABC transporter, permease component 2 (NatD) H281DRAFT_06397 H281DRAFT_04062
natE L-valine ABC transporter, ATPase component 2 (NatE) H281DRAFT_02384 H281DRAFT_04059
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 H281DRAFT_01343 H281DRAFT_06283
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit H281DRAFT_06283 H281DRAFT_01343
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit H281DRAFT_01345
pco propanyl-CoA oxidase H281DRAFT_05174 H281DRAFT_04737
phtJ L-valine uptake permease PhtJ
prpD 2-methylcitrate dehydratase H281DRAFT_06607
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