FoldSeek Search Tool
Examples: wx1, Zm00001eb374230, Zm00001d045055, P16165

Protein overview

Uniprot ID: A0A1D6QC47
Uniprot Description: Non-specific serine/threonine protein kinase, EC 2.7.11.1
AlphaFold ID: A0A1D6QC47
B73 version 5 ID: Zm00001eb192350
B73 version 4 ID: Zm00001d052028
Gene annotation: vps3 - vacuolar protein sorting3

Project summary

Each of the 39,299 AlphaFold predicted protein structure from maize was aligned against eight proteomes using the software FoldSeek. The protein structure data for this project was downloaded from the EBI AlphaFold Protein Structure Database and Google Cloud. Precomputed model organism proteomes are available for four plant species: Arabidopsis thaliana (Arabidopsis), Glycine max (Soybean), Oryza sativa (Asian rice), and Zea mays (Maize). Three well-annotated proteomes were chosen as outgroups: Homo sapiens (Human), Saccharomyces cerevisiae (Budding yeast), Schizosaccharomyces pombe (Fission yeast). A fifth plant species Sorghum bicolor (Sorghum) was downloaded from the Deepmind/Alphafold public dataset on the Goolge Cloud using taxonomy id 4558. The protein structure models are from version 3 released in July 2022. The output HTML from FoldSeek was modified to include the top 25 hits from each species with Uniprot functional annotations, species information, and blue/red color gradient.

AlphaFold structure

Jbrowse view
AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation or a misannotated exon. The 3D image of the protein structure is color-coded based on the confidence score per atom. The JBrowse view shows the B73 RefGen_v5 official gene models along and a track with each exon color-coded based on an average confidence score across the residues in the given exon. Note: the AlphaFold track is based on structures predicted on B73 RefGen_v4 gene annotations and may not match any transcripts in RefGen_v5.

Blue: Very high (average pLDDT > 90) Light Blue: Confident (70 < avg pLDDT < 90) Yellow: Low (50 < avg pLDDT < 70) Orange: Very low (avg pLDDT < 50)

PFAM domains

Protein Alignment start Alignment end PFAM ID PFAM name Type Bit scoreE-value Clan
A0A1D6QC47114318PF00069PkinaseDomain62.21.6e-13CL0016
A0A1D6QC4710761111PF00400WD40Repeat28.70.0057CL0186
A0A1D6QC47566591PF02985HEATRepeat19.92CL0020

Foldseek Structure alignments

Foldseek Alignment Results

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Visualization

Results

Target Species Annotation Sequence Id. Score E-Value Query Pos. Target Pos.