GapMind for catabolism of small carbon sources

 

L-valine catabolism in Lactobacillus silagei IWT126

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) CES79_RS10020 CES79_RS10015
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) CES79_RS10015 CES79_RS10020
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CES79_RS10000
livH L-valine ABC transporter, permease component 1 (LivH/BraD) CES79_RS10005
livM L-valine ABC transporter, permease component 2 (LivM/BraE) CES79_RS10010
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 CES79_RS00720
mmsA methylmalonate-semialdehyde dehydrogenase CES79_RS01180
prpC 2-methylcitrate synthase CES79_RS02950
prpD 2-methylcitrate dehydratase
acn (2R,3S)-2-methylcitrate dehydratase CES79_RS02945
prpB 2-methylisocitrate lyase
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CES79_RS02945
Bap2 L-valine permease Bap2 CES79_RS01340 CES79_RS10735
bcaP L-valine uptake transporter BcaP/CitA CES79_RS03120 CES79_RS02900
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CES79_RS09610
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CES79_RS09615
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CES79_RS09620
brnQ L-valine:cation symporter BrnQ/BraZ/BraB CES79_RS10800 CES79_RS04070
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CES79_RS01180
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CES79_RS09625 CES79_RS04335
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-valine ABC transporter, ATPase component 1 (NatA) CES79_RS10015 CES79_RS10020
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) CES79_RS10005
natE L-valine ABC transporter, ATPase component 2 (NatE) CES79_RS10020 CES79_RS04320
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 CES79_RS05880 CES79_RS03295
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CES79_RS05880 CES79_RS03295
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase CES79_RS05910
phtJ L-valine uptake permease PhtJ
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 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