GapMind for Amino acid biosynthesis

 

Potential Gaps in Amino acid biosynthesis

Found 15 low-confidence and 16 medium-confidence steps on the best paths for 18 pathways x 35 genomes. 31 of 31 gaps have been manually classified.

Pathway Step Organism Best candidate 2nd candidate Class of gap
chorismate aroA: 3-phosphoshikimate 1-carboxyvinyltransferase Echinicola vietnamensis KMM 6221, DSM 17526 Echvi_0122 diverged
chorismate aroC: chorismate synthase Shewanella oneidensis MR-1 SO3078.2 spurious
chorismate aroL: shikimate kinase Azospirillum brasilense Sp245 spurious
cys cysE: serine acetyltransferase Echinicola vietnamensis KMM 6221, DSM 17526 Echvi_0221 Echvi_2964 diverged
his hisC: histidinol-phosphate aminotransferase Synechococcus elongatus PCC 7942 Synpcc7942_1030 Synpcc7942_1109 diverged
his hisD: histidinol dehydrogenase Azospirillum brasilense Sp245 spurious
his hisN: histidinol-phosphate phosphatase Desulfovibrio vulgaris Hildenborough DVU2490 DVU1040 diverged
his hisN: histidinol-phosphate phosphatase Desulfovibrio vulgaris Miyazaki F DvMF_0940 DvMF_3122 diverged
his hisN: histidinol-phosphate phosphatase Synechococcus elongatus PCC 7942 Synpcc7942_1763 Synpcc7942_0125 novel
his prs: ribose-phosphate diphosphokinase Pseudomonas fluorescens FW300-N1B4 spurious
ile ilvI: acetohydroxybutanoate synthase regulatory subunit Dyella japonica UNC79MFTsu3.2 N515DRAFT_0566 diverged
leu ilvI: acetohydroxybutanoate synthase regulatory subunit Dyella japonica UNC79MFTsu3.2 N515DRAFT_0566 diverged
lys DAPtransferase: L,L-diaminopimelate aminotransferase Echinicola vietnamensis KMM 6221, DSM 17526 Echvi_0124 Echvi_0656 novel
lys dapE: succinyl-diaminopimelate desuccinylase Pedobacter sp. GW460-11-11-14-LB5 novel
met metB: cystathionine gamma-synthase Pseudomonas fluorescens FW300-N1B4 Pf1N1B4_4890 Pf1N1B4_4430 spurious
met metC: cystathionine beta-lyase Dyella japonica UNC79MFTsu3.2 N515DRAFT_4305 N515DRAFT_4363 diverged
phe pdehyd: prephenate dehydratase Synechococcus elongatus PCC 7942 Synpcc7942_0881 diverged
ser serA: 3-phosphoglycerate dehydrogenase Desulfovibrio vulgaris Hildenborough DVU0339 DVU1412 novel
ser serA: 3-phosphoglycerate dehydrogenase Desulfovibrio vulgaris Miyazaki F DvMF_1902 DvMF_0209 novel
ser serB: phosphoserine phosphatase Desulfovibrio vulgaris Hildenborough DVU2935 novel
ser serB: phosphoserine phosphatase Desulfovibrio vulgaris Miyazaki F DvMF_1462 novel
ser serB: phosphoserine phosphatase Dyella japonica UNC79MFTsu3.2 N515DRAFT_3581 N515DRAFT_0975 novel
ser serB: phosphoserine phosphatase Synechococcus elongatus PCC 7942 Synpcc7942_2078 Synpcc7942_1501 novel
ser serC: 3-phosphoserine aminotransferase Azospirillum brasilense Sp245 spurious
ser serC: 3-phosphoserine aminotransferase Desulfovibrio vulgaris Hildenborough DVU0494 DVU3121 novel
ser serC: 3-phosphoserine aminotransferase Desulfovibrio vulgaris Miyazaki F DvMF_2809 DvMF_1715 novel
ser serC: 3-phosphoserine aminotransferase Echinicola vietnamensis KMM 6221, DSM 17526 diverged
thr thrB: homoserine kinase Bacteroides thetaiotaomicron VPI-5482 novel
thr thrB: homoserine kinase Dinoroseobacter shibae DFL-12 Dshi_1609 novel
thr thrB: homoserine kinase Phaeobacter inhibens BS107 PGA1_c14090 novel
val ilvI: acetohydroxybutanoate synthase regulatory subunit Dyella japonica UNC79MFTsu3.2 N515DRAFT_0566 diverged

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

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This analysis was run on Jun 28 2019. The underlying query files were built on Jun 28 2019.

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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).

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