GapMind for catabolism of small carbon sources

 

L-valine catabolism in Oceanisphaera arctica V1-41

Best path

brnQ, bkdA, bkdB, bkdC, lpd, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-valine:cation symporter BrnQ/BraZ/BraB UN63_RS05165
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit UN63_RS03100 UN63_RS15430
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit UN63_RS03095 UN63_RS15425
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component UN63_RS03090 UN63_RS07065
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component UN63_RS13455 UN63_RS12615
acdH isobutyryl-CoA dehydrogenase UN63_RS08990 UN63_RS13340
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase UN63_RS10750 UN63_RS14495
bch 3-hydroxyisobutyryl-CoA hydrolase UN63_RS08980
mmsB 3-hydroxyisobutyrate dehydrogenase UN63_RS08975 UN63_RS09270
mmsA methylmalonate-semialdehyde dehydrogenase UN63_RS08995 UN63_RS16535
prpC 2-methylcitrate synthase UN63_RS01195 UN63_RS07100
prpD 2-methylcitrate dehydratase
acn (2R,3S)-2-methylcitrate dehydratase UN63_RS13445 UN63_RS09715
prpB 2-methylisocitrate lyase UN63_RS01190
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) UN63_RS09715
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase UN63_RS03420
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase UN63_RS10750 UN63_RS10745
iolA malonate semialdehyde dehydrogenase (CoA-acylating) UN63_RS16535 UN63_RS08995
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) UN63_RS11740 UN63_RS11735
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) UN63_RS11735 UN63_RS06410
livH L-valine ABC transporter, permease component 1 (LivH/BraD) UN63_RS11725
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) UN63_RS11720
livM L-valine ABC transporter, permease component 2 (LivM/BraE) UN63_RS11730
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit UN63_RS11590
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-valine ABC transporter, ATPase component 1 (NatA) UN63_RS11735 UN63_RS06410
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) UN63_RS11730
natD L-valine ABC transporter, permease component 2 (NatD) UN63_RS11725
natE L-valine ABC transporter, ATPase component 2 (NatE) UN63_RS11740 UN63_RS01085
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
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 UN63_RS13355 UN63_RS08005
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit UN63_RS08005 UN63_RS13355
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit UN63_RS08790
pccB propionyl-CoA carboxylase, beta subunit UN63_RS13345
pco propanyl-CoA oxidase
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