GapMind for catabolism of small carbon sources

 

L-valine catabolism in Acidovorax caeni R-24608

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) BN2503_RS02275 BN2503_RS06720
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) BN2503_RS02270 BN2503_RS06725
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BN2503_RS02255 BN2503_RS06630
livH L-valine ABC transporter, permease component 1 (LivH/BraD) BN2503_RS02260 BN2503_RS06735
livM L-valine ABC transporter, permease component 2 (LivM/BraE) BN2503_RS02265 BN2503_RS06730
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BN2503_RS02910
acdH isobutyryl-CoA dehydrogenase BN2503_RS07075 BN2503_RS07190
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BN2503_RS05070 BN2503_RS12155
bch 3-hydroxyisobutyryl-CoA hydrolase BN2503_RS06080 BN2503_RS05070
mmsB 3-hydroxyisobutyrate dehydrogenase BN2503_RS07175 BN2503_RS06605
mmsA methylmalonate-semialdehyde dehydrogenase BN2503_RS07195 BN2503_RS00905
prpC 2-methylcitrate synthase BN2503_RS02450 BN2503_RS08525
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BN2503_RS02445 BN2503_RS11475
prpF methylaconitate isomerase BN2503_RS02440
acn (2R,3S)-2-methylcitrate dehydratase BN2503_RS02445 BN2503_RS11475
prpB 2-methylisocitrate lyase BN2503_RS08680 BN2503_RS02435
Alternative steps:
Bap2 L-valine permease Bap2 BN2503_RS15280
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 BN2503_RS17110 BN2503_RS03820
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase BN2503_RS07740 BN2503_RS06875
epi methylmalonyl-CoA epimerase BN2503_RS07530
hpcD 3-hydroxypropionyl-CoA dehydratase BN2503_RS05070 BN2503_RS04075
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BN2503_RS03555 BN2503_RS07195
lpd* branched-chain alpha-ketoacid dehydrogenase, E3 component BN2503_RS17105 with BN2503_RS11830 BN2503_RS03815
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BN2503_RS07510
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BN2503_RS07510
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BN2503_RS07510
natA L-valine ABC transporter, ATPase component 1 (NatA) BN2503_RS06725 BN2503_RS01080
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) BN2503_RS02265
natD L-valine ABC transporter, permease component 2 (NatD) BN2503_RS06735 BN2503_RS02260
natE L-valine ABC transporter, ATPase component 2 (NatE) BN2503_RS06720 BN2503_RS02275
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 BN2503_RS07525 BN2503_RS06975
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BN2503_RS07525 BN2503_RS04310
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BN2503_RS07520 BN2503_RS06995
pco propanyl-CoA oxidase BN2503_RS01970
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 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