GapMind for catabolism of small carbon sources

 

L-valine catabolism in Pseudomonas stutzeri RCH2

Best path

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

Also see fitness data for the top candidates

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) Psest_1308 Psest_3854
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) Psest_1309 Psest_1089
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Psest_1312
livH L-valine ABC transporter, permease component 1 (LivH/BraD) Psest_1311 Psest_3855
livM L-valine ABC transporter, permease component 2 (LivM/BraE) Psest_1310
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Psest_3517
acdH isobutyryl-CoA dehydrogenase Psest_2440 Psest_2445
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Psest_2437 Psest_3109
bch 3-hydroxyisobutyryl-CoA hydrolase Psest_2439 Psest_3110
mmsB 3-hydroxyisobutyrate dehydrogenase Psest_2438 Psest_1179
mmsA methylmalonate-semialdehyde dehydrogenase Psest_2436 Psest_3781
prpC 2-methylcitrate synthase Psest_2320 Psest_2499
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Psest_2319 Psest_2521
prpF methylaconitate isomerase Psest_2318
acn (2R,3S)-2-methylcitrate dehydratase Psest_2319 Psest_2309
prpB 2-methylisocitrate lyase Psest_2321 Psest_2567
Alternative steps:
Bap2 L-valine permease Bap2 Psest_1697
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Psest_2219 Psest_1429
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Psest_1427 Psest_2218
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Psest_0447 Psest_2217
brnQ L-valine:cation symporter BrnQ/BraZ/BraB Psest_2489
dddA 3-hydroxypropionate dehydrogenase Psest_2633
epi methylmalonyl-CoA epimerase Psest_4071
hpcD 3-hydroxypropionyl-CoA dehydratase Psest_2437 Psest_3109
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Psest_2436 Psest_3781
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Psest_2492 Psest_1663
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) Psest_1309 Psest_1089
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) Psest_1310
natD L-valine ABC transporter, permease component 2 (NatD) Psest_1092 Psest_3855
natE L-valine ABC transporter, ATPase component 2 (NatE) Psest_1308 Psest_1090
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 Psest_1080 Psest_1019
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Psest_4085 Psest_1019
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Psest_1083
pco propanyl-CoA oxidase Psest_3830
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 17 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