GapMind for catabolism of small carbon sources

 

L-valine catabolism in Herbaspirillum seropedicae SmR1

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) HSERO_RS08290 HSERO_RS14710
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) HSERO_RS08285 HSERO_RS14705
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HSERO_RS08270 HSERO_RS17350
livH L-valine ABC transporter, permease component 1 (LivH/BraD) HSERO_RS08275 HSERO_RS05960
livM L-valine ABC transporter, permease component 2 (LivM/BraE) HSERO_RS08280 HSERO_RS14700
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused HSERO_RS21380 HSERO_RS12755
acdH isobutyryl-CoA dehydrogenase HSERO_RS04640 HSERO_RS12750
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HSERO_RS19405 HSERO_RS20665
bch 3-hydroxyisobutyryl-CoA hydrolase HSERO_RS01610 HSERO_RS20665
mmsB 3-hydroxyisobutyrate dehydrogenase HSERO_RS15390 HSERO_RS21160
mmsA methylmalonate-semialdehyde dehydrogenase HSERO_RS15395 HSERO_RS23245
prpC 2-methylcitrate synthase HSERO_RS15655 HSERO_RS14890
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) HSERO_RS11425 HSERO_RS14940
prpF methylaconitate isomerase HSERO_RS11420 HSERO_RS07335
acn (2R,3S)-2-methylcitrate dehydratase HSERO_RS11425 HSERO_RS14940
prpB 2-methylisocitrate lyase HSERO_RS10565 HSERO_RS15660
Alternative steps:
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
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 HSERO_RS14880 HSERO_RS07310
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase HSERO_RS24000 HSERO_RS23855
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase HSERO_RS19405 HSERO_RS12745
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HSERO_RS24005 HSERO_RS23245
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HSERO_RS07315 HSERO_RS14875
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HSERO_RS21740
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-valine ABC transporter, ATPase component 1 (NatA) HSERO_RS08920 HSERO_RS14705
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) HSERO_RS14700
natD L-valine ABC transporter, permease component 2 (NatD) HSERO_RS05960 HSERO_RS00885
natE L-valine ABC transporter, ATPase component 2 (NatE) HSERO_RS08290 HSERO_RS08925
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 HSERO_RS23460 HSERO_RS01925
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HSERO_RS01925 HSERO_RS20550
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit HSERO_RS23455
pco propanyl-CoA oxidase HSERO_RS23440
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.

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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