GapMind for catabolism of small carbon sources

 

L-valine catabolism in Dechloromonas agitata is5

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) K420_RS0102825 K420_RS0102920
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) K420_RS0101415 K420_RS0102830
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) K420_RS0102845
livH L-valine ABC transporter, permease component 1 (LivH/BraD) K420_RS0102840 K420_RS0101405
livM L-valine ABC transporter, permease component 2 (LivM/BraE) K420_RS0102835 K420_RS0101410
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused K420_RS0102860
acdH isobutyryl-CoA dehydrogenase K420_RS0103915 K420_RS0103895
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase K420_RS0103335 K420_RS0101330
bch 3-hydroxyisobutyryl-CoA hydrolase K420_RS0103335 K420_RS0101385
mmsB 3-hydroxyisobutyrate dehydrogenase K420_RS0109015 K420_RS0109010
mmsA methylmalonate-semialdehyde dehydrogenase K420_RS0106575 K420_RS0109685
pccA propionyl-CoA carboxylase, alpha subunit K420_RS0105525 K420_RS0103940
pccB propionyl-CoA carboxylase, beta subunit K420_RS0105520 K420_RS0103930
epi methylmalonyl-CoA epimerase K420_RS0102715
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit K420_RS0105510 K420_RS0102965
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit K420_RS0105510
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase K420_RS0110820
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit K420_RS0106830
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit K420_RS18355
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component K420_RS0102230 K420_RS0110930
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase K420_RS0103335 K420_RS0101330
iolA malonate semialdehyde dehydrogenase (CoA-acylating) K420_RS0106575 K420_RS0109685
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component K420_RS0102235 K420_RS0110935
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components K420_RS0105510 K420_RS0102965
natA L-valine ABC transporter, ATPase component 1 (NatA) K420_RS0102830 K420_RS20815
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) K420_RS0101405 K420_RS0102840
natE L-valine ABC transporter, ATPase component 2 (NatE) K420_RS0105080 K420_RS0102825
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 K420_RS0105525 K420_RS0105835
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase K420_RS0101730 K420_RS0103895
phtJ L-valine uptake permease PhtJ K420_RS0108980
prpB 2-methylisocitrate lyase K420_RS0116920
prpC 2-methylcitrate synthase K420_RS0110920
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 Apr 09 2024. 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