GapMind for catabolism of small carbon sources

 

L-valine catabolism in Methanospirillum lacunae Ki8-1

Best path

Bap2, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-valine permease Bap2
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH isobutyryl-CoA dehydrogenase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
bch 3-hydroxyisobutyryl-CoA hydrolase
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase DK846_RS11355 DK846_RS05900
pccA propionyl-CoA carboxylase, alpha subunit DK846_RS14185
pccB propionyl-CoA carboxylase, beta subunit DK846_RS13470
epi methylmalonyl-CoA epimerase
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
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
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase
iolA malonate semialdehyde dehydrogenase (CoA-acylating) DK846_RS11355
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) DK846_RS06435 DK846_RS06450
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) DK846_RS06435 DK846_RS06450
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)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit DK846_RS01055
natA L-valine ABC transporter, ATPase component 1 (NatA)
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) DK846_RS10730 DK846_RS12975
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA DK846_RS14410 DK846_RS07590
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB DK846_RS14405 DK846_RS07585
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit DK846_RS14185
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit DK846_RS14190
pco propanyl-CoA oxidase
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
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 DK846_RS07590
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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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