GapMind for catabolism of small carbon sources

 

L-valine catabolism in Burkholderia phytofirmans PsJN

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) BPHYT_RS31755 BPHYT_RS15590
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) BPHYT_RS15595 BPHYT_RS31750
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BPHYT_RS01885 BPHYT_RS31715
livH L-valine ABC transporter, permease component 1 (LivH/BraD) BPHYT_RS15605 BPHYT_RS31740
livM L-valine ABC transporter, permease component 2 (LivM/BraE) BPHYT_RS31745 BPHYT_RS15600
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BPHYT_RS18305 BPHYT_RS02015
acdH isobutyryl-CoA dehydrogenase BPHYT_RS28040 BPHYT_RS02220
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHYT_RS17335 BPHYT_RS28020
bch 3-hydroxyisobutyryl-CoA hydrolase BPHYT_RS28015 BPHYT_RS08630
mmsB 3-hydroxyisobutyrate dehydrogenase BPHYT_RS28025 BPHYT_RS31915
mmsA methylmalonate-semialdehyde dehydrogenase BPHYT_RS28030 BPHYT_RS19500
prpC 2-methylcitrate synthase BPHYT_RS33965 BPHYT_RS30150
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BPHYT_RS30145 BPHYT_RS33980
prpF methylaconitate isomerase BPHYT_RS30140 BPHYT_RS27420
acn (2R,3S)-2-methylcitrate dehydratase BPHYT_RS30145 BPHYT_RS10160
prpB 2-methylisocitrate lyase BPHYT_RS12285 BPHYT_RS26855
Alternative steps:
Bap2 L-valine permease Bap2 BPHYT_RS15500 BPHYT_RS21680
bcaP L-valine uptake transporter BcaP/CitA BPHYT_RS33230 BPHYT_RS01785
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BPHYT_RS29360
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BPHYT_RS29355
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BPHYT_RS12835 BPHYT_RS08115
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase BPHYT_RS19495 BPHYT_RS21745
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase BPHYT_RS25360 BPHYT_RS17335
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BPHYT_RS19500 BPHYT_RS28825
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BPHYT_RS12830 BPHYT_RS08120
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BPHYT_RS02085
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BPHYT_RS02305
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BPHYT_RS02085
natA L-valine ABC transporter, ATPase component 1 (NatA) BPHYT_RS15595 BPHYT_RS04435
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) BPHYT_RS32510 BPHYT_RS15605
natE L-valine ABC transporter, ATPase component 2 (NatE) BPHYT_RS19445 BPHYT_RS15590
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 BPHYT_RS23275 BPHYT_RS17015
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BPHYT_RS17015 BPHYT_RS25975
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BPHYT_RS23265
pco propanyl-CoA oxidase BPHYT_RS11475 BPHYT_RS03780
phtJ L-valine uptake permease PhtJ
prpD 2-methylcitrate dehydratase BPHYT_RS33975
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