GapMind for catabolism of small carbon sources

 

L-valine catabolism in Azospirillum brasilense Sp245

Best path

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

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) AZOBR_RS08250 AZOBR_RS29685
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) AZOBR_RS08245 AZOBR_RS32405
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AZOBR_RS08260 AZOBR_RS29665
livH L-valine ABC transporter, permease component 1 (LivH/BraD) AZOBR_RS08235 AZOBR_RS03565
livM L-valine ABC transporter, permease component 2 (LivM/BraE) AZOBR_RS08240 AZOBR_RS32410
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH isobutyryl-CoA dehydrogenase AZOBR_RS22300 AZOBR_RS22365
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AZOBR_RS01260 AZOBR_RS26485
bch 3-hydroxyisobutyryl-CoA hydrolase AZOBR_RS08460 AZOBR_RS26485
mmsB 3-hydroxyisobutyrate dehydrogenase AZOBR_RS22360 AZOBR_RS26815
mmsA methylmalonate-semialdehyde dehydrogenase AZOBR_RS22500 AZOBR_RS29750
pccA propionyl-CoA carboxylase, alpha subunit AZOBR_RS21105 AZOBR_RS22285
pccB propionyl-CoA carboxylase, beta subunit AZOBR_RS21100 AZOBR_RS22295
epi methylmalonyl-CoA epimerase AZOBR_RS07250
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AZOBR_RS24250 AZOBR_RS21115
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AZOBR_RS24250 AZOBR_RS21115
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AZOBR_RS17090 AZOBR_RS02985
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AZOBR_RS02985
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AZOBR_RS22245 AZOBR_RS04795
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AZOBR_RS04800 AZOBR_RS22250
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AZOBR_RS14080
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase AZOBR_RS26815
hpcD 3-hydroxypropionyl-CoA dehydratase AZOBR_RS26485 AZOBR_RS01260
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AZOBR_RS22500 AZOBR_RS29750
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AZOBR_RS14390 AZOBR_RS03960
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AZOBR_RS24250 AZOBR_RS21115
natA L-valine ABC transporter, ATPase component 1 (NatA) AZOBR_RS32405 AZOBR_RS04130
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) AZOBR_RS29670 AZOBR_RS21005
natE L-valine ABC transporter, ATPase component 2 (NatE) AZOBR_RS19790 AZOBR_RS29685
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB AZOBR_RS02380
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AZOBR_RS21105 AZOBR_RS12015
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit AZOBR_RS22285
pco propanyl-CoA oxidase AZOBR_RS19670
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase AZOBR_RS02405 AZOBR_RS27820
prpC 2-methylcitrate synthase AZOBR_RS24300 AZOBR_RS25925
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase AZOBR_RS24310 AZOBR_RS28105
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB AZOBR_RS02385
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