Data from: A large and phylogenetically diverse class of type 1 opsins lacking a canonical retinal binding site

Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KSY, Yarov-Yarovoy V, Facciotti MT

Date Published: July 20, 2016

DOI: http://dx.doi.org/10.5061/dryad.963hr

 

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Title SI_Dataset_1_Haloarcheal_opsin_seqs
Downloaded 9 times
Description Fasta file containing 170 haloarchaeal opsin sequences recovered by BLASTp searches of haloarchaeal genomes, after correcting for incorrectly called start sites. Sequences are marked with tags noting differences from corresponding NCBI records. Long = sequence is longer than corresponding NCBI record. ID_to = sequence perfectly matches multiple NCBI records, Not_ID = sequence is not identical to corresponding NCBI record, Cap = sequence has alternative annotation as “capsular polysaccharide biosynthesis protein”.
Download SI_Dataset_1_Haloarcheal_opsin_seqs.fasta (50.67 Kb)
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Title SI_Dataset_2_Haloarchaeal_opsins_tree
Downloaded 4 times
Description Nexus formatted phylogeny file for 170 haloarchaeal opsins included in this study. Best opened with FigTree v1.4.0. Corresponds to Fig 2A and SI Fig. 5.
Download SI_Dataset_2_Haloarchaeal_opsins_tree.nexus (96.29 Kb)
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Title SI_Dataset_3_Alignment_halo_trimmed
Downloaded 3 times
Description Fasta formatted alignment file for 170 haloarchaeal opsins included in this study after manual trimming. Remaining 204 positions were used for phylogenetic inference with MrBayes.
Download SI_Dataset_3_Alignment_halo_trimmed.fasta (44.29 Kb)
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Title SI_Dataset_4_Opsin_related_genes_queries
Downloaded 4 times
Description Fasta formatted file containing query sequences used in BLASTp searches for brp, crtE, crtB, crtI, and crtY.
Download SI_Dataset_4_Opsin_related_genes_queries.fasta (11.50 Kb)
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Title SI_Dataset_5_Universal_opsins_tree
Downloaded 7 times
Description Nexus formatted phylogeny file for 1077 Class I opsins collected from the NCBI nr and env_nr databases. Best opened with FigTree v1.4.0. Corresponds to Fig 2C and SI Fig 3.
Download SI_Dataset_5_Universal_opsins_tree.nexus (225.5 Kb)
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Title SI_Dataset_6_Plasmid_sequences.fasta
Downloaded 4 times
Description Fasta formatted file containing sequences for expression vectors pMTFCHIS2 and pDJLCHIS.
Download SI_Dataset_6_Plasmid_sequences.fasta.txt (13.55 Kb)
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When using this data, please cite the original publication:

Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KSY, Yarov-Yarovoy V, Facciotti MT (2016) A large and phylogenetically diverse class of type 1 opsins lacking a canonical retinal binding site. PLOS ONE 11(6): e0156543. http://dx.doi.org/10.1371/journal.pone.0156543

Additionally, please cite the Dryad data package:

Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KSY, Yarov-Yarovoy V, Facciotti MT (2016) Data from: A large and phylogenetically diverse class of type 1 opsins lacking a canonical retinal binding site. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.963hr
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