GapMind for catabolism of small carbon sources

 

L-valine catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

Bap2, bkdA, bkdB, bkdC, lpd, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-valine permease Bap2
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CA265_RS18405 CA265_RS19580
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CA265_RS18405 CA265_RS18860
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CA265_RS09070 CA265_RS19585
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CA265_RS05155 CA265_RS24150
acdH isobutyryl-CoA dehydrogenase CA265_RS22715 CA265_RS02820
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CA265_RS20005 CA265_RS09125
bch 3-hydroxyisobutyryl-CoA hydrolase CA265_RS20005
mmsB 3-hydroxyisobutyrate dehydrogenase CA265_RS01080
mmsA methylmalonate-semialdehyde dehydrogenase CA265_RS14635 CA265_RS19780
pccA propionyl-CoA carboxylase, alpha subunit CA265_RS02215 CA265_RS18365
pccB propionyl-CoA carboxylase, beta subunit CA265_RS16635 CA265_RS10640
epi methylmalonyl-CoA epimerase CA265_RS10815
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit CA265_RS25460 CA265_RS14780
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CA265_RS20010
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase CA265_RS16400 CA265_RS16405
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
bcaP L-valine uptake transporter BcaP/CitA CA265_RS17395 CA265_RS15000
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase CA265_RS20005 CA265_RS09125
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CA265_RS14635
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) CA265_RS25230 CA265_RS04345
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) CA265_RS25230 CA265_RS16020
livH L-valine ABC transporter, permease component 1 (LivH/BraD)
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE)
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CA265_RS14780 CA265_RS25460
natA L-valine ABC transporter, ATPase component 1 (NatA) CA265_RS25230 CA265_RS15245
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)
natE L-valine ABC transporter, ATPase component 2 (NatE) CA265_RS25230 CA265_RS04345
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
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CA265_RS02215 CA265_RS18365
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase CA265_RS14465 CA265_RS09630
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase CA265_RS08845
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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