GapMind for catabolism of small carbon sources

 

L-valine catabolism in Rhizorhabdus wittichii RW1

Best path

Bap2, bkdA, bkdB, bkdC, lpd, 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
Bap2 L-valine permease Bap2 SWIT_RS03485
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SWIT_RS10830 SWIT_RS03985
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SWIT_RS10825 SWIT_RS03980
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component SWIT_RS03975 SWIT_RS10820
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component SWIT_RS06910 SWIT_RS24900
acdH isobutyryl-CoA dehydrogenase SWIT_RS18220 SWIT_RS03310
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SWIT_RS09105 SWIT_RS03300
bch 3-hydroxyisobutyryl-CoA hydrolase SWIT_RS03305 SWIT_RS18205
mmsB 3-hydroxyisobutyrate dehydrogenase SWIT_RS03295 SWIT_RS16510
mmsA methylmalonate-semialdehyde dehydrogenase SWIT_RS26765 SWIT_RS03320
prpC 2-methylcitrate synthase SWIT_RS24200 SWIT_RS16220
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SWIT_RS24185 SWIT_RS13825
prpF methylaconitate isomerase SWIT_RS24190
acn (2R,3S)-2-methylcitrate dehydratase SWIT_RS24185 SWIT_RS13825
prpB 2-methylisocitrate lyase SWIT_RS24205 SWIT_RS21870
Alternative steps:
bcaP L-valine uptake transporter BcaP/CitA SWIT_RS22305 SWIT_RS13040
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase SWIT_RS22820 SWIT_RS24305
epi methylmalonyl-CoA epimerase SWIT_RS14635 SWIT_RS11415
hpcD 3-hydroxypropionyl-CoA dehydratase SWIT_RS03300 SWIT_RS09105
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SWIT_RS03320 SWIT_RS26765
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) SWIT_RS14705 SWIT_RS04010
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) SWIT_RS14705 SWIT_RS00070
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)
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit SWIT_RS14630
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit SWIT_RS14630 SWIT_RS12140
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components SWIT_RS14630
natA L-valine ABC transporter, ATPase component 1 (NatA) SWIT_RS14705 SWIT_RS18740
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) SWIT_RS14705 SWIT_RS18740
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused SWIT_RS09265 SWIT_RS05980
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB SWIT_RS16345
pccA propionyl-CoA carboxylase, alpha subunit SWIT_RS14620 SWIT_RS10920
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SWIT_RS14620 SWIT_RS23720
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit SWIT_RS14645 SWIT_RS10915
pco propanyl-CoA oxidase SWIT_RS04185 SWIT_RS21415
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 SWIT_RS16340
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