GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Escherichia coli BW25113

Found 37 low-confidence and 7 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase b0349
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component b2306 b0809
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 b2307 b0861
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 b2308 b0862
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component b2310 b2309
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase b1619 b2426
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter b2246
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter b2801
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase b1695 b0039
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase b1093 b2842
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit b3256
leucine liuC: 3-methylglutaconyl-CoA hydratase b1393 b0036
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase b2545
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase b1314
myoinositol iolT: myo-inositol:H+ symporter b4031 b2943
myoinositol uxaE: D-tagaturonate epimerase
phenylacetate ppa: phenylacetate permease ppa b4067
phenylalanine ARO10: phenylpyruvate decarboxylase
sucrose ams: sucrose hydrolase (invertase) b4239
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase b0039 b1695
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase b1393 b3846
valine mmsA: methylmalonate-semialdehyde dehydrogenase b1385 b2661
valine mmsB: 3-hydroxyisobutyrate dehydrogenase b3125 b3882
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol PLT5: xylitol:H+ symporter PLT5 b2841

Confidence: high confidence medium confidence low confidence

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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